Mirtron present in all 20 Drosophila species, and contain no substitutions in the mature region.

dme-mir-1006

Species	Coordinate	Alignment
dm3	chr2L:16724787-16724868 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droSim1	chr2L:16422886-16422967 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droSec1	super_7:371577-371658 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droYak2	chr2R:4378137-4378218 +	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droEre2	scaffold_4845:19796352-19796433 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droEug1	scf7180000408961:299575-299656 -	CAACTTCCAGGTGAGTTTGAAATTGAAATATGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droBia1	scf7180000301468:889370-889451 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droTak1	scf7180000415914:451766-451847 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTGCAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droEle1	scf7180000490579:620127-620208 +	CAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droRho1	scf7180000768553:40195-40276 -	TAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droFic1	scf7180000454078:650974-651055 -	GAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droKik1	scf7180000302643:779035-779116 +	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droAna3	scaffold_12943:3938330-3938411 +	CAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTCCAATA
droBip1	scf7180000395973:155856-155937 +	CAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
dp4	chr4_group3:3057665-3057746 +	CAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droPer1	super_1:4544388-4544469 +	CAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droWil1	scaffold_180708:1783976-1784059 +	TAATTTCCAGGTGAGTTTGAAATTGAAATGCCTAAATTGTTTTGTGTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droVir3	scaffold_12963:6536531-6536612 -	CAACTTTCAGGTGAGTTTGAAATTGAAATATGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droMoj3	scaffold_6500:25691044-25691125 -	CAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATA
droGri2	scaffold_15252:9753541-9753622 -	CAATTTCCAAGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATA

dme-mir-1010

Species	Coordinate	Alignment
dm3	chr3R:18118591-18118681 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAA----TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droSim1	chr3R:17925974-17926067 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droSec1	super_0:18476150-18476243 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droYak2	chr3R:18962292-18962386 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droEre2	scaffold_4820:9960771-9960864 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droEug1	scf7180000409768:235941-236034 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droBia1	scf7180000302402:5625521-5625614 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droTak1	scf7180000415711:932912-933006 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droEle1	scf7180000491280:4685180-4685274 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droRho1	scf7180000779175:38996-39089 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droFic1	scf7180000454106:1264894-1264987 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droKik1	scf7180000302461:1947241-1947334 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
droAna3	scaffold_13340:9102983-9103076 +	TGCTTAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTATGAGGAC
droBip1	scf7180000396712:253122-253215 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATAT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAC
dp4	chr2:12275943-12276036 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTTA-TTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGAT
droPer1	super_0:8195071-8195164 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTTA-TTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGAT
droWil1	scaffold_181130:12259764-12259858 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGATACGAGGAT
droVir3	scaffold_13047:8363186-8363279 -	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAATT-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAT
droMoj3	scaffold_6540:27812511-27812603 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAT-T-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGAT
droGri2	scaffold_15074:1256130-1256222 +	TGCTCAACGGGTAAGTGGTGTAGATGAAACAAAACTCTCAACAAT-T-TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGAT

Present in all 20 Drosophila species, but contains substitutions in the mature region.

dme-mir-1003

Species	Coordinate	Alignment
dm3	chr3R:20484317-20484392 +	TGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAG
droSim1	chr3R:20323150-20323225 +	TGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAG
droSec1	super_0:20818709-20818784 +	TGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAG
droYak2	chr3R:26013207-26013282 -	TGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATTTACATATTCACAGGCGTCGTGAG
droEre2	scaffold_4820:7574104-7574179 -	TGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAG
droEug1	scf7180000409881:208845-208920 +	TGCGCAGGAGGTGGGTATC-TTGATGTGGTTGGCTCC-------------G-GCTGTCCTCTCACATCTGTATATTCACAGGCGTCGTGAG
droBia1	scf7180000302402:4263786-4263861 +	TGCGCAGAAGGTGGGTATT-TTGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATCTATATATTCACAGGCGTCGTGAG
droTak1	scf7180000415310:656331-656406 -	TGCGCAGGAGGTGGGTATC-TGGATGTGGTTGGCTCT-------------G-GCGGTCCTCTCACATCTACATATTCACAGGCGTCGTGAG
droEle1	scf7180000491194:539738-539816 +	TGCGCAGGAGGTGAGTATC-TTGATGTGGTTGGCTCT---TC------T-G-GGCGTCCTCTCACATCTACATATTCACAGGCGGCGTGAG
droRho1	scf7180000779488:582448-582523 +	TGCGCAGGAGGTGAGTATC-TTGATGTGGTCGGCTTT-------------A-GCGGTCCTCTCACATCTACATATTCACAGGCGCCGTGAG
droFic1	scf7180000454106:1827853-1827928 -	TGCGCAGAAGGTGAGTATC-TGGATGTGACTGGCTCT-------------T-GCGGTCCTCTCACATCTAGTTATTCTCAGGCGCCGTGAG
droKik1	scf7180000302388:1718915-1718995 -	TGCGTCGAAGGTGAGTATTGTGGGTGTGGGTGGCTCT---GG------C-GGCCAGTCCTCTCACATCACCATATTCACAGGCGTCGCGAG
droAna3	scaffold_13340:4690331-4690413 -	TACGCCGAAGGTGAGTATAGTGGATGTGGGTGGCTCT---TATT----T-GGCCGGTCCTCTCACATCTCCATATTCACAGGCGTCGAGAG
droBip1	scf7180000396359:499296-499379 +	TACGCCGAAGGTGAGTATAGTGGATGTGGGTGGCTCTAAATA------T-GGCCAGTCCTCTCACATCTCCATATTCACAGGCGTCGCGAG
dp4	chr2:1751564-1751642 -	TACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCT---TG--------G-TCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAG
droPer1	super_7:1904975-1905053 -	TACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCT---TG--------G-TCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAG
droWil1	scaffold_181089:9616827-9616906 -	TGCGCCGTAGGTGAGTATC-GGGTTGTGATTGGCTCC---TT------GTG-GTAGTCCTCTCACATCTCTATATTCACAGGCGTCGCGAG
droVir3	scaffold_13047:780937-781014 +	TGCGTCGTAGGTGAGTAAT-CAGTTGTGGGTGGCTTT---TT--------G-AAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGTGAG
droMoj3	scaffold_6540:4775673-4775750 +	TGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTCT---AG--------T-GAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGAGAG
droGri2	scaffold_14906:5529290-5529375 -	TGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTTT---TGTTCTTAGGG-AAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGCGAA

dme-mir-1011

Species	Coordinate	Alignment
dm3	chr3R:16679017-16679090 -	GACCGTGCACGTGAGTTTTTGAGCCAGGAATATA---------GTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCT
droSim1	chr3R:4780979-4781052 +	GACCGTGCACGTGAGTTTTTGAGCCAGGAATATA---------GTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCT
droSec1	super_27:54822-54895 +	GACCGTGCACGTGAGTTTTTGAGCCAGGAATATA---------GTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCT
droYak2	chr3R:5477808-5477881 -	GACCGTGCATGTGAGTTTTTGAGCCAGGAATATA---------ATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCT
droEre2	scaffold_4770:4975833-4975906 +	GACCGTCCACGTGAGTTTTTGAGCCATGAATATA---------ATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCT
droEug1	scf7180000409542:497647-497720 +	TACCATACATGTGAGTCTTTGAGCCAGGAATATA---------ATTA----T-------TAT-TATTGGTTCGAATTGCTCGTAGAATCCACCCT
droBia1	scf7180000302402:9517649-9517722 -	GACCGTGCACGTGAGTCTTTGAGCCAGGAATATA---------ATTC----T-------TAT-TATTGGTTCAAATCGCTCGTAGAACCCTCCTT
droTak1	scf7180000415245:28116-28189 +	GACCGTGCACGTGAGTCTTTGAGCCAGGAATATA---------ATCC----T-------TAT-TATTGGTTCAAATCGCTCGTAGAATCCTCCCT
droEle1	scf7180000491080:558895-558974 -	GACCGTGCACGTGAGTCTTTGAGCCAGGAATATAATTAAC---ATAA----T-------TAT-TATTGGTTCAAATCGCTCGTAGAATCCACCCT
droRho1	scf7180000779659:261338-261411 -	GACCGTGCACGTGAGTCTTTGAGCCAGGAATATA---------ATTC----T-------TAT-TATTGGTTCAAATCGCTCGTAGAATCCACCCT
droFic1	scf7180000453930:97537-97610 +	TACTGCACACGTGAGTCTTTGAGCCAGGAATAAC---------ATCC----T-------TAT-TATTGGTTCGAATCTCTCGTAGAATCCACCGT
droKik1	scf7180000302307:69573-69646 +	AACCGTGCATGTGAGTCTTTGAGCCAGGAATATA---------ATCC----T-------TAT-TATTGGTTCAAATCGCTCGTAGAATCCGCCCT
droAna3	scaffold_13340:7952075-7952149 -	GACGGTGCATGTGAGTCTTTGAACCAGGAATATA---------ATTT----G-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCT
droBip1	scf7180000396708:894004-894078 +	GACTGTTCATGTGAGTCTTTGAGCCAGGAATATA---------ATTT----T-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCT
dp4	chr2:12756668-12756752 +	GACGATGCATGTGAGATTTTGAATCTAATATATA---------ATATAATCCGTACGTGTAT-ATATGGTTCAAATTACTCGTAGAACCCTCCCT
droPer1	super_0:7702117-7702200 -	GACGATGCATGTGAGATTTTGAATCTAATATATA---------ATATAATCT-TACATGTAT-ATATGGTTCAAATAACTCGTAGAATCCTCCCT
droWil1	scaffold_181108:2184471-2184547 +	GACCGTACATGTGAGTCTTTGAATCAGGAATATA---------TTATCA--T-------TATATATTGGTTCGAAATGCTCGTAGAATCCACCTT
droVir3	scaffold_13047:12031336-12031418 +	CACGGTGCATGTGAGTCATTGAACCAGGAATATATGT-ATGTAATTC----T-------TATATATTGGTTCAAATTTCTCGCAGAATCCGCCCT
droMoj3	scaffold_6540:29750594-29750671 -	GACAGTGCATGTGAGTCTTTGAGCCAGGAATATA---------TGTTCATCT-------TAT-TATTGGTTCAAATCTCTCGTAGAATCCTCCCT
droGri2	scaffold_14830:1201864-1201938 +	CACTGAGCATGTGAGTCTTTGAGCCAGGAATATA---------ATTG----T-------TATATATTGGTTCAAACAACTCGTAGAATCCGCCCT

Died

dme-mir-1007 (Died in D. wilistoni but present in all other Drosopholids)

Species	Coordinate	Alignment
dm3	chrX:21167403-21167486 -	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GTTC--T--TGGAC------TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGGA
droSim1	chrX:12920208-12920291 +	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GTTC--T--TGGAC------TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCA
droSec1	super_8:3474410-3474493 -	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GTTC--T--TGGAC------TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCA
droYak2	chrX:20343127-20343210 -	TCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--TAG--GATC--T--TGGAC------TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCA
droEre2	scaffold_4690:17696760-17696843 -	TCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--TGG--GATC--T--TGGAC------TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCA
droEug1	scf7180000408193:314929-315012 +	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GATC--T--TGGAC------TCCTGATAAGCTCAATTAACTGTTT----GCAGCCGACGGCA
droBia1	scf7180000302187:364138-364214 +	TCTGTGCAGTGTAAGCAGTGTTTGAACTCGATC--TT-------------GGAC------TCCTGATAAGCTCAATTAACTGTTT----GCAGCCGACGGCA
droTak1	scf7180000415158:280539-280622 +	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--CCG--GATC--C--TGAAC------TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCA
droEle1	scf7180000490214:749284-749367 +	TCCGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GATC--T--TGGAC------TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGAAGGCA
droRho1	scf7180000780082:45663-45746 +	TCCGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GATC--T--TAGAT------TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGACGGCA
droFic1	scf7180000454077:618956-619038 -	TCCGTACAGTGTAAGCAGTGCTTGAACTCGATC--TTG--GATC--T--TGGAC-------CCCGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCA
droKik1	scf7180000302395:538368-538453 -	TCAGTGCAGTGTAAGCAGTGCTTGAACTCGATC--TCG--TATTAAT--TGGTC------TTCTGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCA
droAna3	scaffold_13334:1054383-1054463 +	TCCGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GAATA-------GC------TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCA
droBip1	scf7180000396733:702541-702621 +	TCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTG--GAATA-------GC------TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCA
dp4	chrXL_group1a:9060612-9060699 +	TCGATACAGTGTAAGCAGCGATTGA--TCAATCAATTG--AATC--GAATCGAA----TCGAATGATAAACTCCATTAACTGTTT----GCAGCCGATGGCA
droPer1	super_15:1454068-1454155 +	TCGATACAGTGTAAGCAGCGATTGA--TCAATCAATTG--AATC--GAATCGAA----TCGAATGATAAACTCCATTAACTGTTT----GCAGCCGATGGCA
droWil1	scaffold_180702:162901-162979 -	TCCATGCAATGTGAGT--TTTTTGATTTT---C--TTG--------T--TTAAT------TTCGAAAAACTTTAATCGACTGTATTCTATCAGCTGATGGCA
droVir3	scaffold_12970:7925731-7925821 -	TCAATGAAATGTAAGCAGTGCTTGAGCTTATTC--TCTGGCTTCA-T--TTGAC--CATTTTCTGATAAGCTCAATTAACTGTTT----GCAGCGGATGCCG
droMoj3	scaffold_6482:1600640-1600728 +	TCCATGAAATGTAAGCAGTGTTTGAACTAAATC--TCTG-GCT-ACT--TGGCC---GTATATTGATAAGCTCAACTAACTGTTT----GCAGCGGACACCT
droGri2	scaffold_15203:11134569-11134659 +	TCAATACAATGTAAGCAGTGTTTGAACTGAATA--TCTG-GTTA--T--CCGACTTCATATACTGATAAGCTCAATTCACTGTTT----GCAGCGGATGGCG

Present outside melanogaster group

dme-mir-1004 (Present in melanogaster group, died in the ananassae subgroup, but present in the obscura group)

Species	Coordinate	Alignment
dm3	chr2L:3767611-3767698 +	TGGACAAAAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCACGGTGC
droSim1	chr2L:3722749-3722836 +	TGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGC
droSec1	super_5:1870690-1870777 +	TGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGC
droYak2	chr2L:3769296-3769383 +	TGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGATGT
droEre2	scaffold_4929:3814035-3814122 +	TGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCAATCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGC
droEug1	scf7180000409554:2307496-2307588 -	TGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGATCGCTGA---------TCC-----------------------------GATTT----AC----TGATCTATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGC
droBia1	scf7180000302261:2154115-2154206 +	TGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC--------ATT-------------------------------CCTT----AC----TGATCCACTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGC
droTak1	scf7180000415709:76423-76515 -	TGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC----------CG-----------------------------ATCT---TTAC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGC
droEle1	scf7180000490728:519650-519743 +	TGGACAAAAGGT-GCGGTT--TCAT------------TGATCTTGGAGACCTTTTC--------GACT-----------------------------ATCCT----AG----TGATCCATTCTC-----TCACATCACT---T--CCCTTATAGCGCGAGGTGC
droRho1	scf7180000777886:5854-5941 -	TGGACAAAAGGT-TGGGGG--ACAT------------TGATCTTGGAGAC--------------GGCT-----------------------------GGCTT----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGC
droFic1	scf7180000453924:1748608-1748700 +	TGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGAATCGCTC--------ATT------------------------------CGCTC----AC----TGATCCATTCTC-----TCACATCTCT---T--CCCTCACAGCGCGCGGGGC
droKik1	scf7180000302401:685590-685681 +	TCGACAAGAGGT--GAAGG--ACAC------------TGATCTTAGAGAAAGGCAA-------CAGCA-----------------------------AATTA----TA----TG--TAATTCTC-----TCACATCACT---T--CCTTCACAGTGCGAGGTGC
droAna3	scaffold_12916:5837620-5837734 +	TGGACAAGAGGT-GAGATA--ACACGTTCTAACCAACTGATAT--GAAACTAC-G-A--------------------ATGTTTTTATCGCTGTC---G--------AT----TCGAACGATCTC-----TCATATAACCGTAC--CTATTACAGTGCGCGGTGT
droBip1	scf7180000396568:1004380-1004458 -	TGGACAAGAGGT-ACG-------AT------------CGAATCT---------------------CTC-----------------------------GTATA----AT----TCAAACGATCTC-----TCATATAACCGTCT--CTCCTACAGTGCCCGGTGT
dp4	chr4_group3:4962043-4962141 -	TGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAAAAA--------AACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGC
droPer1	super_1:6454687-6454783 -	TGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAATA----------ACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGC
droWil1	scaffold_180708:9298768-9298864 -	TGGATAAAAGGT--GGGGT--ACAA------------CAACAACAAAAATAC--G-AATATAATGGTA-----------------------------AACTC----TC------------TCTCTCATCTCTTATCATT---TTCTCCTCACAGTGCGCGTTCA
droVir3	scaffold_12963:14941265-14941359 -	TGGACAAAAGGT-TGGGGC--ACAT------------TGATCTTCAAGAAACTCAC--------AGCC-----------------------------AGCTC----AT----TTACTCACTCTC-----TCTCTCTTCT----CTCCCTCACAGTGCCCGCTGT
droMoj3	scaffold_6500:17898456-17898541 -	TGGACAAGAGGT-AATTGATCACTC------------CTATCTCTGTCTC-----------------T-----------------------------CTTTCTCTTTC----TG----ACTCTC-----TCCCA-CTCT---T--TATTTGTAGTGCTCGCTGC
droGri2	scaffold_15126:4437372-4437492 +	TGGACAAAAGGT-AGGAGAGCACAT------------TGATCTTGAAGAAACTTGC--------AGAAAACTCTCTAATACTCTCAC-----------TCCATTTCTCTAACTCTCCCTCTCTC-----TTATTTAACT---T--C-ATTTTAGTGCGCGCTGT

dme-mir-1014 (Gone in the drosophila group)

Species	Coordinate	Alignment
dm3	chr3R:27579236-27579323 -	TTTTCTCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACTGGATA
droSim1	chr3R:27196225-27196312 -	TTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACCGGATA
droSec1	super_31:233827-233914 -	TTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACCGGATA
droYak2	chr3R:28513873-28513960 -	TTTTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGATA
droEre2	scaffold_4820:396406-396493 +	TTTTCGCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGATA
droEug1	scf7180000409488:324985-325071 +	TTTTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCATC----AGTGG-----TTG--AATTA-------------AATTCATTCTCATTTGCAGTCACCGGCTA
droBia1	scf7180000302035:243909-243996 -	TTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGAC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGCTA
droTak1	scf7180000415712:666826-666913 -	TTTTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGCTA
droEle1	scf7180000491194:1626044-1626125 -	TTTTCCCAAGGTATA---------CGCTTTAAT------CAATTGA--GCTA-------ACAAA----AAT-A-----TTC--AATTTA------------AATTAATTTCCATTTGCAGTCACCGGCTA
droRho1	scf7180000779322:113718-113796 +	TTTTCCCAAGGTAT---------AGATTTTAAT------CGTCG----GC---------GCATT----AGTGG-----ATG--AGTTAA------------AATTTATTTCTGCTTGCAGTAACCGGCTA
droFic1	scf7180000454114:266213-266300 -	TTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----GGTGT-----GTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGCTA
droKik1	scf7180000301641:60802-60889 -	TTCTCCCAAGGTACAATGGAAATCGATTTTAAT------GGCCA----GA---------GAGAG----ACCAA-----TGC--AATTAA------------AATTCATTTTCATTTACAGTCACCGGCTA
droAna3	scaffold_12911:3510623-3510710 +	TTCTCCCAAGGTATAATGAAAATTGATTTTAAT------CACAC----GG---------ATCGG----AGTGG-----CAA--AATTAA------------AATTCATTTTCATTTGCAGTCACGGGATA
droBip1	scf7180000396640:373897-373984 +	TTCTCACAAGGTATAATGAAAATTGATTTTAAT------CACAC----GG---------ATCGG----AGTGG-----CAA--AATTAA------------AATTCATTTTCATTTGCAGTCACGGGATT
dp4	chr2:14711230-14711317 +	TTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGGGT----TT---------CGTTT----GGCGG-----TGA--AATTAA------------AATTCATTTTCATTTACAGTGACCGGCAT
droPer1	super_0:5703127-5703214 -	TTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGTGT----TT---------CGTTT----GGCGG-----TGA--AATTAA------------AATTCATTTTCATTTACAGTGACCGGCAT
droWil1	scaffold_181130:8196920-8197016 +	TTTTCTCAAGGTGAAATGAAAATAAATTTTAATTCGGATAGAAA----GC---------TAATCTAATTGT-A-----TTG--CATTAA------------AATTCGTTTTCATTTGCAGTATCTGGTCT
droVir3	Unknown	TTCTCTCAAGGTATG---TACATATTTTTAAAT----------------------------------------------TT--AACCAG------------TATTTACTTTTGTTCACAGTGACCGGCAT
droMoj3	scaffold_6540:30646892-30646977 +	TTCTCTCAAGGTAAG--------T-GCTTTGACT-----T---------A---------GCAAA----AGTTA-----TTT---ACTAGAAGTGTTTCTCTGCTTTCGTTTCATCCACAGTGACCGGTGT
droGri2	scaffold_14624:997055-997154 -	TTTTCACAGGGTATGCAGAGCT-TGATTA------------TTTGATTGCTCATTTTACACATT----A-TAAATAAATTATATATATA------------TATACATATGTTATTGCAGTGACTGGCGT

dme-mir-2535b (Present in melanogaster group but died in D. kikkawai, D. ficusphila, and the ananassae subgroup. Present in obscura group)

Species	Coordinate	Alignment
dm3	chrX:21169296-21169382 -	CATCACTAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTGAA---CTTA---------GCG-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droSim1	chrX:12918312-12918398 +	CATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTTA---------GCG-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droSec1	super_8:3476303-3476389 -	CATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTTA---------GAG-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droYak2	chrX:20345019-20345105 -	CATCACCAAGGTAAGTGAC--AATGCCG------GGATTGTGGTTATTGAA---AATA---------CCT-TCTCCACT--CACGGCATTAT--ATTCACTTGCAGTACATC
droEre2	scaffold_4690:17698653-17698739 -	CATCACCAAGGTAAGTGAC--AGTGCCG------GGATTGTGGTTATTAAA---AATA---------CCT-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droEug1	scf7180000408193:313033-313119 +	TATCACCAAGGTAAGTGGC--TATGCCG------GGATCGTGGTTGATCTA---TGTA---------CCT-TCTCCACT--CACGGCATTTC--ATTCACTTGTAGTACATC
droBia1	scf7180000302187:362236-362324 +	CATCACCAAAGTAAGTGGC--CATGCCG------GGATTGTGGTTTAA-------CCA---GAGGTTCCT-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droTak1	scf7180000415158:278087-278176 +	CATCACCAAGGTAAGTGGC--TATGCCG------GGATTGTGGTTTACAATA--GAAA-------GATCC-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droEle1	scf7180000490214:747385-747471 +	CATCACCAAGGTAAGTGGG--TATGCCG------GGACTGTGGTTCTAAAT---GCCA---------TCA-CCACCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droRho1	scf7180000780082:43776-43858 +	CATCACCAAGGTAAGTGGG--TATGCCG------GGATTGTGGTTAAT-------ACA---------CCT-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATC
droFic1	scf7180000454077:620851-620929 -	CATCACCAAGGTAAGTTTA--TATTTATTT-GTGTTGG----------------TGTA---------CCT-CCTCCACT--CACAACATTTC--ATTCACCTGCAGTTCATT
droKik1	scf7180000302395:540416-540497 -	CATCACCAAGGTAAGTCTC-------CGAGAACGGGAACG------A----------ATCGCACAGA-TCCATATCTGT--ATC--TGTATC--CTTCTTGTGTAGTACATC
droAna3	Unknown	TATTACAAAGGTAAGT------------------------------------------------------------ATC--CAAGTTATTTC-CTTCAATTTTCAGTTCATA
droBip1	scf7180000396733:700647-700728 +	TATAACAAAGGTGAGAGGGACGAGGT-----------CTATAGCTTTCGG---GTTGT---------GT----AATACT--TTAAATATTTT-ATTCCAATTTCAGTATATA
dp4	chrXL_group1a:9058695-9058781 +	CATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATTG------A----------ACCTCTCATC-TC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATC
droPer1	super_15:1452149-1452235 +	CATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATTG------A----------ACCTCTCATC-TC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATC
droWil1	Unknown	CATTACCAAGGTGAGT------------------------------------------------------------------------TTTG--TTTTTCTTACAGTACATT
droVir3	Unknown	CATTACCAAGGTAAG--------------------------------------------------------CCTCTTCT--CACGACATCCCTTAATCCCTTGCAGTACGTT
droMoj3	Unknown	CATAACCAGGGTAAGTGCTCAGCTGC---------TtTTtTttTttTtgt--------------------------tTT--TTttTTtTTTC--GTCGCCTTACAGTACATC
droGri2	scaffold_15203:11132621-11132707 +	CATTACTAAGGTATGTT--------CGA------TGATTTTGGTTTTTTTTGGCTTTA---------CTT-TCACCGTTTACACGACAATTT-CATCCTTTTGCAGTACGTG

Present within melanogaster group

dme-mir-1005 (Present in the melanogaster group except D. kikkawai and the ananassae subgroup)

Species	Coordinate	Alignment
dm3	chr2L:4343686-4343766 +	ATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACGAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droSim1	chr2L:4265549-4265628 +	ATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGTTTTTGG-CC-ACAAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droSec1	super_5:2441100-2441180 +	ATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACAAAT----------------------------------------G---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droYak2	chr2L:4375643-4375723 +	ATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droEre2	scaffold_4929:4420546-4420625 +	ATTCTGACCTGTGAGTT--CA-TCGA-TTTCGAGGTTT-GC-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droEug1	scf7180000409554:1722178-1722258 -	ATCCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CTCTTAGAA----------------------------------------A---------CAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droBia1	scf7180000302261:2802465-2802546 +	ATCCTGACCTGTGAGTT--GA-TCGA-TTTCGGGGTTTTTGGCTGCCTTCA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGA
droTak1	scf7180000414050:34782-34863 -	ATTCTGACCTGTGAGTT--GT-GAGA-TTTCATGGTTCCTTTCGGTCATTT----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTCCCCACCGA
droEle1	scf7180000490458:268806-268889 +	ATTCTGACCTGTGAGTT--TA-TGGA-TTTCCAAGTTTTTT-TGA-CATTTTACA------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGA
droRho1	scf7180000778291:9913-9993 -	ATCCTCACCTGTGAGTT--GA-TCGA-TTTCGAGGTTGTGG-CATCTAACA----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGA
droFic1	scf7180000453904:1262368-1262449 -	ATCCTGACCTGTGGGTT--GA-TCGA-TTTCGAGGTTGCGGGTTGGCGCTT----------------------------------------C---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGA
droKik1	scf7180000302570:979768-979846 -	TTGCTGTACTGTGAGTT--GA-AAAT-CCTTGAGGATCTTG-ATACCTTAA----------------------------------------T---------CTAGCAGAATTCT-CT--TTCTTAGTTCCCTCGGA
droAna3	scaffold_12916:13781304-13781390 -	GTTTTGACTTGTAAGAA--CC-AAAA-CTAC---TTTCTGT--A-TCAAAG---------------------------------CCAGAAACTAATCG---TAAT-TGA-AATT-ATCTTAACCAGTCCCCATTGA
droBip1	scf7180000396728:639365-639444 +	ATTCTCTCATGTAAGCGGTGT-TAGA-TTCCGAC-TGGTTC-TTC-CGTATAATA------------------------------------A---------CTCTTT---GTAT-CCA--TTTCAGTCCCGCTCGA
dp4	chr4_group2:339134-339247 +	ATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGA
droPer1	super_8:3550420-3550533 -	ATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGA
droWil1	scaffold_180772:1844879-1844964 -	ATTCTATCATGTAAGTT--AAAACGA-TTAAGTAATTTCAC--ACTTACAT------------------------------------ATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGA
droVir3	Unknown	GTATTGACCTGTAAGTA---------------------------------------------------------------------------------------TGTTGAATTT-TCTTACTGCAGTTCCGCTGGA
droMoj3	scaffold_6500:22625697-22625724 +	ATATTGCTCTGCGTGCA--AG-ATGC-GCCCG--------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:16827858-16827943 -	ATTCTGACATGTAACC----A-CTGA-TCCTGATCCTT-GA-TT-GCACTG---------------------------------CCCATTTTGAATGCGTTTTC-------TTT-CTGCTTTGCAGTTCCCACGGA

dme-mir-1008 (Present in the melanogaster group except in the ananassae subgroup. Died in D. takahashii and D. elegans.)

Species	Coordinate	Alignment
dm3	chr2R:6773028-6773104 +	CCTCATCTATGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CCAATGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droSim1	chr2R:5362607-5362683 +	CCTCATCTATGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droSec1	super_1:4360097-4360173 +	CCTCATCTATGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droYak2	chr2R:2355906-2355982 -	CCTGATATACGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAAT
droEre2	scaffold_4845:19001857-19001933 -	CCTCATATACGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droEug1	scf7180000409672:4238931-4239007 -	TCTTATATACGTAAATAT-CTAAA-------------------GT-TGA-----ACTTCG-------------------TCAATGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droBia1	scf7180000301506:492626-492701 +	CCTCATCTACGTAAATAT-CTAAA-------------------GT-TGA-----ACTTGG-------------------CC-GTTGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droTak1	scf7180000415870:8900-8976 +	CCTAATCTACGTAAATAC-CCTAA-------------------GT-TGA-----ACTTGG-------------------CCAACGGCAAGTCACAGCTCTTCGTGTTTACAGGAGAACGAGT
droEle1	scf7180000491201:224449-224509 +	CCTCATCTATGTA--TAT-CT----------------------GT-TGA-----ACTTGG-------------------C-AACGGCAAGTCACAGC----------GGCAGGAGAACGAGT
droRho1	scf7180000777760:20996-21071 +	CCTAATTTATGTAAATAT-TTAAA-------------------GT-TGA-----ACTTGG-------------------CC-ACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droFic1	scf7180000454066:908249-908325 -	TCTCATCTATGTAAATAT-TTAAA-------------------GT-TGA-----ACTTGG-------------------TTAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGT
droKik1	scf7180000302481:290804-290880 +	TCTCATCTACGTAAATAC-ATTAA-------------------GT-TGA-----GCTAGG-------------------CGATGTTGAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAAT
droAna3	scaffold_13266:18269908-18269984 +	TCTTATCTACGTAAGGAA-CTCAA-------------------TTTTTA-----CATTAA-------------------ACCGAAGCAATTTAACACGTTTCTTATTT-CAGGAGAACGAGT
droBip1	scf7180000396735:1548333-1548409 +	TCTTATCTACGTAAGGGA-CTCTG-------------------TTTTTA-----CATTGA-------------------TTAAAAAAAACTCAAAACTTTTCATGT-TGCAGGAAAACGAGT
dp4	chr3:12187380-12187463 +	TCTCATTTATGTAAGGGA-TCGGC-------------------GA--GAGTTTTT----CCCAC--GGAATA---TCAT-------TATATTATATTGTTATGTGCCTGCAGGAAAACGAGT
droPer1	super_44:370827-370910 +	TCTCATTTATGTAAGGGA-TCGGC-------------------GA--GAGTTTTT----CCCAC--GGAATA---TCAT-------TATATTATATTGTTATGTGCCTGCAGGAAAACGAGT
droWil1	scaffold_180697:3635911-3635996 -	TCTTATCTATGTAAGACAATCCAC-------------------GA--GGTGGTTG----GGAAG---ACAAATTTTGAA-------TA-ATTGGATTTTGATTTTTCTACAGGAAAACGAAT
droVir3	scaffold_12875:11727604-11727672 +	TCTCATCTATGTAAGTGA-TGA---------------------------------TGCGTCCATTGGGAATA---TCAT------TTA----------ATTTGTGTTGGTAGGAAAACGAAT
droMoj3	scaffold_6496:15129882-15129962 -	TCTCATCTATGTAAGTAG-TAATA-------------------GG-TGT-----TTGTAG-------ACATAT--TCA------GTTAATTTTCGCATTTGTGTATTGGCAGGAAAACGAAT
droGri2	scaffold_15245:6497408-6497485 -	TCTCATCTATGTAAGTGA-TGCAAATGAATAAATATTAATCATAT-TGC-----CTTTAA-------------------TCAATGGT------------------CTTGCAGGAGAATGAGT

dme-mir-1009 (Present in the melanogaster group except in the ananassae subgroup)

Species	Coordinate	Alignment
dm3	chr2R:19880568-19880647 -	CATTCAAGACGTAAGTGTAAGACTTTCTTG-AGTTAC---CCGCG-ATGAGTATCTCAAAA---ATTGT-----TACATTTCAGAGCGATAGC
droSim1	chr2R:18425645-18425724 -	CATTCAAGACGTAAGTGTAAGACTTTCTTG-AGTTAC---CCGCG-ATGAGTATCTCAAAA---ATTGT-----TACATTTCAGAGCGATAGC
droSec1	super_9:3164542-3164621 -	CATTCAAGACGTAAGTGTAAGACTTTCTTG-AGTTAC---CCGCG-ATGAGTATCTCAAAA---ATTGT-----TACATTTCAGAGCGATAGC
droYak2	chr2R:19858952-19859031 -	CATTCAAGACGTAAGTGTAAGACTTTCTTG-AGTTAC---CCGCG-AGGAGTATCTCAAAA---ATTAT-----TACATTTCAGGGCGATAGT
droEre2	scaffold_4845:21253651-21253730 -	CATTCAAGACGTAAGTGTAAGACTTTGTTG-AGTTAC---CCACG-TAGAGTATCTCAAAA---TTTGT-----TACATTTCAGAGCGATAGC
droEug1	scf7180000409464:253227-253305 -	CATTCAAGACGTAAGTGTAA-ATTTTCTTG-AGTTAC---CACCG-AAAAGTATCTCAAAA---ATTGT-----TACATTTCAGAACGACAGC
droBia1	scf7180000302143:411852-411931 -	CATTCAAGATGTAAGTGTAAGACTTTCTTG-AGTTAC---CATCG-AAAAGTATCTCAAAA---TTTGT-----TACATTTTAGAACGACAGC
droTak1	scf7180000415878:1005536-1005616 -	CATTCAAGATGTAAGTGTAAGAGTTTCTTG-AGTTAC---CTTTCCAAAAGTATCTCAAAA---ATTGT-----TACATTTCAGAACGATAGT
droEle1	scf7180000491214:5200370-5200449 +	CATTCAAGATGTAAGTGTAAGACTTTCTTG-AGTTAC---CATCG-AGGAGTATCTCAAAA---ATTGT-----TACATTTCAGAACGATAGC
droRho1	scf7180000767536:44385-44464 +	CATTCAAGATGTAAGTGTAAGACTTTCTTG-AGTTAC---CATCG-AAAAGTATCTCAAAA---ATTGT-----TACATTTCAGAACGATAGC
droFic1	scf7180000453858:1616364-1616443 -	CATTCAAGACGTAAGTGTAAGACTTTCTTG-GGTTAC---TGTCA-AGGAGTATCTCAAAA---ATTGT-----TACATTTCAGAACGACAAC
droKik1	scf7180000302355:470337-470417 -	GATCCAAGACGTAAGTGTAAAAGTTTGTTG-AGTTAC---CGCCGCAAATGTATCTCAAAA---GACGT-----TACATTTTAGAATGAAAGC
droAna3	scaffold_13266:5750537-5750615 -	GATTCAAGATGTAAGTTTTGAATACTTCTA-CTCTAT---CTTG--GAATGTCTCTCATAA---TTGTC-----CATCTTCTAGAACGATAGC
droBip1	scf7180000396372:363890-363969 -	TATCCAAGATGTAAGTTTTAAATGCTTCCT-ATTTTT---ACAAA-AAATATATCTTATAA---TTTAA-----AATCTTCCAGAACGATAGC
dp4	chr3:7562606-7562681 -	CATACAAGATGTAAGTTCGAGAATCCCA---------AACACATA-AGTTCTTTTTTAACA---T----CCAAATATTTTGTAGAGCGACAAC
droPer1	super_2:7758009-7758084 -	CATACAAGATGTAAGTTCGAGAATCCCA---------AAAACATA-AGTTCTTTTTTAACA---T----CCAAATATTTTGTAGAGCGACAAC
droWil1	scaffold_180700:5103988-5104069 +	TATCCAGGATGTAAGTATTTAAAGTTATTTTCATAAT---GACG--GGAA---A-TCAATGATTTGCATTCA--CTCATTGCAGAGTGATAAC
droVir3	Unknown	---------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:14788221-14788303 +	TCTACAGGAGGTAAGGACCAATTGGTA--A-AGTGAGAAATTGGA-AGAAATTTATTGAAA---TTTAT---ACTCGTGTTTAGGACAAGGAG
droGri2	Unknown	---------------------------------------------------------------------------------------------

dme-mir-1012 (Present in the melanogaster subgroup, in D. eugracilis and D. biarmipes)

Species	Coordinate	Alignment
dm3	chr3R:22687061-22687139 -	CAAAAGAACGGTGGGTAGA-ACTTTGATTAATATTG-------------------------------C---TTGAAAAATATT--------------------------------------AGTCAA-----------A--GATTTTCC-CCATAGATTTATCAAT
droSim1	chr3R:22517520-22517597 -	CAAAAGAACGGTGGGTAGA-ACTTTGATTAATATTG-------------------------------C---TTG-AGAATATT--------------------------------------AGTCAA-----------A--GATTTTCC-CCATAGATTTATCAAT
droSec1	super_13:1460555-1460632 -	CAAAGGAACGGTGGGTAGA-ACTTTGATTAATATTG-------------------------------C---TTG-AGAATATT--------------------------------------AGTCAA-----------A--GATTTTCC-CCATAGATTTATCAAT
droYak2	chr3R:23804850-23804929 +	CAAAAGAACGGTGGGTAGA-ACTTTGATTAATATTG-------------------------------C---TTGCAAGATATT--------------------------------------AGTCAA-----------A-GG-TTTTTCCCCATAGATTTATCAAT
droEre2	scaffold_4820:5353894-5353973 +	CAAAAGAACGGTGGGTAAA-TCTTTGATTAGTATTG-------------------------------G---TTTCAATATATT--------------------------------------AGTCAA-----------A-TG-TTTTTCCCACTAGATTTATCAAT
droEug1	scf7180000409770:137927-138002 -	CTACAGAACGGTGGGTAAA-CTTTTGACTTATATTG-------------------------------T---T---AAAATATT--------------------------------------AGTCAA-----------A--CTTTTTCC-CCCTAGATTTATCAAT
droBia1	scf7180000302113:2951574-2951651 -	CAAAGGAACGGTGGGTATT-CATTTAACTAGTATAA-------------------------------A---TCGAGTTATATT--------------------------------------AGTCAA-----------ATG--GATT-C-CCATAGATTCATCAAC
droTak1	scf7180000415286:732115-732193 -	CAAAAGAACGGTGGGTACTTACTTTGATTAATACTA-------------------------------C---TTGCAAAATATT--------------------------------------AGTCAA-----------ATGG--AT-TC-CCACAGATTTGTGAGC
droEle1	scf7180000491280:725180-725257 -	TAAAAGAGCGGTGGGTAAA-C-ATTGATTAATACTT-------------------------------T---ATG-TGGATGTT--------------------------------------AGTCAA-----------T-GG-ATTTCCTACTCAGATTTATAAAT
droRho1	scf7180000779166:13483-13560 +	TAAAAGAACGGTGGGTAAA-C-ATTGATTAATATTT-------------------------------T---ATG-CGGATATT--------------------------------------AGTCAA-----------T-GG-TTTTTCCCATCAGATTTATCAAT
droFic1	scf7180000454055:2583625-2583701 -	CAAAGAAACGGTGGGTGAG-C-ATTGGTTAATACAG-------------------------------T----GG-TGCATATT--------------------------------------AGTCAA-----------T-GA-TATTCCCCACTAGATTTATCAAT
droKik1	scf7180000297719:58341-58418 +	TGAAGCAGCGGTGAGTTTT-AATT-GGTTGTATATT-------------------------------G---AAA-TTGCTGAT--------------------------------------TATAAA-----------G-GG-TTTCTCTTTATAGTTTCATCAAT
droAna3	scaffold_13340:16646762-16646838 +	TAAAAAAGCGGTAGGTTTC------AACCAAATTTC-------------------------------C----TTTGAGAGTTC--------------------------------------AGTTAA-------CTTTATA--TATTCT-TTTTAGCTTCACTAAC
droBip1	scf7180000396424:162684-162765 +	TTAAAAAACGGTAGGCATT-ATTTAAATTACTATGG-------------------------------G---CTA-CTACTATT--------------------------------------AGCTTA-------CTCCATA--CTTTCA-TTTCAGCTTCACCAAC
dp4	chr2:4781326-4781413 +	ATTCAGAGCGGTGGGTAGT-CTCTCA-TATATAGT---------TATAAAAG---------------A---ACGAACACCAGT--------------------------------------GGTTAA--------GCAATG--CATTTC-TTGTAGATTCATCAAT
droPer1	super_19:478313-478400 +	ATTCAGAGCGGTGGGTAGT-CTCTCA-TATATAGT---------TATAAAAG---------------A---ACGAACACCAGT--------------------------------------GGTAAA--------GCAATG--CATTTC-TTGTAGATTCATCAAT
droWil1	scaffold_181130:2629013-2629089 +	TGTCAGAACGGTATGGT---------------AGTG------------CAAG----AAAGCCGAAATT-----------------------------------------------------CAAAAACACCCTAA---T-TGTAACAAT-TTGCAGATTTGTCAAC
droVir3	scaffold_13047:12018106-12018186 -	TAAAGAAACGGTACGGATT-G-TTTATTT-AAATG--------------------------------CTTTAT-----ATATT----------------------------------TATCTATAAGCTA--------T--CTTTTTGT-TTGCAGTTTCATTAAC
droMoj3	scaffold_6540:29763932-29764036 +	TAAAAAAACGGTGTGTAAA-TA-TGGATTATTATT---------TATAAATTATCGAAAACTTAACTTCTAAT-----GTTTT----------------------------------TATATTTATATTT--------T--CAACATAC-TCTCAGTTTCATCAAC
droGri2	scaffold_14624:2192652-2192780 -	TCAAGAAGCGGTACGTTCTACATTTGGTTGAACTATTCTTGAACTTGAGCCG---------------A---A---AAAACTTTAGCTGTATTTTAAACATTCTTTTTCAATCTCTTTTGTG---TGT-----------G-TGTTTTTAT-TTGCAGTTTCATTAAC

dme-mir-1013 (Present in the melanogaster group except in D. eugracilis and the ananassae subgroup)

Species	Coordinate	Alignment
dm3	chr3R:26617348-26617428 -	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droSim1	chr3R:26257491-26257571 -	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droSec1	super_4:5435205-5435285 -	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTTTGCCGAACTCGC-------AGGCGACGGATG
droYak2	chr3R:27538988-27539068 -	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATT---GGGA---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droEre2	scaffold_4820:1381509-1381589 +	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATT---GGAG---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droEug1	scf7180000409679:78781-78854 -	TGCTGGAAAGGTGAGTT-----CATAGACTA----AATCAGTA---TGAA---AAGT-----------G---ACTA-----------AT------ATACCGAATTCGC-------AGGAGACGGATG
droBia1	scf7180000302113:733291-733370 +	TGCTGGAGCGGTGAGTT----TCGTACACTT----AGTTAATT---CG-G---AGGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGGCGGATG
droTak1	scf7180000415367:120666-120746 +	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATA---TGGA---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droEle1	scf7180000491280:2970976-2971056 -	TGCTGGAGAGGTGAGTT----TCGTACGCTT----AATTAATA---AATG---AAGC-----------A---ATTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droRho1	scf7180000774800:25022-25102 -	TGCTGGAGAGGTGAGTT----TCGTACACTT----AATTAATA---AAGG---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCGC-------AGGCGACGGATG
droFic1	scf7180000453782:677618-677701 +	TTCTGGAGCGGTGAGTT----TCGTACACTT----AATTAATA---CAAGAAGCGGG-----------G---ATTA-----------ATAAAAGTATGTCGAACTCGC-------AGGCGGCGGATG
droKik1	scf7180000302390:601165-601254 -	TGCTGGAAAGGCGAGTT----TTGTATATTT----AATTAATT---TTCA---AAGT-----ATCGTTCATAATTA-----------ATAAAAGTATGCTGAACTCGC-------AGGCGGCGAATG
droAna3	scaffold_12911:4366276-4366351 +	TGCTGGAGAGGTAATCT----TTGAATAATT----ATCTGTGA---GTTG---TGGC-----------A---TCTA-----------ATGATTGT-----TATCTTCC-------AGACGTCGCATG
droBip1	scf7180000396640:1207121-1207194 +	TGCTGGAGCGGTAAGTT----GGA-G-GAAT----GCCTATGAGTCACG-------------------------TC-----------ATGTACTGATCTTTATCTTCC-------AGACGACGGATG
dp4	chr2:577095-577179 +	TGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCAT-------AGACGACGGATG
droPer1	super_7:3361279-3361363 +	TGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCAT-------AGACGACGGATG
droWil1	scaffold_181130:10168436-10168515 -	TATTAGAAAGGTATAAT----GAATAAACCA----ATTTGAAT---AG-C---AAAC-----------C---ATTA-----------AATCAATTTCCTTTTTTGTCT-------AGACGACGTATG
droVir3	scaffold_13047:11434933-11435023 -	TGCTGGAGAGGTGGGTG-----CATCCACAT----CAGCTGCT---TG-A---TAAC-----------C---ATTTGTAAA--TGTA---AATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATG
droMoj3	scaffold_6540:30312693-30312782 +	TGCTGGAGAGGTGGGAG-----CATTGATTTCACCACCCATAAGACACA-------------------------TTCTCAC--AGTT---TTTCTTGC-TTAATTCC-TTTGTACAGGCGGCGCATG
droGri2	scaffold_14624:1473567-1473660 -	TGCTGGAAAGGTGATTCAAATCCATA----------------AGCCACAA---TCTTCTT-AAATATTATTT-------TCGCT------AATGCTATTTGTACTCGCTTTGATTAGGCGTCGCATG

dme-mir-1015 (Present in the melanogaster group)

Species	Coordinate	Alignment
dm3	chr3R:20164944-20165027 +	GGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droSim1	chr3R:19998547-19998630 +	GGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droSec1	super_0:20503501-20503584 +	GGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGTCTGAGTGAG-A--------C----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droYak2	chr3R:26340576-26340659 -	GGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGACTGGGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droEre2	scaffold_4820:7895698-7895781 -	GGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTGAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCT
droEug1	scf7180000409798:215834-215917 -	GGCTACAATGGTGAGTG----ATGCTCCAGATAGCTTCGCAAAGTAAG-G--------A----TA------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droBia1	scf7180000302136:526700-526783 +	GGCTACGACGGTGAGTG----ATGCTCCAGATGGCTGGGCTAAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droTak1	scf7180000415769:2262022-2262105 -	GGCTACGACGGTGAGTG----ATGCTCCAGCTGGCTTGGCAAAGCGTG-G--------A----TC------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droEle1	scf7180000491008:477710-477799 +	GGCTACGACGGTGAGTG----ATGCTCCAGAAAGCTTGGCCAAGTGAC-C--------A----CCCATACTTAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCT
droRho1	scf7180000779477:268227-268312 +	GGATACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTAAGTGAG-G--------A----TTAA----TAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCT
droFic1	scf7180000453912:1339930-1340015 +	GGCTACCAAGGTGAGTG----ATGCTCCAGATAACTTGGAAAAGTGGG-A--------ATACGGA------TAAGTCC--GGAC-----TTCTCTCTTGCAGTCAAGATTCT
droKik1	scf7180000302387:55063-55149 +	GGCTATGACGGTGAGTG----ATGCTCCAGATAGCTTAGTTTAAAAAAAG--------A----TTCA----AAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCT
droAna3	scaffold_13088:204250-204334 +	GGCTACGACAGTGAGTG----ATGCTCCAGATAGGTTGGCTTAGGAAGTC--------A----TT------AAAGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCT
droBip1	scf7180000396413:258469-258553 +	GGCTACGATAGTGAGTG----ATGCTCTAGATAGGTTAGCTGATGAAG-T--------C---TTT------CAAGCCCTAGGTC-----ATCTCTCTTGCAGTTAAAATCCT
dp4	chr2:18646211-18646293 -	GGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACT
droPer1	super_3:1376411-1376493 -	GGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCT
droWil1	scaffold_181108:4541730-4541803 -	GGTTATGACAGTAAGTTA--GCTGGTAAAGTTGATTTCT------------------------TT------TAACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTT
droVir3	scaffold_13047:3497495-3497585 +	GGCTACGAAAGTAAGTA----T-TTACTTGATAACTCGTT------AA-ACCTAAAGTC----TGTT----AACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACT
droMoj3	scaffold_6540:20508346-20508426 +	GGCTACGATGGTAAATG-CTGATGTTCATGAATATTTATCCAAGTAAT-T--------T----------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTT
droGri2	scaffold_14906:156642-156726 +	GGCTATGATAGTGAGTTG---ATTCTATTGT--AATAATC-AAATC-G-T--------T----TTTG----TTATTTTATAAAC---ATGCCATTTTAACAGTCAAGATACT

dme-mir-1016 (Present in the melanogaster subgroup and in D. eugracilis)

Species	Coordinate	Alignment
dm3	chr2R:10120625-10120702 -	AGCTTTTCCAGTAAGTATAGAG---AG----GATGTGA-TT---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGG
droSim1	chr2R:8883303-8883380 -	AGCTTTTCCAGTAAGTACAGAG---AT----GATGTAA-TG---CGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGG
droSec1	super_1:7628251-7628328 -	AGCTTTTCCAGTAAGTATAGAG---AG----GATGTAA-TG---CGTA-----------------TA-T---------------TCCAATGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGG
droYak2	chr2R:10057673-10057750 -	AGCTGTTCCAGTAAGTATAGAG---GG----GATGTGA-TG---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGG
droEre2	scaffold_4845:15723076-15723153 +	AGCTGTTTCAGTAAGTATAGAG---AG----GATGTGA-TG---GGCA-----------------AA-A---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGG
droEug1	scf7180000409462:2724072-2724150 +	AGCTTTTCCAGTGAGTATAGAG---AG----GATGTGA-TGG--TGTA-----------------AT-T---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGTGGC
droBia1	scf7180000301506:3144553-3144629 +	AGCTCTTCCAGTGAGTATAAAG---AG----GACGTGA-TG----CCA-----------------AG-T---------------GCCAAAGTTTACCTGTCTCCA--TA-CTTAGTCGGCGCGGA
droTak1	scf7180000414111:24451-24531 -	AGCTTTTCCAGTGAGTATAGAG---AG----CATGTGA-TGCAAGGTA-----------------AT-G---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGGCGCGGA
droEle1	scf7180000491349:753079-753159 +	AGCTTTTTCAGTGAGTATCGAA---GG----CATATGC-AA---GATA-----------------T--------GA--T-GTATACTAAGATTAACCTCT--TTA--AA-CTTAGTCGTCGCGGA
droRho1	scf7180000777200:436785-436865 -	AGCTTTTCCAGTTAGTATCAAATTTAT----GATATGA-TT---GGTA-----------------AA-T---------------ACTTAAATTGACCTCTCTCCA--TT-CTTAGTCGTCGCGGA
droFic1	scf7180000453948:312452-312529 +	AGCTTTTCCAGTAAGTATAGAG---CA----GATGTGA-TG---GGTC-----------------AG-A---------------ACCAAACTTCACCTGCCTCTG--TA-CTTAGTCGTCGCGGA
droKik1	scf7180000302366:807250-807326 -	AGCTGTTCCAGTGAGTAACGAG---AA----AGGGGAG-TT---GGAA-----------------GC-C---------------ACATAAACTAACATGCATCC---TT-CGTAGTCGCCGAGGT
droAna3	scaffold_13266:5804283-5804355 +	AACTTTTTCAGTGAGTACTTGT---AA------TATAAATC---CATA-----------------A------------------ATCAAAACTCACTTT-TTCCA---A-CTTAGTCGCCGTGGT
droBip1	scf7180000396372:418175-418251 +	AACTGTTTCAGTGAGTACATGC---AA--TGGATATATGTA---CATA-----------------A--A---------------TCCA-GACTTACTT-TCTCC---TA-CTTAGTCGCCGTGGT
dp4	chr3:17369371-17369465 -	AGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATCGTCTGAAAC----TAATT----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGTCGCGGC
droPer1	super_31:422917-423011 +	AGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATTGTCTGAAAC----TAATG----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGGCGCGGC
droWil1	scaffold_180700:1839748-1839823 +	AATTGTTCCAGTAAGTTAAAAT---GA------T---C-TA---AAAT-----------------CATTTC------AA-----ATT--GATTCAATAATCTCTT--CC-ATTAGTCGACGCGGT
droVir3	scaffold_12875:17586462-17586536 +	AACTATTTCAGTAAGTAGCAGG---T----------GC-TG---AGTG-----------------CA-TGATTGTC--------TCTATATCTTGATTATC------T-TTGCAGTCGACGCGGG
droMoj3	scaffold_6496:11208555-11208637 +	AGCTGTTTCAGTAAGTAGAGCA---CG----CATTTCC-AG---TACCCAACTAT----------------TCGTT--------ACTATATCTGTACAATT------T-TTGTAGTCGACGCGGG
droGri2	scaffold_15245:14096520-14096597 -	AACTGTTTCAGTAAGTGGTAAC---ACAACTACTATGT-TT-------------------------G-TGC-----AACA----TTTAATG-------GACAGTATCT-TTGCAGTCGACGGGGA

dme-mir-2500 (Present in melanogaster subgroup, D. eugracilis, D. biarmipes, and D. takahashii)

Species	Coordinate	Alignment
dm3	chr3L:16991548-16991633 -	TTTCTGCAGGTAAGGAA------CACAC------------------ATATAC--------------------------AATACCGTTTGA-------------------------A-----------------------TTTCAAATAATCAGGAT-----------TTTGTGTGTGGA-----C-CTCAGATCATGTTCC
droSim1	chr3L:16333279-16333362 -	TTTCTGCAGGTAAGGAA------CACAC------------------ATAC----------------------------AGTCCCTGTTGA-------------------------A-----------------------TTTCAAATAATCAGGAT-----------TTTGTGTGTGGA-----C-CTCAGATCATGTTCC
droSec1	super_0:9052562-9052645 -	TTTCTGCAGGTAAGGAA------CACAC------------------ATAC----------------------------AATCCCTGTTGA-------------------------A-----------------------TATTAAATAATCAGGAT-----------TTTGTGTGTGGA-----C-CTCAGATCATGTTCC
droYak2	chr3L:17082646-17082729 +	TTTCTACAGGTCAGGAT------CACAC------------------ATAC----------------------------ATTCCCTGTAGA-------------------------A-----------------------TTTAATTTAATCAGGAA-----------TTTATGTGTGAA-----C-TTTAGATCATGTTCC
droEre2	scaffold_4784:16851464-16851547 +	TTTCTGCAGGTAAGGAT------CGCAC------------------ATAC----------------------------AATCCCTGTCGC-------------------------A-----------------------TTTTATGTAATCAGGAT-----------TTTGCGTGTGAA-----C-TTTAGATCATGTTCC
droEug1	scf7180000409711:344223-344305 +	TTCCTTCAGGTAAGGAT------CACAC------------------ATAC----------------------------TATCCC-GTTAT-------------------------T-----------------------TAGGAAATAATCAGGAT-----------GTTCTGTGTGAC-----C-CTCAGATCATGTTCC
droBia1	scf7180000302428:3118519-3118599 +	TTTCTGCAGGTAAGGAA------CACAC------------------ATAC----------------------------AACTCCTGTCGC---------------------------------------------------CAAAGTAATCAGGAA-----------TTTTTGTGTGTC-----C-CTCAGATCATGTTCC
droTak1	scf7180000415352:367402-367485 +	TTTCTGCAGGTAAGGAT------CACAC------------------AGACAC--------------------------AATC-CTGTAA--------------------------AA----------------------T-GTAAATAACCAGGAT-----------TTTTTGTGCGAT-----C-CTCAGATCATGTTTC
droEle1	scf7180000491255:3429589-3429682 -	TTTCTGCAGGTTAGAAT------AACAG------------------ATATAT-ATATATGCATAT-GA------------------TTGT-------------------------G-----------------------TCTCTATTAATCAGTGG-----------TTTTTGTTTAAA---TCC-CCCAGATCATGTTCC
droRho1	scf7180000779902:73528-73612 +	TTTCTGCAGGTAAAGAT------CCCAC------------------TAAC----------------------------ATATTCGGTTTT-------------------------C-----------------------TCTTAAATAAACAGAAT-----------TATTTGTTCGAT-----CAACCAGATCATGTTCC
droFic1	scf7180000454113:3613700-3613786 +	TTTCTGCAGGTAAGGAT------CGCAC-----------------------------------TCC-ATTAACATTTA---------------------GTTTCTCTGG-----------------------------------ATTAATCTGGAT-----------TTCCTGTTTGGA----TC-TTTAGATCATGTTCC
droKik1	scf7180000302486:836784-836802 -	TTCCTGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATCATGTTCC
droAna3	scaffold_13337:13625781-13625860 +	TTTCTGCAGGTGAGCAG------TTCA------------------------------------------------------------------------AGCTTAGCGAG------GTCTGT-TCCAGTTTCCTAACAT---------------------TC----T----TC------CGCTCC-TTTAGATCATGTTCC
droBip1	scf7180000395832:570054-570135 +	TTCTTGCAAGTGAGGAT------TAGG--------G----TCTT------AGGATTTAAGCATTC-------------------------------------------------------C-----------------------ACTGACCACCAT-----------TTTCCCCGCTTA-----T-TCCAGATCATGTTCC
dp4	chrXR_group8:4827172-4827256 -	TTTTTGCAGGTAAGCCATCACC------A-----G-------------------------------------CATTGA---------------------AAGCCATTGA------AATGCG-----------------------TCTAAATAGCAG-----------TCTCTCTC------CTCC-CACAGATCATGTTCC
droPer1	gnl\|ti\|780630171:520-605 -	TTTTTGCAGGTAAGCCATCACC------A-----G-------------------------------------CATTGA---------------------AAGCCATTGA------AATGCG-----------------------TCTAAATAGCAG-----------TCTCTCTC------CTCC-CACAGATCATGTTCC
droWil1	scaffold_180955:197092-197176 -	TTTTTACAGGTAAGCCACAAC------GATGAATG-------------------------------------GCTCGA---------------------GGGAGATTGA------ACTCTA-----------------------TGTA--------ATCTCTTCA--------------CTTTCT-TGCAGATAATGTTTC
droVir3	scaffold_13049:10166528-10166610 +	TTTCTGCAGGTGCGTTCCCCCT------G-----G-CTGATCACATATGT----------------------------------------CGTTTATAC---------------------------------TATAT--------------------TTT-CG-CCTTT----------TGCTCC-TGCAGATCATGTTCC
droMoj3	scaffold_6680:10629198-10629274 -	TTTCTCCAGGTGAGTTACGG---------------T----TC----ACAT----------------------------AATTC---TCGT-------------------------A-----------------------TTCCAAATAACGAA--A-----------TCTTTG--------TCCT-TGCAGATCATGTTCC
droGri2	scaffold_15110:9071740-9071825 -	TTGCTGCAGGTGAGATTTT---G------------ATCGATTAATT-----------A---------------------------------------------------AGTCTG------GCTCTCTTTGCTAAATAT---------------------GC-CAC-TTTTTG--------TGTT-GGCAGATCATGTTCC

dme-mir-4916 (Present in the melanogaster group except in the ananassae subgroup)

Species	Coordinate	Alignment
dm3	chrX:9130484-9130561 -	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-GATC--------G-GTAGCTAA-ATTTCTGAT--------TACTCCTAAAAGCCTTT-TGGA
droSim1	chrX:7292600-7292671 -	-----GATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-GATC--------G-GTA-CTAA-ATTTCTGAT--------TACTCCTAAAAGCCTTT-TGGA
droSec1	super_68:18219-18296 -	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-GATC--------G-GTAGCTAA-ATTTCTGAT--------TACTCCTAAAAGCCTTT-TGGA
droYak2	chrX:17726642-17726720 -	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCTTC-GATC--------G-GTTGCTAA-ATTTCTGAT--------TACCCCTAAAAGCCTTT-TGGA
droEre2	scaffold_4690:5984823-5984900 +	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-GTTC--------G-GTAGCTAA-ATTTCTAAT--------TACTCCCAAAAGCCTTT-TGGA
droEug1	scf7180000409032:831252-831328 +	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-G-AAT---------G-GGAGTTAA-ATTTCTGAT--------TACTCCTAACAGCTTTT-TGGA
droBia1	scf7180000301760:5099763-5099840 -	CTCAAGTTAAG--TGGGTGTTCTTG---GA-AATTCGTCT-C-GATC--------G-GGAGTTAA-ATTTCTGAT--------TACTCCTAATAGCCTTC-TGGC
droTak1	scf7180000415696:84248-84326 -	CTCAAGCTGAG--TGGGTGTTCTTG---GA-AATTCGTCT-C-GATC--------GAAGAGTTAA-ATTTCTGAT--------TACTCCTGACAGCCTTT-TGGA
droEle1	scf7180000491018:142963-143044 +	CTCAAGATTAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-CATC-GCGG---C-GCAGTTTA-ATTTCTGAT--------TACTCCTAACAGCCTTC-TGGA
droRho1	scf7180000779966:24004-24081 -	CTCAAGATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-AATC--------G-GCAGCTTA-ATTTCTGAT--------TACTCCTAACAGTCTTC-TGGA
droFic1	scf7180000454073:2043164-2043241 -	CTCCAGATAAG--TGGGTGTTCTCG---GA-AATTCGCCT-C-AGTC--------G-GCAGTTAA-ATTTCTGAT--------TACTCCTAACAGCCTTT-TGGG
droKik1	scf7180000302704:132397-132474 +	CTCAAAATAAG--TGGGTGTTCTTG---GA-AATTCGCCT-C-GATT--------G-AGAGATAA-ATTTCTGAT--------TACTCCTAATAGCATTT-TGGA
droAna3	scaffold_13047:993027-993099 -	CTGAGAATAAG--TGGGTAGTTCCGAGCGA-AAGACTCCT-C-CATC--------T-TAACATCC-ATTTC----------------CCGTTCAGCCTTT-TGGA
droBip1	scf7180000396431:767428-767505 -	CTAAGGATAAG--TGAGTTATTTCGATCGAAAGATCACTC---CAAC--------A-----CTACATCCATCCGT--------TACCCTTCTCAGCCTTT-TGGA
dp4	chrXL_group1e:1170766-1170851 +	CTCAAGATAAG--TGGGT---TCCG---CA-GATACGTTTTTCC-TCTGCAGACTCGAGAGTCTCTTTTTTTGGC--------TTTCGCCCACAGCCTTT-TGGA
droPer1	super_30:24282-24367 -	CTCAAGATAAG--TGGGT---TCCG---CA-GATTCGTGTTTCC-CCTACAGACTCGTGAGTCTCTTTTTTTGGC--------TTTCGCCCACAGCCTTT-TGGA
droWil1	scaffold_181096:7487013-7487053 +	TACTAC-------------------------------------------------------ATTG-ATTTCAACT------T-TCATTTGATAAGCCTTT-TGGA
droVir3	scaffold_13052:1731758-1731823 +	TTAAATAAATA--TATGTGTAATTT---GA-ATACTGCCT-C-GATG--------G-TTAGCTAC-GTTTTTTAT--------------------TCTTA-TGTA
droMoj3	scaffold_6498:2397373-2397453 +	TTTGAAATTAGGCTTATTGTTATTA---AT-AAAGCCTCATT-TTTC--------T-GCA-CTTG-GCTTTAAAT--------TATTTTTCAAAATTTGGAGATA
droGri2	scaffold_15203:7061825-7061912 +	CTTAAGATAAG--TATGTGTTCCGT---GT-GATAAAAG--GAA-TCTTCA----G-ACAGCGAA-CTGATCGCCTTACTGAATCCG-CTTGCAGTCTTT-TGGA

dme-mir-4919 (Present in the melanogaster subgroup and in D. eugracilis)

Species	Coordinate	Alignment
dm3	chr2R:11833382-11833461 +	ATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCTATAATT----TCTCACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTT
droSim1	chr2R:10571962-10572041 +	ATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCTATAATT----CCTCAAT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTT
droSec1	super_1:9333414-9333493 +	ATACTAAATGGTGAGTCTTT---AGGGG--ATTAGC-A-------------------AGCCATAATT----CCTCACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTT
droYak2	chr2R:17148716-17148795 -	ATACTGAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCCATGATT----CCTCCCT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTT
droEre2	scaffold_4845:14024568-14024647 -	ATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCCATATTT----CCACACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTT
droEug1	scf7180000409672:743657-743735 +	ATTCTAAATGGTGGGTCTCT---AGGGG--ATTTACTA-------------------AA--TTATTT----CCTTGTT-AAATCTC----TTAAC-------------------------------------------CA-TTTACAGAAGCCGTTTT
droBia1	scf7180000302292:2006186-2006264 +	ATACTAAATGGTGAGTCGCC---AGGGG--ATTTCCTA---------AAGGGTAGTAAGCTACA---------TCATT-TAAAC------------------------------------------------------CC-TTCGCAGAGGCCGTTCT
droTak1	scf7180000415795:733163-733243 -	ATACTAAATGGTGGGTCTCC---AAAGG--AATTTATA-------------------CCCATTATAT----CTCTACC-TAATCTT----TAAAC-------------------------------------------CC-CTTACAGAAGCCGTTTT
droEle1	scf7180000491107:834455-834540 +	ATACTTAATGGTGAGTCTTT---GAGGG--TCTAGC-AAGAAACTTGAT-------------AAGCT----CTTGAAT-AAATCCC----TAATC-------------------------------------------CG-CTTACAGAGGCCGTTTT
droRho1	scf7180000779911:267597-267680 -	ATTCTAAATGGTGAGTCTTT---AGGGG--ATTTCT-T-------------------A-CTGTAGTTTTCTCCTAAAT-AAACCCA----TACCC-------------------------------------------ACCTTAATAGAAGCTGTTTT
droFic1	scf7180000453948:1083552-1083633 +	ATACTAAATGGTGAGTCTCT---AGGAG--ATTTAT-A-------------------AGCCCCATTTCAATCCCTAA--TAATACT----TG-AC-------------------------------------------CA-TTTTTAGAGGCCGTTTT
droKik1	scf7180000302385:1064074-1064158 +	ATACTAAATGGTGAGTCTCT---AGAGAGGATTAGT-T--------------------TCTCCTGGT----CATCAAC-TAACCTCTATATGACT-------------------------------------------TA-CCCACAGAGGCCGTTCT
droAna3	scaffold_13266:11891006-11891088 -	ATACTGAATGGTGAGTTTAC---AAG----------------------------------------T----CGGCAC--TAATTTT----TGAAGCGGGAATGTGAATATGAGC---------------------CGTAA-ATTGCAGAAGCGGTGCT
droBip1	scf7180000396547:586646-586723 +	ATACTGAATGGTGAGTCTGG---AGGTC--AATATT-G-------------------AATAAAGGAA----TCTGAA------------------------------TATCGAC---------------------CGTAACATTGCAGAAGCGGTGCT
dp4	chr3:18992465-18992544 -	ATCTTAAATGGTGAGTCTTC---CATTC---------CAGTTCCTTTGCGTTTT-----------------GTCCACT-GATTCAC----TCAAA-------------------------------------------CT-TATACAGAGGCCGTTTT
droPer1	super_242:24179-24258 -	ATCTTAAATGGTGAGTCTTC---CATTC---------CAGTTCCTTTGCGTTTT-----------------GTCCACT-GATTCAC----TCAAA-------------------------------------------CT-TATACAGAGGCCGTTTT
droWil1	scaffold_181150:1332690-1332764 -	ATAATAGCGGGTGAGTGAAA-----GAG--ATA-CG-A-------------------GATTACAATT------TGGATTACATTT-----TTGGT-------------------------------------------TG-GTCGCAGAAACGTCAAT
droVir3	scaffold_12875:17265806-17265878 +	GTGCTGAATGGTGAGCTTTGCCTGA-------G-----------------------------TGGGT----CCACACC-AAATCCTAATCCCATT-------------------------------------------TA-TTTGCAGAGGCTGTGCT
droMoj3	scaffold_6496:10745162-10745253 -	GTGCTAAATGGTAAGTCCCACTTCAGGC--ACTTCT-A-------------------ATCT-------------GAA------------------------------TATTAATACTCTTTCTTTCTCTCTCTCTCCTGT-CTTGCAGAGGCTGTACT
droGri2	scaffold_15245:16779334-16779414 +	GTTTTAAATGGTGCGTGCTT---AACTT--GAAAGAGA-------------------TCTCACAAAT----CCAATCT-TAATTAA----GTGAT-------------------------------------------TC-ATTGCAGAGGCTGTTCT

Present within the melanogaster subgroup

dme-mir-2489 (Present only in D. melanogaster, D. simulans, and D. sechellia)

Species	Coordinate	Alignment
dm3	chr2L:13609978-13610065 +	TAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACGTAAG--T------TCTAATGTATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATA
droSim1	chr2L:13379258-13379345 +	TAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATA
droSec1	super_16:1746055-1746142 +	TAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATA
droYak2	chr2L:10029711-10029796 +	TAAGTTAGATGTGAGTATGGC-------TATT-T----AAATCAACC-----G--A---------ACGTATG--T----ATGTTAT---ATAGT----TTGCA-TTT-TGTATTTGCAGTTTTATGATA
droEre2	scaffold_4929:11847841-11847922 -	TAAGTTAGACGTGAGTATGGC-------TATC-T----AAATCAGCC-----G--A---------ACGTGTA--T------TCTAATGTTT---------GCA-CTT-TGTATTTGCAGTTTTATGATA
droEug1	scf7180000409452:191309-191389 +	TAAGTTAGACGTGAGTATAGTA------CTTA-A----ATTATAAT----TTT-AA----------ATCACA--T------TATAAT-------------GTA-CTTTGTACTTTTCAGTTTTATGATA
droBia1	scf7180000302408:2742697-2742781 -	TAAGTTAGAGGTGAGTACTCCTAAAATA--TA-C----T-------------AAAAATAA-----GAAAACA--T------TCTAACAACC---------AAT-ATT-TGCCCTTGCAGATTTATGATA
droTak1	scf7180000415285:144406-144491 +	TAAGTTAGACGTGAGTATATA-------AATA-T----ATATTAATT-----A-AA---------ATTTAAA--T------CTTAAAT--CGTA----ACATT-TGT-TGTACTTTCAGTTTTATGATA
droEle1	scf7180000491338:1217914-1217998 +	TAAGTTAGACGTGAGTATTGT-------CATTAAGATAGAACAA-----------C---------ATAAACA--T------GTTAA-A--CATA---TTTGTA--TT-TTTTTTTTCAGTTTTATGATA
droRho1	scf7180000780107:475249-475330 -	TAAGTTAGACGTGAGTATTTTTTAAATA---------------ATTT-----A-AA-AA------ACTTACA--A------CTTAATGTGT---------ACA-CCT-TGTATTTTCAGTTTTATGATA
droFic1	scf7180000453925:389433-389515 -	TAAGTTAGACGTGAGTATTGCTCTCAAG-ATT-A----AAATCA-----------A---------AAACCCT--T------ACTAAGACAT----------AC-TTT-TTTATTTTTAGTTTTATGATA
droKik1	scf7180000302656:77460-77543 +	TAAGTTAGACGTGAGTATTACATACGCA------------ATTATATTAATTTTAA---------------G-----------TAATGCTCGTA----TT-TC-CTT-TACTTTTCCAGTTTTATGATA
droAna3	scaffold_12943:1670004-1670098 +	TAAGTTAGACGTGAGTATTGTC------TCTG-T----CAAGTGTAT-----G-GT--ACTAATATTTA------------ACTAATTCTTGTATTA-ACTTG-TTT-TTAATTTCCAGTTTTATGATA
droBip1	scf7180000396728:1558166-1558252 -	TAAGTTAGACGTGAGTATTAATATAATC-CTTAA------A--ATAT--------A---------AAATCAA--T------AATTAAT--CAAA----ACCTC-TTT-CTGATCCATAGTTTTATGATA
dp4	chr4_group1:1879336-1879425 -	TAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAA---------ACAATCA--T------TTTCATATACATA----TATAT-TTT-TGTGTGTTTAGTTTTATGATA
droPer1	super_5:3326179-3326272 +	TAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAAATA------TTTTATATTTTTATATA---TTACATATA----TT-----TT-TTGGTGTTTAGTTTTATGATA
droWil1	scaffold_180772:852556-852643 -	TAAGTTAGATGTGAGTATATTATATCTT--TT-------GTCCCAT----TTTGGA---------ATATGTT--T------TTGAATACCT---------TTT-CTT-TGGGATTTCAGTTTTATGATA
droVir3	scaffold_12723:5236360-5236443 -	TAAGTTAGACGTGAGTATTATCAACATA--TA-T----GAATTATT-----TTAAA---------AT-AATA--A------------T--CGAA----T-TTA-ATT-TGTTATCCCAGTTTTATGATA
droMoj3	scaffold_6500:16444113-16444192 +	TAAGTTAGACGTGAGTATTACAGAGGCC-CTA-------------------TCAAA---------AT---------------ATCATTCGTGTA----TCTAATATA-ATATTTTTCAGTTTTATGATA
droGri2	scaffold_15126:8263498-8263582 -	TAAGTTAGACGTGAGTATTTATTAACTT--CA------------------TTCAACGTA------ATATACA--T------ACTAAAATATGAA-------TA--CA-TCATTTTGCAGTCTTATGATA

dme-mir-2494 (Present only in the melanogaster subgroup)

Species	Coordinate	Alignment
dm3	chr3R:12444500-12444591 +	CCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGG
droSim1	chr3R:9022613-9022704 -	CCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGG
droSec1	super_12:1702842-1702936 -	CCGGCGATCAGTAAGTGCACCATA-GTAAA-TGGAA------TAAC------------C-TTCAAAATCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCGCTTACAAGGAGCCCCTGG
droYak2	chr3R:11948238-11948329 -	CCGGCGATCAGTAAGTGCACC-----AGATTGGGAT------TAAC------------C-TTCAAAAGCTGCAGCT-TAACTA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGG
droEre2	scaffold_4770:9193005-9193096 -	CCGGCGATCAGTAAGTGCAAC-----AGATTGGGAG------TAAC------------C-GTCAAAAGCTACAACT-TCAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGG
droEug1	scf7180000409557:86567-86658 -	CCAGCGATCAGTAAGTCCACC-----AGATTGGGAT------TAAT------------C-TTCAAAAGTTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCTCTGA
droBia1	scf7180000299102:379926-380017 +	CCGGCGATCAGTAAGTGCATC-----AGATTGGAGT------TAAT------------C-TTGAACAGCTGCAACT-TAAATA--------TTC---CCAGTTATGTCCACCTACAAGGAGCCCGTAA
droTak1	scf7180000415580:230326-230424 -	CCGGCGATCAGTAAGTGCTTTACC-CCGCATGGGAT------TAAC------------C-TTCAAAAGCTGCAACT-TGAATA--------TTCCATCCAGTAATGTCCACCTACAAGGAGCCACTGA
droEle1	scf7180000490967:720382-720473 +	CCGGCGATCAGTAAGTGCTCC-----CGATTGGAAT------TGAC------------A-TTCA-AAGCTACAACCACAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCACTGC
droRho1	scf7180000778413:42188-42278 -	CCGGCAATCAGTAAGTGCACC-----AGATTGGGGT------GGAC------------C-TT-AAACGCTGCAACT-TAAATA--------TTC---ACAGTAATGTCCACCTACAAGGAGCCTTTCG
droFic1	scf7180000453796:140225-140317 -	CCGGCGATCAGTAAGTGCACC-----AAACTTATAT------TGTC-----------TC-TTCAAAGGCTGCCACT-TGAATC--------TTT---ACAGTAATGTCCACCTACAAGGAACCCCTGC
droKik1	scf7180000302475:105646-105739 -	CCGGCGATCAGTAAGTTA-AT-----AAATTAGGATACCCCAG---------------A-ATCTGGCGCTGCAACT-AACTTA--------TCC---TTAGTTATGCCTACCTACAAGGACCCCGTCG
droAna3	scaffold_13340:7435245-7435333 -	CCTTCCATAAGTAAGTACTAT-----ATACGTCCTG------CTGT------------C-TTATAAAATTGTTATT-T---TT--------TTT---CTAGTAATTGCCACATATAAGGAGCCATTAG
droBip1	scf7180000396708:1418523-1418611 +	CCTGCCATAAGTAAGTGCTGT-----A--TTAATATTT----CTGT------------G-TTCTGAAACTGTTATT----GTT--------TCT---CTAGTAATTGGCACTTACAAGGAGCCATTAG
dp4	chr2:5294070-5294176 -	CCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACCAGGAGCCCGTCG
droPer1	super_19:1006198-1006304 -	CCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACAAGGAGCCCGTCG
droWil1	scaffold_181108:4575794-4575887 -	CCTGGTGTCAGTAAGTCCTCA-----AAATTCAACT------TGTA-----------AC-TAT---AGCT----GT-TAAATTTTCTCCTTATT---ATAGTTATTGCCACCGCCAAGGAGCCAGTTT
droVir3	scaffold_13047:18500385-18500490 -	CCTTCCATCGGTATGTAGGTCCCG-CTAA--CTGGT------TGGGCTTGACAAGTA-ACCATATTTATTTTTTTT-TTTGTT--------CGC---CCAGTGACGGCGGCCATACACGAGCCCATGC
droMoj3	scaffold_6496:22335114-22335203 -	CCATCCATAGGTGAGTCG---------AAGTATAAA------TCTA-----------AT-TGAGAAGGCCCTAACT-GA-CTG------CTATT---ACAGTATACGGTACACTGGAGCACCCCATGA
droGri2	scaffold_15074:333852-333944 -	CCGGGTGTCAGTAAGTTCGTC-----GAATCATTAA------GATC-----------AG-TAAGAAGATGTTCTC----AGTC-----TCCATT---TCAGTTATTGGCAGCTACAAGGACCCCCTCC

dme-mir-4914 (Present in D. melanogaster, D. yakuba, and D. erecta)

Species	Coordinate	Alignment
dm3	chr2L:2737558-2737671 +	AGCCCACAACGTGAGTGAG-A----GC--GAGTTCCAATG--TGGT--------------CCT---------C-------------------------GAAACCAGT-----TGTGCTTCGA--TCAGATT--CCAAAATTG-A-------CACAT--TCCGACCTTGAA----------------------T----------------------------------------------------------------------CA-CC-CACAGCGGATTGGAC
droSim1	chr2L:2697917-2698030 +	AGCCCACAACGTGAGTGAG-A----GC--GAGTTTCATTG--TGGT--------------CCT---------C-------------------------GAAACCAGT-----TGCGCTCCGA--TCAGATT--CCAAAATTG-A-------CACAT--TCCGACCTTGAA----------------------T----------------------------------------------------------------------CA-CC-CACAGCGGCTTGGAC
droSec1	super_5:903640-903753 +	AGCCCACAACGTGAGTGAG-A----GC--GAGTTCCATTG--TGGT--------------CCT---------C-------------------------GAAACCAGT-----TGCGCTCCGA--TCAGATT--CCAAAATTG-A-------CACAT--TCCGACCTTGAA----------------------T----------------------------------------------------------------------CA-CC-CACAGCGGCTTGGAC
droYak2	chr2L:2732716-2732828 +	AGCCCACAACGTGAGTG-----------AGAGGTCCATTGTGTGAT--------------CCC---------C-------------------------AAAACCAGT-----TCTACTCAGA--TCTGATT--CCA-AATTG-A-------CACATTCTCTGACCTTGAA----------------------T----------------------------------------------------------------------CA-CC-CACAGCGGATTGGAT
droEre2	scaffold_4929:2790155-2790264 +	AGCCCACAACGTGAGTG-----------AGAGGTCCATTG--TGGT--------------CCT---------T-------------------------GAAACCAGT-----TCCGCTCGGT--TCATGAT-GCCA-GATTG-A-------CACAT--TCCGACCTTTAA----------------------T----------------------------------------------------------------------CA-CC-CACAGCGGATTGGAC
droEug1	scf7180000409554:3374619-3374738 -	AGCCCACAACGTGAGTG-----------AGAGGTCCATTG-------------------TCCT---------C-------------------------GAAACCAGT-----TCAA-TACGATCGCAG-----CCA-GATTG-A-------CACATTCATTGACCTTGGATCCCTTC-----ATTC---TGAT----------------------------------------------------------------------CT-CC-CACAGTGGATTGGAC
droBia1	scf7180000302188:1736412-1736539 +	AGCCCACAACGTGAGTGAG-A----G---GAGGTCCCTTG--T--C--------------CCCC--------G-------------------------AAAACCTGT-----TCTG-----T--GCAGATT--CCC-GACTG-G-------CACAT--TCCGACCTTGAACCGAACCTCATGATCCCCTTGAT----------------------------------------------------------------------CT-CC-CACAGCGGATTGGAC
droTak1	scf7180000415705:481732-481854 +	AGCCCACAACGTGAGTG-----------AGAGGTCCATTG-------------------TCCT---------C-------------------------GAAACCAGT-----TTAGC-------TCAGCTT--CCA-GATTG-A-------CACAT--TCCGACCTTGAACCGAACCCCTTGACTCCCTTGAT----------------------------------------------------------------------CT-CC-CACAGCGGATTGGAC
droEle1	scf7180000491273:444408-444525 -	AGCCCACAACGTGAGTG-----------AGAGGACTATTG-------------------TCCT---------C-------------------------GAAACCTGT-----TGG--------CGTAGCCCAATCG-AACTGAA-------CATAA--ACCAACCTTGAACCTCTT----TAATTC---TGAT----------------------------------------------------------------------CT-TA-AACAGTGGTCTGGAC
droRho1	scf7180000766156:89928-90042 -	AGCCCACAACGTGAGTG-----------AGAGGTCCACTG-------------------TCCT---------C-------------------------GAAACCAGT-----TGT--------TGCAG-----TCA-CAGTGAC-------CACAT--CCGAGCCTTGAACCCTTT--CTTAATTC---TGAT----------------------------------------------------------------------CT-CC-CACAGTGGCCTGGAC
droFic1	scf7180000453924:665447-665570 +	AGCCCACAACGTGAGTGGT-G----GTGAGAGGACCATTG-------------------TCCT---------C-------------------------GGAACCTGT-----TCCCC-CCAT--TAAGAAT--------CAG-T-------TGCAT--TCAGACCTTGAACCCTTTCTCT----TTCCATGAT----------------------------------------------------------------------CC-AC-CGCAGTGGCCTGGAC
droKik1	scf7180000302473:48907-49013 -	AGCCCACAACGTGAGTG-----------AGAGGTGCCCCA-------------------TCCTCGGTG----C-------------------------AGAACCAGT-----T----------------------------G-A-------CAGAA--CCCGACCTTGAACCTGATCTCTGATCTC---CATT----------------------------------------------------------------------CT-CC-CACAGCGGCCTGGAC
droAna3	scaffold_12916:13439495-13439576 +	AGCCAACAACGTAAGT-----------------------------T--------------CTC---------T-------------------------GAAACCATT----------------------------------------------------CCAATTTTCAAACTTAT--------------------------------CAAGTTGTTAATG--T-------------------------------------CTTT-CA-CACAGGGGCTTGGAT
droBip1	scf7180000396580:12679-12769 -	AACCCACAACGTAAGTT----------------------G-------------------TCTT---------T-------------------------------CGTAAGGTTTCGTTTG--------------------------------------TATAATCTTGAATTTATTA-----A----------------------------ACTGTTGATA--T-------------------------------------CTTT-AA-CGCAGGGGCTTGGAC
dp4	chr4_group4:2073909-2074055 +	AGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCAGA------CCAGAGGCAGCA--TCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGT-----TGC--------T-------------GACTG-A-------CATTC--CACAACCTTGAAC--------------------------------------------------------------------------------------------CATCC-CACAGAGGCCTGGAT
droPer1	super_10:1078993-1079139 +	AGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCAGA------CCAGAGGCAGCA--TCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGT-----TGC--------T-------------GACTG-A-------CATTC--CACAACCTTGAAC--------------------------------------------------------------------------------------------CATCC-CACAGAGGCCTGGAT
droWil1	scaffold_180772:1508928-1509016 +	AGCCCACAACGTAAGTAAT-A----AC--AAA----------------------------------------A-------------------------AAGACCGGT-----TAT--------T-------------TCCT-----------------GTTAGCCTTGAACTTAACC-----AAC------AT--------------------------------------------------------------------CTCAACC-AACAGAGGCCTGGAC
droVir3	scaffold_12963:11356889-11356992 +	AGCCCACAACGTAAGCAAG-A----AT--AGAGAATGCAA-----T-----------CAATGC---------G-------------------------GAAACCAGT-----TGC--------T-------------GACTA-A-------CATGT--GCTTACCTTGAAAT------------TG---TAAC----------------------------------------------------------------------CA-TT-CGCAGGGGCCTGGAT
droMoj3	scaffold_6308:1548471-1548583 -	AGCCCACGTCGGGCCTG---------------------------------------------------------------------------------GACTCCTTT-----A-------------------------------------------------------------------------------CCGCCCACAGCGTCGTCCAGGTGCTGAAGAAGCTATCGCAAAAGGGCAAGACCGTCATACTGACCATACATCA-GC-CATCG----TCGGAG
droGri2	scaffold_15252:5474365-5474478 +	AGCCCACAACGTAAGTG-----------AAACACCGAAAC-----A------CCACAC--AATC--------G-------------------------AGAACCAGT-----TAC--------T-------------GACTA-AGCATTATTATTT--TTTAACCTTGAAATT------------GCATCG------------------------------------------------------------------------CATCCATACAGGGGCCTGGAC

Present within the D. melanogaster only

dme-mir-2497

Species	Coordinate	Alignment
dm3	chr2L:16678240-16678327 +	GCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATG-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATCATTAACA-ACA-TTTACAATGT--TTGCAGGCTGTCAACG
droSim1	chr2L:16366238-16366317 +	GCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACG
droSec1	super_7:325115-325194 +	GCATGTTATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------CTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACG
droYak2	chr2R:4424631-4424712 -	GCACGTCATCGTAAGCTTTGCTAT--------------------------------------------ATA-----T-----------GTAG------------------AT------------------------------------------------------------------GTGAATTTCGAGCTTCAATTCTTTT-------C---TATTCT--CTTCAGGCTGTCAATG
droEre2	scaffold_4845:19748465-19748542 +	GCACGTTATTGTAAGCTGCGCCA----------------------------------------------TA-----T-------------AG------------------TT------------------------------------------------------------------CGTAAATTCGAGCTTCAATTATGTT-------C---TATTCT--CTCCAGGCTGTCAATG
droEug1	scf7180000408961:253917-253999 +	GCAACTTATTGTAGGCAACATAAT--------------------------------------------TTA-----A-------------TA------------------AT----------------------GT-------------------------------------------TGAATCTCAGATTCTAATCCTACT-------TTT-ACTTCC--TTTTAGGCAGTCAATA
droBia1	scf7180000301468:836919-836998 +	GCAAGTCATTGTAAGCTACTAAAC--------------------------------------------T--GCCTGT---TTAT----AT-------------------------------------CCAAATTACT---------------------------------------------------------GACTATA---------ATTCTCGTCC--AACCAGGCTGTCAATG
droTak1	scf7180000415914:402905-402995 +	GCAAGTTATTGTAAGCTACACATT--------------------------------------------TTA--TCTT---TTGCAACCAA-------------------------------------AGAG--AGCC------------------------------------------TA-TTCTAATAC-----------T--CTATTC---CACGCAACCCACAGGCAGTCAATG
droEle1	scf7180000490579:668435-668611 -	ACAAGTTATTGTGAGTCCAAAT--TTAAGGCTTTTTTAAGTACGAAAACTATCATCA-TTAATCCGTTAC----------ATTT--------------------------TTGACATGGGCTAGCTTTAACTAGGCTGAAAATTGAATATTATTACGATTACTAATATATATACTAATAC--------------GAACTTACT--TTG-TC---TTTTCT--CCTCAGGCGGTCAACG
droRho1	scf7180000777347:13388-13508 -	ACAAGTTATTGTAAGTAAGGAATT--AAGGCTTCTTTGAGTAA-----------TCA-T--AT-----TCG-----A-------------CAAGAGCAATTCACATATTTTTGACATGTTTTG----------------------------------------------------------------ACCT---ACTTCATCG------CT---ATATTT--TTCCAGGCTGTCAACG
droFic1	scf7180000449814:1579-1704 -	ACAAGTCATCGTAAGTAATCAAGG------CTTTCTTCATCAGAAAGGTTATTTTTAGCCAAA-----ATA-----CAGGATTT----TT-------------------------------------GGATTAAACTAA-----TAA--------------------------------TA-TTTTTACAT-----------T--TTGTACT--GCTTGT--CCCCAGGCTGTTAATG
droKik1	scf7180000302382:508891-508970 +	GCAAGTGATTGTAAGTTAAGCGAA--------------------------------------------TTC-----A-------------AG------------------AT------------------------------------------------------------------TTTCTAGCCCTAGTACGACCCTTCT-------C---GTTTCT--GACCAGGCTGTCAACG
droAna3	scaffold_12916:15881694-15881776 -	GCAAGTGATTGTAAGATGTAAACTCTTAGACCCTCCTAACTG----------------------------------------------CT-------------------------------------ACA---AGCT---------------------------------------------------------AATACTTTT-------G---CTTTGA--ATCCAGGCTGTTAACG
droBip1	scf7180000396717:120666-120748 -	GCAAGTGATTGTAAGTTTCGAACTCTAAGACCCAAGTAGGTG----------------------------------------------CC-------------------------------------ACAAACTATA---------------------------------------------------------AGT---TTT-------G---CTTTCA--ATCCAGGCTGTTAACG
dp4	chr4_group3:8422196-8422274 +	GCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TTAATC--TTCTAGGCTGTCGAAT
droPer1	super_1:9873279-9873357 +	GCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TGAATC--TTCTAGGCTGTCGAAT
droWil1	scaffold_181132:892507-892591 -	AGAAGTGATTGTAGGTGTCAATGA-------T------------------------------------T--------------T----CA-------------------------------------AACTAACATC--------AA------------------------------TTTTTTATTAAC-----GTCTTTATT-------T---TTTCCT--ATTCAGGCTATCAATG
droVir3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

dme-mir-4908

Species	Coordinate	Alignment
dm3	chr3R:26332541-26332619 +	GAT---GAACTTG-----------------GTAG-GATTTTAAGCATTA--A----GC--AT-GTAT--ATAGTT--T-TTGCTGTGCTCA------------------------------------------------TAAAGTTCTATAGGT-------TCTCGATA
droSim1	chr3R:25978445-25978517 +	GAT---AACCTAG-----------------GTAG-GATTTTAAGCATTA-------GC--------T--ATAGTT--T-TTGCTGTGACCA------------------------------------------------TAAAGTTCTACAGGC-------CTTCGATT
droSec1	super_4:5152162-5152234 +	GAT---AACCTAG-----------------GTAG-GATTTTAAGCATTA-------GC--------T--ATAGTT--T-TTGCTGTGACCA------------------------------------------------TAAAGTTCTACAGGC-------CTTCGATT
droYak2	chr3R:27249459-27249526 +	GAT---GAACTAG-----------------GTAG-GACTATGAGCATAT--------------TGGATG-----------TACCATACTCA------------------------------------------------TAAGGTTCCACAGGT-------ACTAGGTA
droEre2	scaffold_4820:1676554-1676621 -	GAT---GAACTAG-----------------GTAG-GATAATGAGTACAA--------------GGCATT-----------GGCCGTTCTTA------------------------------------------------TAGAGCTACACAGGT-------ACTCGATT
droEug1	scf7180000409555:835193-835260 +	GAA---GGACTTG-----------------GTAG-GTTTTTATAGTAAA--------------GGG--------G--TTCTGATATTATGG------------------------------------------------TT-GCTCTTTAAGGT-------TCGAGAAC
droBia1	scf7180000302113:1039325-1039400 -	GAT---GCACTAG-----------------GTGG-GATTTGGTATATAA--------------ATCAGT--CG-G--TACTGAT-----TA-------------TAGAAGG----------------------------TGATATCCTTTAGGC-------TCTCGACA
droTak1	scf7180000415367:489031-489106 -	GAT---GGACTAG-----------------GTGG-GAATTTGTAGATAA--------------GTGT--ATGG-GTTTACTGACTTATAAG------------------------------------------------TTATTTCCCATAGGA-------TCGCGAAC
droEle1	scf7180000491280:2646578-2646653 +	GAT---GCACAAG-----------------GTAG-GATTTTATAATCAA--------------ATGATT--TG-TTACTCTGATGAAGACT------------------------------------------------AAAAACATTACAGGT-------AAGAGAGG
droRho1	scf7180000779405:3534-3609 +	GAT---GCTCTAG-----------------GTAG-GATTTTATAATCGA--------------GAGT-T-TTCTG--TTCTGATAAAGACT-------------------A----------------------------AAAAACTCTGCAGGT-------GAGCGGAG
droFic1	scf7180000454106:145949-146023 -	GAT---GCACTAG-----------------GTAG-GGCTTTCCAGCTCA--------------GAGT--CTAGTG--TACTGACTTGTTGG------------------------------------------------TAAAATGACACAGGT-------TCGCGAGC
droKik1	scf7180000302390:290587-290663 -	GTG---GAACAGG-----------------GTGA-GTAAACAGGGAA-----------ACCGAT-TC-----------TCAGAGAT------------TTCTAT-TAAATAAG----------------------------TTTTCATTTAGGA-------GAAGTGGA
droAna3	scaffold_12911:4648848-4648929 +	GTTTTGGGACTTATTAGGATAAAA--CGGCGTG---------AGTAAAA--------------GAGTTT-----------AAACCAAC-TA-------------A----------------------------------GAAAACT-CATTATTATTTAAACA--TGTA
droBip1	scf7180000396360:4732-4811 +	TAC---CAAAACA-----------GT----TTGA-AGTTCTAGGCATTC-------CT--------T--ATCG-G----------------------------------TTTATCTTGATATTGCTGATGAAATCAGCAAAAAGTTCTGGA------------------
dp4	chr3:12022576-12022652 +	TTT---GAACATG-----------------AGTAAGGAATCGGGATCGA-------CG--------T-----------GTAGATCCATCCG--T----CCA-----CTGAC----------------------------AACGTCTTTGCAGAC-------AAGAAGGA
droPer1	super_20:1381645-1381715 +	GGT---GAGTGTT-----------------GAAG-GGAAGCAAGCTTTG--A----GC--------C-----------AAAGATCTGCAGG--T----TTTCAT-TTGACAGG----------------------------CCTTG------GT-------TT----GT
droWil1	scaffold_181130:9833045-9833120 -	CACT--GAATCAG-----------------GTGG-GTAATAAGAAATTG-------GC-------CT--ACAG-G-------CTAAATACTGAAATTC------TGGA-------------------------------GAAAGATCCA---AA-------TCACGA--
droVir3	scaffold_13049:21775414-21775489 +	CAG---AGCGCGT-------------CT--ATTG-CAAGGTAGGTGGTG------GA-ACGC----------ATC--TATTGATATGCCCG------------------------------------------------TACCTGATCAACTGT-------TGGCTAGG
droMoj3	scaffold_6540:13565420-13565495 -	GAA---TTA---A-----------------GTTC-AAAACGATCGACTAACGCTTAA-ACGC----------------ATATACATATA-----------------TAAAT----------------------------ATATTCCCTGTGTAT-------ACAATGTG
droGri2	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------

dme-mir-4909

Species	Coordinate	Alignment
dm3	chr2R:3598912-3598991 +	TTAGGACAGGGTAGGTTGAAATC--GGATACAACTAAA--AG---T---------TATTTTTAATTGTA-----TCCG------GTCT---TC-ATTTTAGGTCTTCGATT
droSim1	chr2R:2322899-2322978 +	TTAGAACAGGGTAGGTAGAAATC--GGATTAAACTAAA--AC---T---------TATTTTTGATTGTC-----TCTT------GTTT---TC-ATTTGAGGTCTTCGATT
droSec1	super_1:1254451-1254530 +	TTAGAACAGGGTAGGTAGAAATC--GGATTAAACTAAA--AC---T---------TATTTTTGATTGTC-----TCTT------GTCT---TC-ATTTGAGGTCTTCGATT
droYak2	chr2L:16271886-16271964 +	TTAGGACAGGGTAGGTAGAT-TC--GGGTTTAACTAAA--AG---T---------AAGATTTAATAGTT-----TTCT------TTCC---AC-ACTTTAGGTCTTCAATT
droEre2	scaffold_4929:19008524-19008602 -	TTAGAACAGGGTAGGTAGGT-TC--GGATATAACTAAA--AG---T---------AAGATTTAATAGTT-----TTCT------TGCA---TC-ACTTTAGGTCTTCGATT
droEug1	scf7180000409672:5617604-5617678 +	TTCGAACGGGGTAAGTAAAAATC--TTAAAAAGTTAAG--GG---T---------AATTTGCAATATT----------------ATTA---TT-CTTAAAGGTCATCGATT
droBia1	scf7180000301506:717920-717996 -	TTCGAACGGGGTGAGTTTGGA------ATTCAACTAAA--GA---G---------CATCTTAAATTATA-----ATCT-----TATCC---TG-ATTATAGATCCTCAATT
droTak1	scf7180000415870:258337-258416 -	TTCGAACGGGGTAAGTAAAGATC--TGTTAAAGCTAAG--AG---A---------AATAGTCATATATT-----TTCC------ATCA---TT-ATTTAAGGTCATCGATT
droEle1	scf7180000491347:490801-490877 +	TTCGAACGGGGTGAGTAGTTAGT--TGAAAAAACAAAG--AA---A---------AAT-TATGAAAATA-----TCT--------CTC---TA-TTTATAGCTCATCTATA
droRho1	scf7180000780226:27086-27161 +	TTCGGACGGGGTAAGTAGCTAAT--T--TAAAACTTAT--AA---A---------AACCATAAATAATA-----TCC--------CTG---TT-GTTAAAGCTCATCGATA
droFic1	scf7180000453215:617399-617475 -	TTCGAACGGGGTGAGTACAGGGC--TTTCTAAATTAAA--TG---G---------ACTTATTAACAGTT-----TC---------ATA---TG-GTTATAGGTCTTCGATT
droKik1	scf7180000302277:1217173-1217250 +	TTCGAACAGGGTGAGTTATAATC--AAAAAAAATATAT--AT---A---------AACTGGTATTTATA-----TAA--------CGT---TG-TTTGTAGGTCATCGATA
droAna3	scaffold_13266:10106463-10106544 +	TTCGAACGGGGTGAGTGAAAATTATTATGGAAATTGAT--GG---C---------AGAATCT------C-----TCTAAAAAACTCTT---TT-ATTGCAGTTCCTCAATT
droBip1	scf7180000396428:525891-525970 +	TTCGAACGGGGTAAGTGGAGATT--TAATG--TCAATT--CG---T--------ATTAATCTTTCAATA-----ACTA-----TTATT---TT-ATTTCAGTTCCTCAATA
dp4	chr3:6515151-6515232 -	TAAGAACAGGGTGAGTGTATAAT--GGAAGTAGCACAT--TG---T--------TTAAATACGAAAGTA-----ACCT-----TGTTC---CT-GATGCAGTTCATCGATT
droPer1	super_2:6735411-6735492 -	TAAGAACAGGGTGAGTGTATAAA--GAAAGTAGCATAT--TG---T--------TTAAATACGACAGTA-----ACCT-----TGTTC---CT-GATGCAGTTCATCGATT
droWil1	scaffold_180700:1009017-1009113 +	TACGTACGGGGTAAGTGAGGGGG--TATGAAAAATAAGTTTATAGAATGGCAGTTAATATTTGTTTTTC-----TTTT------TTCTTTTTA-TGTATAGTTCCTCTATA
droVir3	scaffold_12875:823177-823258 +	TACGCACGGGGTGAGTACGGCTGACTGCGATAACTGCA--CG---C--------ACATTCACGGCATTC-----ACT---------CT-C-CCATGAGCAGTTCGTCGATT
droMoj3	scaffold_6496:3846146-3846245 +	TGCGAACAGGGTGAGTAGACAGG--AGA-AAAACTAACTGTATAACGCTTCCA-TTACATTCAACTATCCTCTCTCTT-----TGTCT-CTTG-TGAACAGTTCTGCTATT
droGri2	scaffold_15245:10130935-10131010 -	TACGCACGGGGTAAGTGTATCTG--ATACTGGGCATCG--AA---T---------AAAATCTGACACTA-----AT----------CC---AT-GGCTCAGTTCGTCCATT

dme-mir-4910

Species	Coordinate	Alignment
dm3	chr2L:4817806-4817891 -	AAACAGGCAGGTTTGTATGGAA------------TTCCATGAGCT-TC---AAAGTAATGCTTCTAACTCTGTGG----TT--TTTCATATTTCCCAGTGGCAAGAGC
droSim1	chr2L:4687590-4687676 -	AAACAGGCAGGTTTGTATGGAA------------TTCCAGAAGCT-CC---AAAGTAATCTTTCTAACTCTGCGG----GT-TTTCTATCTTTCCCAGTGGCAAGAGC
droSec1	super_5:2913663-2913749 -	AAACAGGCAGGTTTGTATGGAA------------TTCCAGGTGTT-CC---AAAGTAATCTTTCTAGCTCTGTGG----TT-TTTTCATATTTCCCAGTGGCAAGAGC
droYak2	chr2L:4827667-4827754 -	AAACAGGCAGGTTTGTTTGGAA------------CTCCACAAGATTTC---AAGGTATTCCTTCTAACTCTGTGG----TT-TTTCCACATTTTCCAGTGGGAAAAGC
droEre2	scaffold_4929:4898745-4898832 -	AAACAGGCAGGTGTGTATGCAA------------TTCCAAAAGGTCTC---AATGTATTCCTTCTAACTCTGTGG----TT-TTTCTATATTTCCCAGTGGCAAGAGC
droEug1	scf7180000409005:695847-695925 -	AAACCGGCAGGTTAGTAAA----------------------AGTCATT---AAATGAGACTTATTAATATATTGG----TATCCCCTGTGATTTTCAGTGGTAAGAGC
droBia1	scf7180000302188:1388505-1388590 -	AGACAGGCAGGTTCGTTTGATG--------------CTGGGACTTCCC---AAAGCAGTCTTCTTTACTAAAAGG----TT-TTCCTATGTTTTCCAGTGGCAAGAGC
droTak1	scf7180000415705:108883-108969 -	AAACAGGCAGGTAAGTGAGGTT------------T-TCAGGAGTCCCC---AAAG-AGTGTTCTTAACTTTTTGTG---TT-TTCTAATGTTTTCCAGTGGCAAGAGC
droEle1	scf7180000491046:2470328-2470414 -	AAACAGGCAGGTTTGTATGGAG------------TTCTAGACGAA-CT---AGAAAAGGCGCCTTAATTTTCACT----AT-TTTCTGTGTTTTCCAGTGGCAAGAGC
droRho1	scf7180000779189:220715-220726 +	------------------------------------------------------------------------------------------------TGCGGCAAGAGC
droFic1	scf7180000453842:1437048-1437130 +	AAACCGGCAGGTTAGTATGGAA------------TTCTAGGAATC-CC-A-TAAAACAGCATGTTAACTTTAT---------TAATTAT-ACCCCCAGCGGCAAAAGC
droKik1	scf7180000302472:3494720-3494804 -	AGACGGGCAGGTGAGAGAGATGTTAA--TGC---------AAG---TC---AA-GGAATTACTTTAACTTGTTGG----TTTTTTGTAT-GTTTTCAGTGGCAAGAGC
droAna3	scaffold_12916:9386291-9386370 -	AGACCGGCAGGTGAGAATACAA------------TTCTACAACCC-AT---A---CCC--TTGTTTTCA-TATC-----AT-TTTTTCAATTTTTCAGTGGCAAGAGC
droBip1	scf7180000396535:1954132-1954213 -	AAACAGGCAGGTAGGATTGGAA------------TGCATA-AA---CC---AA--TAACCATGTTTTCATATCGT----AT-TTCACATTTTTTTCAGCGGAAAGAGC
dp4	chr4_group3:3567835-3567915 -	AAACAGGAAGGTGAGTGAGAAGCAAATATGTATGCCC----------C----AAGAAATCC---TAACGATCA---------TATTTTC-CCCTTCAGCGGCAAGAGC
droPer1	super_1:5048034-5048114 -	AAACAGGAAGGTGAGTGAGAAGCAAATATGTATGCCC----------C----AAGAAATCC---TAACGATCA---------TATTTTC-CCCTTCAGCGGCAAGAGC
droWil1	scaffold_180772:7924026-7924108 +	AGACGGGCAGGTAATTAAA----------------ACCATAAGGTTACCTTAATGTAT-AT-------TTAAAGTATTTAT-GTACGATATTTTGCAGTGGAAAGAGC
droVir3	scaffold_13246:521383-521402 +	AGACGGGC----------------------------------------------------------------------------------------AGCGGGAAGAGC
droMoj3	scaffold_6500:7585091-7585110 -	AGACGGGG----------------------------------------------------------------------------------------TCTGGCAAAACG
droGri2	scaffold_15252:16729559-16729578 -	AAACTGGC----------------------------------------------------------------------------------------AGTGGGAAGAGC

dme-mir-4911

Species	Coordinate	Alignment
dm3	chr3R:11661999-11662086 -	ATTCTGTCAGGTGAGGAGGAG----CAAAGTG--GCGCCACA--------------------------ATTTACTAGAAACTA-------ATTGCATC----------TTTTTGT-----C-CCCCCGCGTAGGAAGCCTGTC
droSim1	chr3R:9814140-9814226 +	ATTCTGTCAGGTGAGGAGGAG----CGCAGTG--GCGCCACT--------------------------ATTTACTAGAAACTA-------ATTGGATA----------TTCTTGT-------CCACCCCGCAGGAAGCCTGTC
droSec1	super_0:10292642-10292728 +	ATTCTGTCAGGTGAGGAGGAG----CGCAGTG--GCGCCACT--------------------------ATTTACTAGATACTA-------ATTGGATA----------TTCTTGT-------CCACCCCGCAGGAAGCCTGTC
droYak2	chr3R:14775394-14775478 +	ATTCTGTCAGGTGAGGAGGAG----CACACTC--TTGCCACT--------------------------GTTTACGGGAAAATA-------ATTGCATT----------TCCTTA--------C-CCCCTTCAGGAAGCCTGTC
droEre2	scaffold_4770:11186822-11186906 -	ATTCTGTCAGGTGAGGAGAAG----CACAGTG--GTGCCACT--------------------------GTGAAATGGAATCTT-------ATAGCAAA----------TCCTTT--------C-CGCCTTCAGGAAGCCTGTC
droEug1	scf7180000409797:1876330-1876415 +	ATTCTGTCAGGTGAGGAAGTG----ATTGGCT-GCACTAATT--------------------------AGTTACTGTTCACTA-------ATGGCGTT----------TATTTA--------T-CCTCTGCAGGAGGCTTGTC
droBia1	scf7180000302136:1263805-1263892 -	ATTCTGTCAGGTGAGGAGGAG----ATA-CTCCCGTGTATCC--------------------------TGTTAATGGCGACTA-------ATGGCTGT----------TATTTGT------AA-CCCCTGCAGGAGGCCTGTC
droTak1	scf7180000415170:59923-60007 +	ATTCTGTCAGGTGGAGAGGAT----TATTCAT--TTTATTCT--------------------------AGTTACTAGAGACTA-------ATCATGTT----------TATATC--------G-CACCCACAGGAGGCCTGTC
droEle1	scf7180000491080:1438901-1438986 -	ATTCTGTCAGGTGACGAATCG----CTAGCTC--CTGTAATC--------------------------AGCCAGTTGTCACTT-------ATTGCTAT----------TACTTA--------CCAACCCACAGGAGGCCTGTC
droRho1	scf7180000758667:66704-66789 -	ATTCTGTCAGGTGACGAAGGG----CTTACTT--TTGTAACC--------------------------AGAGAATAGGCACTA-------ATAGGTTT----------TATTTA--------CTATCTCACAGGAGGCCTGTC
droFic1	scf7180000452523:1034857-1034941 -	ATTCTGTCAGGTTGTGTGGAT----ACA------------TA----------------ATTTTGAGCCAGTCTCAGGTTACTA-------ATA-TACT----------TATTTA--------TTACCCCGCAGGAGGCTTGCC
droKik1	scf7180000302639:1021889-1021977 +	ATTCTGTCAGGTGAGTGGTGA----TTTAGTC--TCGTTTCTGATA----------------------AAGAACTGAATTCAA-------AGTGTCAT----------TATTTA--------T-CGCCTGCAGGAGGCCTGCC
droAna3	scaffold_13340:16266865-16266954 -	TTTCTGTCAGGTGAGGAACCT----TTCAATT--TAA-------------------------------ATTTATAAGAAGCAA-------GTTC--------TAAATATTCTTGTATCATCAA-TTTACACAGGAGGCTTGCC
droBip1	scf7180000396708:3777834-3777932 +	TTTCTGTCAGGTGGGAAACAT----TTCTTTG--AACATAAA--------ATTTAA------------AATTGCAAGAAT---------------CAATATCTAAAAATT--GGTATCTTCCA-TTTATACAGGAGGCATGCC
dp4	chr2:20340735-20340818 -	CTTCTGTCAGGTAAGGAATGGGAGTCGAAATT--TTTACATA--------------------------ATTTCAAGTCGATTC-------ATTGA---------------CTTT--------T-TGCTCGTAGGAGGCCTGCC
droPer1	super_3:3092226-3092309 -	CTTCTGTCAGGTAAGGAATGGGAGTCGAAATT--TTTACATC--------------------------ATTTCAAGTCGATTC-------ATTGA---------------CTTT--------T-TGCTCGCAGGAGGCCTGCC
droWil1	scaffold_181130:15806464-15806546 +	ATTCTGTCAGGTGAGTGTGAC----TGAAATT--CCAATTCA--------------------------GCATATTTGAACTAT-------ATTAT--A------------TTTT------CTG-CCCCTGCAGGAAGCTTGTC
droVir3	scaffold_12855:5731325-5731399 +	TTTTTGTCAGGTAATTATTA-------------------------------------------------CCCATAAGTATCCCATATAAAACTCATGG----------TGTGTT--------T-CCTTTGCAGGAGGCCTGTC
droMoj3	scaffold_6540:6055060-6055136 +	TTTTTGTCAGGTAATTTAT--------CCATA--TGGATATA----------------ATTTTGAGTG-------GGG--TT-------------CATG---------ATTCTT--------C-CATTAATAGGAGGCTTGCC
droGri2	scaffold_14906:8272381-8272472 -	TTTTTGTCAGGTAATCTATTA----TTCTATA--T---GTCCAGCAAGAAATTTAACAATTTTAATTA-------TGT--T--------------CCA----------CATTT--------AA-ATGTTGCAGGAGGCCTGTC

dme-mir-4912

Species	Coordinate	Alignment
dm3	chr2L:4829970-4830049 -	GCAGCTTTAAGTGAGTAGTCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TTACTTTCTATAAAT----------------------------------------------------T-AATGT--CC-----ACTACTTTTAGTCTCTATGAC
droSim1	chr2L:4699802-4699881 -	GCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGAC
droSec1	super_5:2925678-2925757 -	GCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGAC
droYak2	chr2L:4839799-4839882 -	GCAGCTTTAAGTGAGTAAAACT---ATGTCTATTA--------------------------------------------GGT---------------------------------------------------------------------------------------------------------------------GA----AAT-TAACTTTCTATAAAT----------------------------------------------------T-ACTTT--TC-----TTTATTTTTAGTCTATATGAC
droEre2	scaffold_4929:4910725-4910823 -	GCAGTTTTAAGTGAGTAAAATT---AGGTTTAATTT--------------------------------GG-TTTATTA-GGAGAA--------------------------------------------T-TTTAA------------------------------------------------------------AATT----------A-C-TTTTTTAAAT----------------------------------------------------T-GCTTT--TC-----ATTATTTGCAGTCTCTATGAC
droEug1	scf7180000409005:708025-708172 -	GCAGCTTCAAGTAAGTATATGT---ATATATGTATATATTATTC-------------------------------------------------------AAATCGA------------------------------TGA--------------------------------------------TTAAATATAGATTAG----GTCAATTC--------------C-------TATTTGAATCCATTTATTCATAAAGGTTCCTTTTTATTCAAAA-TA--TTCCTAT-----TTTATTTTCAGACTCTACGAC
droBia1	scf7180000302188:1402574-1402693 -	GCAGTTTCAAGTGAGTGGGGAT---TT----------------------TGGGGAG-------------------------------------------------------------------------TCATTAAAGC-CTTTAAAGATGTCGAACTTTATGGTA-----------------TTAAG--------C------------AAGCAT--------------------------TTAATGGA-------------------------TT-T-ATG----AACGTATATACTTCCAGACTCTACGAC
droTak1	scf7180000415705:123604-123779 -	AAAGCTTCAAGTGAGTGGGGATAGCAAGTTTATA---------------------------GCACATAGGTTCTATTA---------------------CAA---------------------------CAGATCTACATATCTAAAGTCATTGAAATTT--GGCCTAAAATTGCTTTTATATTAGTTATTTTATTA----------------------------------------------------ACATAAATGATAAAGCTTTAATAAAT-TC--TCCCCAT-----TGTAATTCCAGACTCTACGAC
droEle1	scf7180000491046:2483313-2483390 -	ACAT--TCAATCAAGTTTTTGT---TC------------------------------------------------------------------------------------------------------------AAGT--------------------------------------------TTAAGTACTTATTGA----CTCAATTT--------------CACT-----------------------------------------------------TT--TT-----TAAATTTATAGACTCTATGAC
droRho1	scf7180000768274:29812-29992 +	GTACCTTCAAGTGAGTGGGGAT---TTGGGAA-----------------------TTCATTCCAAATAGATTTTATAAAGGG-GACATTTATAATGTTCAAATTCAAGACCCCCAGACAATTTTGTTCCTTTTTAAAGTTATTTATTTC------------------------------AAGTTCGTTAATTTACTAA----TTTAATTT--------------TGCC-------------------------------------------------TTACT----A----ATGTTTTTCCAGGCTCTTCGAC
droFic1	scf7180000453842:1425514-1425595 +	GCACCTTCAAGTAAGTGGTTGT---ACATT----------ATAC-------------------------------------------------------A--------------------------------------------------------------------------------------AATATCGA--AATGAGTTCAATAC--------------------------------------------------------------------CATTC--CT-----ATTATCTCCAGGCTTTATGAC
droKik1	scf7180000302472:3508962-3509042 -	GCACCTTCAAGTGAGTCTAATTATTA-------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------C------------------------TCTTTTTTTGTAT----GTTTTA-------------------------AATT-CAGTCT--CT-----GATCCTTGCAGCCTCTATGAT
droAna3	scaffold_12916:9399294-9399369 -	GAAGCTTCAAGTATGTTAAGAA---AT----------------------CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TTTTA------------------------TAT----T------TTCATACA---------------AA---------------ATTCA-TTTTTTCAGCTTGTACGAC
droBip1	scf7180000396535:1966696-1966774 -	GGAGTTTCAAGTGGGTTAAGAA---AT------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCATAGCTTT----ACTTA------------------------TAT----T------TTCATTAA-----------------------GA-------ATTCG-TTATTTCAGCCTGTACGAT
dp4	chr4_group3:3587827-3587928 -	GCACATTTAAGTGAGTAGGAAA---AA----------------------TCG-----------------------------------------------------------------------------TTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGAT
droPer1	super_1:5067403-5067503 -	GCACATTTAAGTGAGTAGGAAA---AT-----------------------CG-----------------------------------------------------------------------------CTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGAT
droWil1	scaffold_180772:1562224-1562308 -	AAACGTTTAAGTGAGTAGTAAA---TC-------------TTGGTTAACCCA-----------------------------------------------------------------------------A------------------------------------------------------------------TAC------GATT--------------------------------TCATTGGCGTTT--------------------------ATA----AATTCCT-CCACCTTAGCCTTTACGAC
droVir3	scaffold_12963:8507052-8507133 +	GCACATTCAAGTATGTCAACTA---T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT------------AAAATGCTTTGCAGTAC----TCTTTAAA-------------------------TA-TTGTAT--TC-----TCATTCGATAGCCTCTATGAC
droMoj3	scaffold_6500:1118885-1118966 +	GTACATTCAAGTAAGCCCAATTCGCCG------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------GT----TAT------------------------GGTAT----T------CATATACA---------------AATGCT-AATCA--TT-----TATCCCTTTAGCCTCTATGAC
droGri2	scaffold_15252:11699282-11699373 +	GCACCTTCAAGTATGTGCAATGGGTAA--------------------ACCAT-----------------------------------------------------------------------------ATGTGAGAGATTTAAACCTT--------------------------------------------------------AATTT--------------TACTTTCCTATAT-----------------------------------------------------CTG-CCCAAACAGTCTGTACGAT

dme-mir-4913

Species	Coordinate	Alignment
dm3	chr3L:8347274-8347351 -	AACTACTTGAGTGAGTTCGATT----------------G-----G-A-------------------------------------------------------------------------------------------------------------------------------------AAATT-TAAATTTAATGTTTAATTA------ACCAAT-------TCGAAT--TGCTTAGATTGCTATAT
droSim1	chr3L:7807270-7807352 -	AACTATTTGAGTGAGTTCGATT----------------G-----A-A-----------------------------------------------------------------------------------------------------------------------------AATTTGGAAAATT-TAAAT---ATGTTTAATTA------ACCAAT-------TCAATT--TGCATAGATTGCTACAT
droSec1	super_0:643751-643833 -	AACTATTTGAGTGAGTTCAATT----------------G-----G-A-----------------------------------------------------------------------------------------------------------------------------TATTTAGAAAATT-TAAAT---ATGTTTAATTA------ACGAAT-------TCAATT--TGCATAGATTGCTACAT
droYak2	chr3L:3551202-3551283 +	AACTACTTGAGTGAGTTCGATT----------------G-----G-A-----------------------------------------------------------------------------------------------------------------------------CATTCGGAATATT-TCAAT---ATGTATAATCT------C-CAAT-------TCCAAT--GGTTTAGATTGCTACAT
droEre2	scaffold_4784:5683612-5683691 +	AACTATTTGAGTGAGTTCGATT----------------G-----A-A------------------------------------------------------------------------------------------------------------------------------GTTCGGAATATA-TTAAT---A-GTTTAATTG------T-CAAT-------TCCAAT--GGCTTAGATTGCTACAT
droEug1	scf7180000409524:297432-297569 +	AACTATTTGAGTGAGTACTAGC----------------A-----G-AAAATTTAATGGGTTTTTATTTTGAA-----------------------------------------------AAAAATGGCTTTAAAAATTTTAAATAA----A--------------C-TTTAACC----ACATATA-TTAAT---------AATAT------ACCATTTCTGTT-AACTTT--GGCTTAGATTGCTACAT
droBia1	scf7180000302428:10291387-10291558 -	AACTATTTGAGTAAGTTGGAAA---------C------A-----C-CCAATCTTAAATGTTCTTATTTTCGAAATTAAACTTTCCTCTGATCCGGGAAAAAGCCTTCTTAAAATCAAGAAGAAGAAGCTCTCAAGTTTTCGAGTGT----A--------------G-G-TAGCT----ACATATA-TAA--------------C------TG---------TGTTCCTAT--CGCTTAGATTGCTACAT
droTak1	scf7180000415703:565110-565177 +	AACTATTTGAGTGAGTACGATC----------------GTTA--A-A-------------------------------------------------------------------------------------------------------------------------------------AAATT-TAAT--------TTTATT------AA---------TAGAATTTTATGGTAGAAAT-----TAT
droEle1	scf7180000491268:341343-341391 +	AAATAATACAATAAT----------------------------------------------------------------------------------------------------------------------------------------------------ATTT--------------------------AAT--------------AT---------A-TTTCAAA--TACCTAGATTGCTACAT
droRho1	scf7180000780039:15490-15564 +	AACTATTTGAGTGAGTTTGACC----------------T-----A-A-----------------------------------------------------------------------------------------------------------------------------AACTAGGAAGAGT-AT------------AATCTTAAATAA---------GA---GCCT--GGTTTAGATTGCTACAT
droFic1	scf7180000453833:523600-523681 -	AACTATTTGAGTGAGTAGTATT---------CATTATTC-----A-A-----------------------------------------------------------------------------------------------------------------------------GATC-TGAAGAGATTA----------AGTATTC--------AAA-----TT-ACCCTC--GCTCTAGATTGCTATAT
droKik1	scf7180000302486:1222136-1222211 +	AACTATTTGAGTAAGTGTGCTG----------------G-----G-A-----------------------------------------------------------------------------------------------------------------------------GAGT-AGAAGATG-AA------A---GGCATAA---AGGA---------AA-ATCCTT--AACTTAGATTGCTACAT
droAna3	scaffold_13337:7445996-7446068 +	AACTATTTGAGTGAGTATCTTC----------------CTAAGAA-G----------------------------------------------------------------------------------------------------GAAGT------------------------------------------GTCATTTATT------TA---------TGATATTAC--TGCATAGATTGCTACAT
droBip1	scf7180000395543:108584-108656 +	AACTATTTGAGTAAGTCTGTTT----------------CAAAGAA-G----------------------------------------------------------------------------------------------------GAATT------------------------------------------ACCCTTAAAT------AA---------TATCCCTAT--TCCGTAGATTGCTATAT
dp4	chrXR_group6:12821050-12821123 -	AACTATTTGAGTGAGTACCACG----------------A-----G-A----------------------------------------------------------------------------------------------------GATCCCTCCTTCTGATTGTT--------------------------AAT--------------GT---------T--TTTTGT--GCCGCAGATTGCTATAT
droPer1	super_33:845501-845574 -	AACTATTTGAGTGAGTACCACG----------------A-----G-A----------------------------------------------------------------------------------------------------GAACCCTCCTTCTGATTGTT--------------------------AAT--------------GT---------T--TTTTGT--GCCGCAGATTGCTATAT
droWil1	scaffold_181009:3090047-3090133 +	AATTATTTGAGTGAGCGAGGCTACGAATATTCTC----T-----AGA---------------------------------------------------------------------------------------------------GG------------------------AATTTGGAATGCT--------AAG--------------AT-----TCGTT-TTTCTTT--TCCGTAGATTGCTACAT
droVir3	scaffold_13049:4752945-4753021 -	AACTACTTGAGTGAGTGAGGCT----------------T-----AGA---------------------------------------------------------------------------------------------------GGCTG--------------T-CGA----------CTACT-TTCGCT-TAT--------------GC---------CTGAATCTC--TCTGCAGATTGCTATAT
droMoj3	scaffold_6680:3143582-3143657 -	AATTATTTGAGTGGGTAGAGTG----------------A-----A-G----------------------------------------------------------------------------------------------------TATT--------------T-CTT----------ATACT-CCAGCCTAAT--------------GT---------TGGTCTCTC--CTTATAGATTGCTATAT
droGri2	scaffold_15110:10166034-10166119 +	AACTATTTGAGTGAGTACTTTG----------------A-----G-T-----------------------------------------------------------------------------------------------------TTG--------------T-CTTAATCCCCTGGATAGG-TG------------AGTGCTGAGTGG---------TG-ATCTCT--TTCACAGATTGCTATAT

dme-mir-4915

Species	Coordinate	Alignment
dm3	chrX:29762-29899 +	TGCCACCCAGGTGAGAAA-AAGTA-------------GTAAATTAAGCAT---ATCACGCAAG-----GACAAACATTAAGTTAAGG----------CCTAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TC--AA----TCCTACTTATGCCTC-TTATT---CTT---CT-TTTCTCAGACCTCCGCCA
droSim1	chrX:14356-14493 +	TGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCGCGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTACTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCA
droSec1	super_108:19646-19783 +	TGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCACGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTCCTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCA
droYak2	chrX:20609-20730 +	TGCCACCCAGGTGAGAGA-ACTAA-------------GTAAAATAAAAAT---ATCCTGCCAA-----G-----TTAAAAGTGAAATCTTATAATTGCAT------------------------------------------------------------------------------------------------------AG--TTTTCCTACTAATGTCCCTTTCTT---CTT---CT-TTTCCCAGACCTCCGCCG
droEre2	scaffold_4644:14897-15009 +	TGCCGCCCAGGTGAGAAA-ATTTA-------------GTCAAATAAGCATCTTATCCTGCAAA-----GAA-------AAGTTAACT----------TAT-----------------------------------------------------------------------------------------------------AAG--TTTCCCTACTAATGCCCC-TTTTT---CTT---CT-TTTCCCAGACCTCCGCCA
droEug1	scf7180000409277:365477-365576 +	TGCCACCCAGGTGAGTGA-ACTATGAGCTATGAACTA----T-------------------------------------GTCTAGGT----------AGT-----------------------------------------------------------------------------------------------------AGT--TACCCTTACTAATATCTC-TCCTT---TTTGCATT-CATTGCAGACCTCCACCA
droBia1	scf7180000301760:995905-995989 +	TGCCACCCAGGTGAGCCA-GTT------------------------------------------------------TTAAGTGATTC----------TAC-----------------------------------------------------------------------------------------------------CGA--TTTCCCTACCAATAACCCCGCCTC---TTC---GC-CCCCACAGACCTCCGCCA
droTak1	scf7180000415151:113073-113153 -	TGCCACCCAGGTGAATAA-CCCATTTAAT-TATATAA----CCTATAA-------------------------------------------------------------TTTACTA-------------------------AGAA-------------------------------------------------------------------------AA-------ACC---CTC---TC-TTTCACAGACCTCCGCCA
droEle1	scf7180000491011:1024812-1024900 +	TGCCACCCAGGTGAGTGA-ACCAT-------------GTGGGTTAATCCT---GTAGAGGAAGCTTGGGCCAGGCCTCAAGAGACAT----------TAGGTTT-----------------------------C----GATT------------------------------------TAATA---------------G------------------------------C------------------------------
droRho1	scf7180000779506:817617-817797 +	---------GTTGAGAAATGAATA-------------GAAGATTAAACAC---CACCTACAAA-----TTCGATTATTTAGTGATTT----------TCC---------------CACTTTTACATTAGCTTAGAACCTAATTCCTTACTCACGATATATCTAAAAATGTTCCATTTGTGATTTCCCAATTTTATACAT----G------TACATGTACG-------CTT---GTT---CC-ATCTGCAGACCTCCGCCA
droFic1	scf7180000453927:476232-476332 +	TGCCACCAAGGTGAGCAA-TACCT-------------TCCTGACAATCCT---CTCTAG----------------------------------------------------------------------------------------------------------TTTGGTTTTTTTGTGAATA--------------T----GT----TCTTACATATG-------TTT---TAT---AC-CCTCGCAGACCTCCGCCA
droKik1	scf7180000302610:258639-258667 +	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C-TTCCC---CCT---CT-TCCTACAGACCTCCGCCC
droAna3	scaffold_12929:1781927-1782005 -	TGCCACCCAGGTGAGTCT-GTCTAGAGTT-T-G----ATGGGATTGGA-----------------------------------------------------GTT-----------------------------G----AAAT------------------------------------TAATG---------------G------------------------------A---TTG---TG-ATTTTCAGACCTCCGCCA
droBip1	scf7180000396543:239477-239557 -	TGCCACCCAGGTGAGTCT-ATCGCGAGTC-TGGATGG----GATTGGG-----------------------------------------------------ATT-----------------------------G----GAAT-------------------------------------------------------------------------TAATG-------ATT---CAT---TA-TGTTGCAGACCTCCGCCA
dp4	chrXL_group1a:594383-594466 +	TGCCACCCAGGTGAGTGT-CCGAGGTGCC-T-------------------------------------------------------T----------CAA-----------------------------------------------------------------------------------------------------TGG--ACTACTGACCAATATCGTCTT--TGATCCT---TT-CCCGGCAGACCTCCTCCA
droPer1	super_157:12438-12452 +	AGCCACCCAGGTGAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181150:2495753-2495842 +	TGCCACCAAGGTGAGTGA-GATAA-------------GTTAT------------------------------------------------------------TTCCTTTTTTTCTC------------------------------A----------------------C-----------------------------AG--TTA----A---CTAATTACCGTTTCCA---CTT---CTTATTTTCAGGCCACCGCCT
droVir3	scaffold_12928:440193-440228 +	TGCCACCCAGGTAAATGC-GCGTA------------------------------------------------------TGTTGATTA--------------------------------------------------------------------------------------------------------------------------------------------------------------ACCA-----------
droMoj3	scaffold_6328:1398760-1398780 +	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---CC-CATTGCAGACCGCCGCCA
droGri2	scaffold_15203:6869203-6869243 +	TTG--------------------------------------------------------------------------------------------------TTT-----------------------------T----TTTT------------------------------------TGATT---------------T------------------------------G---TTG---TT-ATCTGCAGACCGCCGCCA

dme-mir-4917

Species	Coordinate	Alignment
dm3	chrX:14093568-14093663 +	CCCCAGCAGAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGAAGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC--CC-----CCTTACTACTAT-----------------------------------------------CGTCTG--C-T----CAACAGGAAAGCA----A----------A
droSim1	chrX_random:3764310-3764401 +	CCCCA---GAGTGAGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------G
droSec1	super_20:697982-698069 +	CCCCA---GAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------G
droYak2	chrX:8347474-8347558 +	CCCCA---GAGTAAGTAGCCAGGGGGATCAGGAG----GCCGCGGAAGG---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------AC-----------------------------------------------CCTCCG--A-T----CCACAGGAAAGCA----A----------C
droEre2	scaffold_4690:12836873-12836957 -	CCCCA---GAGTGAGTACGCAGTCGGGTCAGAAG----GCCGCGGAAGA---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------CC-----------------------------------------------CCTCCG--A-T----CAACAGGAAAGCA----A----------C
droEug1	scf7180000409008:504396-504468 +	CCCCA---GAGTGAGTAGAAGTGGGGGCGAGAAA----TCTACGGAAGA---------------------------------------------------------------------GATATGATCC--------A---TATGATT------------------------------------------------------------------------------------------------------------ACAGGAAAGCA----A----------C
droBia1	scf7180000302041:1138740-1138815 +	TCCTA---GGGTGAGTAGCGCCGC----CAT------------------------------------------------------------------------------------------ATGATCCATGACGCAC---GATGATT---------------------AC---------CCTA-------------------------------------------------------CCTCCG--A-T----CAGCAGGAAAGCA----A----------C
droTak1	scf7180000415667:540036-540106 -	CCCCA---GAGTGAGTAGTTTATA--TTT--------------------------------------------------------------------------------------------AAGATTC--------AAGAGATGATT---------------------TT---------TATA-------------------------------------------------------AATTTG--G-T----TAGCAGGAAAGCA----A----------C
droEle1	scf7180000491011:415441-415547 -	CCCCA---GAGTGAGTGAATGCATGGA----------------GAAAGC---------------------------------------------------------------------TACACGATCC--------C---AATGATA---------------------AC---------CATC--------CATCCAAC-----TATCCA--------TCCAACCAACCATCCG----GCGCCG--C-A----CAACAGGAGAGCA----G----------C
droRho1	scf7180000776513:33447-33527 +	CCCCA---GAGTGAGTAGTAGTGGTAGTAGA--G----ATCACCAATGA---------------------------------------------------------------------TTACC-----------------AATGATA---------------------AC---------CTTA-------------------------------------------------------CCTCCG--C-C----CAACAGGAAAACA----G----------C
droFic1	scf7180000454073:905657-905732 -	CCCCA---GAGTGAGTAGCGGGGA----------------------GAA---------------------------------------------------------------------TATGTGATCC--------A---ATTGATT---------------------GC---------CCTA-------------------------------------------------------ACTCCGTAC-C----AAGCAGGAAAGCAGCC-A----------C
droKik1	scf7180000302517:390479-390549 -	CCCCA---GAGTAAGTTTTAATTT-------------------------------------------------------------------------------------------------------------------------------------------------C---------TC-----------TCTAAAAAGCAATTTTTAAAG-------------------------CTTTTT--C-T----TTACAGGCAAGCAGCA-A----------C
droAna3	scaffold_13047:1616603-1616743 +	CCCGA---GAGTGAGTTAAATAGGTAGACT----------------------GGGTTTTACGGGTTTTGG-GGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTAGAAGGACCAAAGGACTT--------A---AGAACTA---------------------AC---------AAAA------AT-----------------------------------------------TCACCA--T-T----CCACAGGCAAGCA----C----------G
droBip1	scf7180000396740:414610-414750 +	CCCGA---GAGTGAGTTAAATAGGTAGAATT--T----ATCGTAA--CCTATGGGGTTTACGGGTTTTTGGG--------GCAAAGGGCTTAAGGGTTA----------------------AAGATTA--------AA--ATCAAAA---------------------AC---------TTTA-------------------------------------------------------ATAACTTAA-C----GGGTTAAAAGTCAGACAATCGAACGGATG
dp4	chrXL_group1e:6144265-6144386 -	CTCCA---GAGTGAGTTGAGTGAG--GTT--------------------------------------------------------------------------------------------GAGAGCCGGGGTGCTC-G-GAAGACCATCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTC------------------TCTCTC--G-T----CCGCAGGCAAGCG----A----------A
droPer1	super_21:1109359-1109487 -	CTCCA---GAGTGAGTGGTTGAGA--GCCGGG---------------------------------------------------------------------------------------------------GTGCTC-GCAA-GACCTTCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTCTCTCTCTCTCTCTC----GCTCTC--G-T----CCGCAGGCAAGCG----A----------A
droWil1	scaffold_180702:2428506-2428584 +	CACAA---GGGTGAGTGGGAGGAGAGATGAGAGG----AGAATGGAC---------------------------------------------------------------------------------------------TTTAACC---------------------GC---------CATTATT----------------------------------------------------TCTTTC--T-T----CCACAGGGAAGTG----A----------A
droVir3	scaffold_12932:1910959-1911050 +	CGGCA---GCAGCAGCGGCAGCGGCGGCGGCGCC----ACC---GTCAG---------------------------------------------------------------------TTGGT-----------------GCTGCGC---------------------CC---------GCTG-------------------------CACAG------------------CC-----GCCGCC--CTCGGCAGGCGAAGCAGCCG----C----------T
droMoj3	scaffold_6359:2739414-2739512 -	CACAA---GAGTGAGTGACAAGATTTATATATAT----TTA-------------------------------------------------------------------------------TAGGAATA--------T---AATACTA---------------------ATTCTTATCTACGT--------------------------TATTC------------------CCGTCTCACTCAA--T-C----AATTAGTCGAGCC----G----------A
droGri2	scaffold_15081:1312794-1312808 -	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAGTCGAGCG----A----------A

dme-mir-4918

Species	Coordinate	Alignment
dm3	chr3R:4134143-4134217 -	CATGTCTAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCAATGAA----------TT---CC-CGCCTGCCCACAGGTTCACTCG--G
droSim1	chr3R:17124444-17124516 +	CATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--G
droSec1	super_0:17695142-17695214 +	CATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--G
droYak2	chr3R:8209601-8209673 -	CATGTCCAAGGTGAGCAC-GG-----CGGCCCCAA--------------AATCAAAGT----------TCT----------CTGACCAA-------------AA----TCCCGCCCACAGGTTCACTCC--G
droEre2	scaffold_4770:17439364-17439443 +	CATGTCCAAGGTGAGCAC-GA-----TGGCCCCGA--------------CATCGAAATTCTAAATCCCC----------AATCCA---A-------------AA----TCCCGCCCACAGGTTCACTCA--G
droEug1	scf7180000409490:587166-587239 +	CATGTCCAAGGTGAGCAT-TG-----TTTCCCGTTAATTCT------------GAA------------TT--T--------CTCTA--A-------------AATC-CGTCTGTCCACAGGTTCACTCT--G
droBia1	scf7180000302402:6823677-6823761 -	CATGTCCAAGGTGAGCGC-GA-----TTTCCCGCCAATCCT------------GGGGA----------CTCCTCTCTGAAATCCA-GAG----------T-----C-CTCCTGCCCACAGGTGCACTCG--G
droTak1	scf7180000415750:47174-47264 -	CATGTCCAAGGTAAACAC-GA-----TTTCCCGCCAAT-TA------------AGAAG----------CATCTCTCTGCAATCCAAGAATCCCCC---------TT-TCCACATCCACAGGTTCACTCG--G
droEle1	scf7180000491212:1694404-1694499 +	CATGTCCAAGGTGAGCTT-GA-----TGTTCCCAGAGGTTC------------AAAGA----------TTTCTTACTAAAAATTGAGACTTGTCTTCATTGAAA----TC--CTTTCCAGGTTCACTCC--G
droRho1	scf7180000779995:99587-99680 -	CATGTCCAAGGTGAGCTT-GA-----TTTCCGTTCCAC-TT------------AAAGA----------TTCCTCTCTAAAACTTGTAACTCCCAT---TTGAAA----TGCTGTCCACAGGTGCACTCC--G
droFic1	scf7180000454073:3313776-3313852 +	CATGTCCAAGGTGAGCTT-GG-----CTTCCCTGCAATCCTTTGGTGC--------------------C----------GATCTGTAAA----------------C-CTCCCTTTTATAGGTTCACTCT--G
droKik1	scf7180000302810:169519-169594 +	CATTTCCAAGGTAGGAGT-GA-----ATTCTGTGGGCTCTAGCG--GA--------------------CTT----------GCCACTGA----------T-----T-CTCCTGGTTGCAGGTCCATTCG--G
droAna3	scaffold_13340:13231721-13231798 -	TCTGAACAAGGTAATTTG-AA-----TTTGTGT--TTTTGGCCAGGAGCA-A-----------------------------TTGATGTA----------TT---TG-TTTATGTTCGAAGGTACACTCT--G
droBip1	scf7180000396691:2102180-2102257 -	TCTGAACAAGGTAATTGG-AA-----TTGATGT--TTTTAGCCTGTCAAA-A-----------------------------TGTATGCA----------TT---TT-TTTATATTTGAAGGTACACTCG--G
dp4	chr2:14657779-14657853 -	CACGTCCAAGGTAAGAAG--C-----TAGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAA--T--TGTCTGAGGCAGGTTCACTCC--G
droPer1	super_0:5758131-5758205 +	CACGTCCAAGGTAAGAAG--C-----TGGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAAA----TGTCTGAGGCAGGTTCACTCC--G
droWil1	scaffold_181089:2794448-2794533 +	TATGTCCAAGGTAATCAA-AT-----TTAATGT--AATTTACCA--GACAAGCGTTCC----------CTT----------TTTACAAA----------TT---TT-CTTTCCCTGGCAGGTTCACTCG--G
droVir3	scaffold_12822:435892-435967 +	CATGTCAAAGGTGGGTAT-AA-----AACCATT-TAGTCTGTCGGTGG--------------------CAT----------TTAATTGG----------------T-TTTCTTTTCGTAGGTGCATTCG--G
droMoj3	scaffold_6540:27855891-27855966 -	ATAG-CAACAGCAACAGC-AA-----TAGCAAC--AGCAA-CAG-CAGCA-A-----------------------------CACCTGCA----------AG---CCGCGGCAGCCCAAAGTCTCGTTCG--C
droGri2	scaffold_15245:11304339-11304418 -	CAGCTCCTTAAGCAATATGAACAGCAGAGCCTGGG--------------TAGTGATGT------------------------ACCTGGA----------TC---CC-GGCCCATCTACACGTTCAGTGGACA