Secondary structure and small RNA-seq evidence for dme-mir-989

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:10032841-10033044 -	ATT-TTATTTAAGTACAA-------AGATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTACAAG-CAACA------CGAA-GT---GA
droSim1	chr2R:8799008-8799211 -	ATT-TTATTTAAGTACAT-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAG-CAACA------CGAA-GT---GA
droSec1	super_1:7540579-7540782 -	ATT-TTATTTAAGTACAG-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCTTG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCCGAAATTGCAAG-CAGCA------CGAA-GT---GA
droYak2	chr2R:9968911-9969114 -	TTTTTTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTGGTGG-ACCCATTCTC-ATT-----------------------------CCGAGATTAGTTTTATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGGA-GT---AA
droEre2	scaffold_4845:15804995-15805201 +	ATT-TTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACCCAGGTGACACTGATC---CGGATTTGGTAGTCGTACAAATCCTCCATT-----------------------------CCGAGTTAAGTTTCATTCTGCGTCTTTTGAA------TTCGAACAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGTA-GGCA-TA
droAna3	scaffold_13266:5886554-5886734 +	A--------------CCA-------ACGTTTCGGGAAGTGGCCACTACCTCGCAGTCACGTGATGCC---AAAATGCAACTGACACTGATC---CGGAGATGGT------------CCTCCATC---------C-------------------TTGGGATTAGTGTTAATTTGTGTTTTTTTTA------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTCCTAA-CAACA------AAAA-GT---GA
dp4	chr3:2729279-2729420 -	A-------------------------CGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droPer1	super_2:2918784-2918948 -	TTG-TAAACCAAGAAGAACCAAACAACGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droWil1	scaffold_180745:1541090-1541255 +	TAC-GAGTTCGAGTACAA----TAAATGTTTTGGGAATTGGCCACTACCTCGCAGTCACGTGATGAG---AGA---------------------------------------------------GATGCAAGA------------------------GGACTTTG------TATGCCATTTGCATTTAATATTTCATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGAGCTTTAAAGTCATCA------AGAA-GG---AA
droVir3	scaffold_12875:1889282-1889470 +	A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCAGTCACGTGATCCA---CAAACGCAGC--------------CGGCTCTGGTGCTTG-GGAAA---------AATACAATTTTCTTTTGTTTTCCTGGGCGCCGCA-------ACGTTTTGCGT----TCA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTGCAG-CCACA------GCGC-GAAGTG-
droMoj3	scaffold_6496:23382296-23382464 -	A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCACTCACGTGATGCACTCAAAACGCCGACGAGGACGT---------------------CCAAATT--CCAT---------TTTCT--CGTTTTCCTC--------------TGTCGTTTTGCGT----TGA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGCC-----CCAGCAATCCG----------
droGri2	scaffold_15112:3992495-3992691 +	ATG-TAAT-----GAA------AAAGCGTTCCGGGAATTGGCCACTACCTCGCAGTCACGTGATGCC---ACAAGGCGGGC-ACGCCGTGCAACATCCTCTCTTCGTTT-ACACATCTCCTCTT-----------------------------GAGAGGATTGCGTCGTTCCGCCT----TGAA-------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTCCCA-CAACA------AGAA-CA---AC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:10032841-10033044 -	ATT-TTATTTAAGTACAA-------AGATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTACAAG-CAACA------CGAA-GT---GA
droSim1	chr2R:8799008-8799211 -	ATT-TTATTTAAGTACAT-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAG-CAACA------CGAA-GT---GA
droSec1	super_1:7540579-7540782 -	ATT-TTATTTAAGTACAG-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCTTG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCCGAAATTGCAAG-CAGCA------CGAA-GT---GA
droYak2	chr2R:9968911-9969114 -	TTTTTTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTGGTGG-ACCCATTCTC-ATT-----------------------------CCGAGATTAGTTTTATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGGA-GT---AA
droEre2	scaffold_4845:15804995-15805201 +	ATT-TTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACCCAGGTGACACTGATC---CGGATTTGGTAGTCGTACAAATCCTCCATT-----------------------------CCGAGTTAAGTTTCATTCTGCGTCTTTTGAA------TTCGAACAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGTA-GGCA-TA
droAna3	scaffold_13266:5886554-5886734 +	A--------------CCA-------ACGTTTCGGGAAGTGGCCACTACCTCGCAGTCACGTGATGCC---AAAATGCAACTGACACTGATC---CGGAGATGGT------------CCTCCATC---------C-------------------TTGGGATTAGTGTTAATTTGTGTTTTTTTTA------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTCCTAA-CAACA------AAAA-GT---GA
dp4	chr3:2729279-2729420 -	A-------------------------CGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droPer1	super_2:2918784-2918948 -	TTG-TAAACCAAGAAGAACCAAACAACGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droWil1	scaffold_180745:1541090-1541255 +	TAC-GAGTTCGAGTACAA----TAAATGTTTTGGGAATTGGCCACTACCTCGCAGTCACGTGATGAG---AGA---------------------------------------------------GATGCAAGA------------------------GGACTTTG------TATGCCATTTGCATTTAATATTTCATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGAGCTTTAAAGTCATCA------AGAA-GG---AA
droVir3	scaffold_12875:1889282-1889470 +	A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCAGTCACGTGATCCA---CAAACGCAGC--------------CGGCTCTGGTGCTTG-GGAAA---------AATACAATTTTCTTTTGTTTTCCTGGGCGCCGCA-------ACGTTTTGCGT----TCA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTGCAG-CCACA------GCGC-GAAGTG-
droMoj3	scaffold_6496:23382296-23382464 -	A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCACTCACGTGATGCACTCAAAACGCCGACGAGGACGT---------------------CCAAATT--CCAT---------TTTCT--CGTTTTCCTC--------------TGTCGTTTTGCGT----TGA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGCC-----CCAGCAATCCG----------
droGri2	scaffold_15112:3992495-3992691 +	ATG-TAAT-----GAA------AAAGCGTTCCGGGAATTGGCCACTACCTCGCAGTCACGTGATGCC---ACAAGGCGGGC-ACGCCGTGCAACATCCTCTCTTCGTTT-ACACATCTCCTCTT-----------------------------GAGAGGATTGCGTCGTTCCGCCT----TGAA-------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTCCCA-CAACA------AGAA-CA---AC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATTTTATTTAAGTACATAAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACTGGTGACACTGATCCGGATTTGGTAGTTGACAAATCCTCCATGCCGAGATTAGTTTCATTTTGCGTCTTTTGAATTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAGCAACACGAA-GTGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................................................................................................TGTGATGTGACGTAGTGGAAC...............................	21	1	10.00	10	10
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACA..............................	22	1	9.00	9	9
.........................................................................................................................................................TGTGATGTGACGTAGTGGAA................................	20	1	3.00	3	3

dp4

AC-----------------GTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATCGGAATG--------------------------------CAATGATCTACGTTAAATTGTGTTTCTTTTT---------------GAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAGCAACAGAAATGTAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACA..............................	22	1	245.00	245	68	177
.........................................................................................................................................................TGTGATGTGACGTAGTGGAAC...............................	21	1	187.00	187	29	158
.........................................................................................................................................................TGTGATGTGACGTAGTGGAA................................	20	1	70.00	70	9	61
.........................................................................................................................................................TGTGATGTGACGTAGTGGA.................................	19	1	9.00	9	0	9
........................................................................................................................................................ATGTGATGTGACGTAGTGGAA................................	21	1	4.00	4	3	1
........................................................................................................................................................ATGTGATGTGACGTAGTGGAAC...............................	22	1	3.00	3	2	1
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACAT.............................	23	1	1.00	1	0	1
..........................................................................................................................................................GTGATGTGACGTAGTGGAACA..............................	21	1	1.00	1	1	0

Secondary Structure

dm3

-57.8	-57.8	-57.8	-57.8	-57.8	-57.8

droSim1

-54.1	-54.1	-54.0	-54.0	-53.7	-53.7

droSec1

-55.9	-55.9	-55.8	-55.8	-55.6	-55.5

droYak2

-63.9	-63.9	-63.9	-63.8	-63.8	-63.8

droEre2

-60.0	-60.0	-60.0	-60.0	-59.9	-59.9

droAna3

-70.0	-70.0	-69.8	-69.8	-69.7	-69.7

dp4

-49.8	-49.6	-49.4	-49.4	-49.4	-49.2

droPer1

-56.5	-56.3	-56.1	-55.9	-55.8

droWil1

-48.3	-48.3	-48.3	-48.1	-48.0	-48.0

droVir3

-68.6	-68.2	-67.9	-67.8	-67.7	-67.7

droMoj3

-55.4	-55.2	-55.2	-55.1	-55.0	-55.0

droGri2

-72.6	-72.5	-72.4	-72.3	-72.2	-72.1

Generated: 01/05/2013 at 05:36 PM