dme-mir-4984- Best orthologs

dme-mir-4984	chr2L:8141539-8141662 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 8141568-8141589
   star strand at position 8141608-8141632
   mutations
   read mismatches

Notes: "droPer1 ortholog missing looks genuine (this region looks properly assembled). However, this is another interesting case. There has been large insertion and deletions since droKik1 and earlier that case the hairpin to gradually dissappear as we move up the tree"

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:8141524-8141677 -		1	TTAAAATAGTCTC--AA------------------------------------CTTCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSim1	chr2L:7922185-7922338 -	LASTZ	1	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------G--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSec1	super_3:3638638-3638791 -	LASTZ	1	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droYak2	chr2L:10772572-10772720 -	LASTZ	4	TTAAAATAGTCTC--GA------------------------------------G----------------------ACGAGGTGTGAAAACC--------------TTTTGGCCG-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEre2	scaffold_4929:17047208-17047355 -	LASTZ	4	TTAAAATAGTCTC--TA------------------------------------C----------------------TCGAGGTGTGAAAACC--------------TT-TGGCCA-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCT--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEug1	scf7180000409461:136449-136599 -	LASTZ	5	TTAAAATAGTCTC--AA------------------------------------G----------------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CTC-GCCTCGT---TG-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----AG-CCAAATGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droBia1	scf7180000302408:3185378-3185528 -	LASTZ	5	TTAAAACAGTCCC--AA------------------------------------G----------------------TGGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--GCC-CGTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGCATTTGCT-----GG-CCAAACGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droTak1	scf7180000415287:134548-134699 +	LASTZ	5	TTAAAATAGTCGC--AA------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCAAAT----------------------------------------------A--CTC-ACTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCC-----GGTCCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATAGCTTTC----------ATT
droEle1	scf7180000491338:774218-774368 +	LASTZ	5	TTAAAATAGTCTC--AG------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CCC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAGATGACACGTTTGCCATGTTTT----ACG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droRho1	scf7180000770662:26011-26160 -	LASTZ	5	TTAAAATAGTCTC--AA------------------------------------G----------------------TTGAGGTGTGAAAACC--------------TTTCGGCCA-GCA-AT----------------------------------------------A--CTC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droFic1	scf7180000453925:826752-826904 -	LASTZ	5	TTAAAATAGTCTC--AA----------------------------------TAG----------------------TCGAGGTGTGAAAACC--------------ATTTGGCCA-GCA-GT----------------------------------------------A--CTC-ACTTCGG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGGATTTGCT-----GG-ACAAACGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------TCTC------------AATTGCTTTC----------GTT
droKik1	scf7180000302468:119229-119407 -	LASTZ	5	TTAAAATAGTCGC--GG------------------------------------T----------------------TAGAGGTGTGAAAACC--------------TTTCGGCCG-GCAAAAAAGAACAAGAAATAAGTCCAAGCTCAAAGAACTCAAGCTGCAGCTCA-GCAG-CTCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-GCAAACGGCACGTTTGCCATGCTTT------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_12916:9486383-9486598 -	LASTZ	5	TTTAAATAGTCTCTCGA------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGTTA-GCCAGCCAGCGAGACACTT--------------------------------AA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTCTGACATGGAAT----GGCATGGCATGAGATGGGCATGGTATGGT-TGGTTGGTGCG------------------------------------------AC-T--------AAAT-AATGGTTTC----------ATT
droBip1	scf7180000396580:1551536-1551742 +	LASTZ	5	TTTAAATAGTCTC--GG------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCCGAG-------ACACTT--------------------------------TA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTTTGGCATGTCAT----CCCACCGCATGGCAC-GGCATGGCATGGCATGGTTGGTGCG------------------------------------------GC-A--------AAAT-AATGCTTTC----------ATT
dp4	chr4_group3:2877715-2877892 +	LASTZ	5	TTAAAATAGTTGC--AGCCCACAAGTCACATGCCGCCGCCGGCGCATTGGACAT----------------------TGGAGGTGTGAAAACC--------------A-------------AT----------------------------------------------A--TTC-GCTTCAG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TG-GCAAATGACACGTTTTGGACCT--------GC-------------------------------------------------------------------------AATTTCCAG-C------------ATTTACTTTC----------ATT
droPer1	super_1:4362183-4362198 +	LASTZ	5	TTAAAATAGTTGC--AG------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180703:2787401-2787579 -	LASTZ	5	TCTC------------------------------TCCACCAACATAATA--TGG----------------------ACAAGGTGTTAAGGTC------------TCTTTTGGATG-GTAGTC----------------------------------------------A-GTTGCTAGTTAA---CT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AG-CGAAATGACACGTTT----TGTCTTAACCCGCACCGG-------------------------------------------------------------------------CCGG-CCCCCACTTACATAGATATTTTT----------AGT
droVir3	scaffold_12963:13862249-13862454 +	LASTZ	5	TTAAAGCGGCTTC--AA------------------------------------------------------------CAAGGTGTTAAAATC------------G-CAAAGGCCG-TCACAG----------------------------------------------CCACAG-TCCACAG---TC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAG-CCAAATGGCACGTTTTCAATGGGCT----GGCA----------------------------------------GCAGCCCCAAGCCCTCAGCCAGCTTCATCTGCAATTGCGAC-G------------ACTTTCTTTCTGGCCCAACGAAC
droMoj3	scaffold_6500:5788118-5788309 -	LASTZ	5	TTGGAATACTTGA---A----------------------------------CA--CTGGTTACAGCGGCTAC---AACAAGGTGTTAAAAACAGAAAAAAGCGAACCAAAGGCCG-GCACAC-----------------------------------------AGC-CACACAG-TCCACAG---TT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAG-CCAAATGGCACGTTTGCCATGGCAT-----CG--------------------------------------------------------------------------------CT-C------------AACAGCTTTA----------AGC
droGri2	scaffold_15126:6028218-6028422 -	LASTZ	5	TTTGAATACTTGA---A----------------------------------CA--CTGGTTACACCGACTTCAGCAACTAGGTGTTAAAGCC------------ACCAAAGGCCTTGCAGAC----------------------------------------------A--CAG-TTCACAG---TC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAG-CCAAATGGCACGTTTGCTAAGCATG----GAC--------------------------------AGATCCCCAAGAGCCCCAAGCTCTAA----------------------GC-C-------------AGTTCCATC----------ATC

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	TTAAAATAGTCTC--AA------------------------------------CTTCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSim1	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------G--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSec1	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droYak2	TTAAAATAGTCTC--GA------------------------------------G----------------------ACGAGGTGTGAAAACC--------------TTTTGGCCG-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEre2	TTAAAATAGTCTC--TA------------------------------------C----------------------TCGAGGTGTGAAAACC--------------TT-TGGCCA-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCT--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEug1	TTAAAATAGTCTC--AA------------------------------------G----------------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CTC-GCCTCGT---TG-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----AG-CCAAATGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droBia1	TTAAAACAGTCCC--AA------------------------------------G----------------------TGGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--GCC-CGTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGCATTTGCT-----GG-CCAAACGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droTak1	TTAAAATAGTCGC--AA------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCAAAT----------------------------------------------A--CTC-ACTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCC-----GGTCCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATAGCTTTC----------ATT
droEle1	TTAAAATAGTCTC--AG------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CCC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAGATGACACGTTTGCCATGTTTT----ACG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droRho1	TTAAAATAGTCTC--AA------------------------------------G----------------------TTGAGGTGTGAAAACC--------------TTTCGGCCA-GCA-AT----------------------------------------------A--CTC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droFic1	TTAAAATAGTCTC--AA----------------------------------TAG----------------------TCGAGGTGTGAAAACC--------------ATTTGGCCA-GCA-GT----------------------------------------------A--CTC-ACTTCGG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGGATTTGCT-----GG-ACAAACGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------TCTC------------AATTGCTTTC----------GTT
droKik1	TTAAAATAGTCGC--GG------------------------------------T----------------------TAGAGGTGTGAAAACC--------------TTTCGGCCG-GCAAAAAAGAACAAGAAATAAGTCCAAGCTCAAAGAACTCAAGCTGCAGCTCA-GCAG-CTCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-GCAAACGGCACGTTTGCCATGCTTT------------------------------------------------------------------------------------------------------------------------------
droAna3	TTTAAATAGTCTCTCGA------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGTTA-GCCAGCCAGCGAGACACTT--------------------------------AA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTCTGACATGGAAT----GGCATGGCATGAGATGGGCATGGTATGGT-TGGTTGGTGCG------------------------------------------AC-T--------AAAT-AATGGTTTC----------ATT
droBip1	TTTAAATAGTCTC--GG------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCCGAG-------ACACTT--------------------------------TA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTTTGGCATGTCAT----CCCACCGCATGGCAC-GGCATGGCATGGCATGGTTGGTGCG------------------------------------------GC-A--------AAAT-AATGCTTTC----------ATT
dp4	TTAAAATAGTTGC--AGCCCACAAGTCACATGCCGCCGCCGGCGCATTGGACAT----------------------TGGAGGTGTGAAAACC--------------A-------------AT----------------------------------------------A--TTC-GCTTCAG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TG-GCAAATGACACGTTTTGGACCT--------GC-------------------------------------------------------------------------AATTTCCAG-C------------ATTTACTTTC----------ATT
droPer1	TTAAAATAGTTGC--AG------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	TCTC------------------------------TCCACCAACATAATA--TGG----------------------ACAAGGTGTTAAGGTC------------TCTTTTGGATG-GTAGTC----------------------------------------------A-GTTGCTAGTTAA---CT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AG-CGAAATGACACGTTT----TGTCTTAACCCGCACCGG-------------------------------------------------------------------------CCGG-CCCCCACTTACATAGATATTTTT----------AGT
droVir3	TTAAAGCGGCTTC--AA------------------------------------------------------------CAAGGTGTTAAAATC------------G-CAAAGGCCG-TCACAG----------------------------------------------CCACAG-TCCACAG---TC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAG-CCAAATGGCACGTTTTCAATGGGCT----GGCA----------------------------------------GCAGCCCCAAGCCCTCAGCCAGCTTCATCTGCAATTGCGAC-G------------ACTTTCTTTCTGGCCCAACGAAC
droMoj3	TTGGAATACTTGA---A----------------------------------CA--CTGGTTACAGCGGCTAC---AACAAGGTGTTAAAAACAGAAAAAAGCGAACCAAAGGCCG-GCACAC-----------------------------------------AGC-CACACAG-TCCACAG---TT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAG-CCAAATGGCACGTTTGCCATGGCAT-----CG--------------------------------------------------------------------------------CT-C------------AACAGCTTTA----------AGC
droGri2	TTTGAATACTTGA---A----------------------------------CA--CTGGTTACACCGACTTCAGCAACTAGGTGTTAAAGCC------------ACCAAAGGCCTTGCAGAC----------------------------------------------A--CAG-TTCACAG---TC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAG-CCAAATGGCACGTTTGCTAAGCATG----GAC--------------------------------AGATCCCCAAGAGCCCCAAGCTCTAA----------------------GC-C-------------AGTTCCATC----------ATC

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image																None
UNAFold Image																None

Small RNA-seq read pileup

Species

Alignment

droSim1

TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------G--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----G.........................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----GG-C......................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----GG-.......................................................................................................................................................	22	1	37.00	19.00	9.00	9.00
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----GG-T......................................................................................................................................................	23	1	5.00	2.00	0.00	3.00
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----GT-.......................................................................................................................................................	22	1	2.00	1.00	0.00	1.00
...............................................................................................................................................................................................................GAGGTGAATTCTTGGACC.......................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................AATTCTTTGACGTATTCGCT-----GG-AA.....................................................................................................................................................	24	1	1.00	1.00	0.00	0.00

droYak2

TTAAAATAGTCTC--GA------------------------------------G----------------------ACGAGGTGTGAAAACC--------------TTTTGGCCG-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................................................................................................TTCAAGTTCGAGGTGAATCCT.............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTAAAATAGTCTC--TA------------------------------------C----------------------TCGAGGTGTGAAAACC--------------TT-TGGCCA-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCT--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TTAAAATAGTCTC--AA------------------------------------G----------------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CTC-GCCTCGT---TG-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----AG-CCAAATGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT

Size

Hit Count

Total Norm

droBia1

TTAAAACAGTCCC--AA------------------------------------G----------------------TGGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--GCC-CGTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGCATTTGCT-----GG-CCAAACGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT

Size

Hit Count

Total Norm

droTak1

TTAAAATAGTCGC--AA------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCAAAT----------------------------------------------A--CTC-ACTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCC-----GGTCCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATAGCTTTC----------ATT

Size

Hit Count

Total Norm

droEle1

TTAAAATAGTCTC--AG------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CCC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAGATGACACGTTTGCCATGTTTT----ACG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT

Size

Hit Count

Total Norm

droRho1

TTAAAATAGTCTC--AA------------------------------------G----------------------TTGAGGTGTGAAAACC--------------TTTCGGCCA-GCA-AT----------------------------------------------A--CTC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT

Size

Hit Count

Total Norm

droFic1

TTAAAATAGTCTC--AA----------------------------------TAG----------------------TCGAGGTGTGAAAACC--------------ATTTGGCCA-GCA-GT----------------------------------------------A--CTC-ACTTCGG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGGATTTGCT-----GG-ACAAACGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------TCTC------------AATTGCTTTC----------GTT

Size

Hit Count

Total Norm

droKik1

TTAAAATAGTCGC--GG------------------------------------T----------------------TAGAGGTGTGAAAACC--------------TTTCGGCCG-GCAAAAAAGAACAAGAAATAAGTCCAAGCTCAAAGAACTCAAGCTGCAGCTCA-GCAG-CTCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-GCAAACGGCACGTTTGCCATGCTTT------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droAna3

TTTAAATAGTCTCTCGA------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGTTA-GCCAGCCAGCGAGACACTT--------------------------------AA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTCTGACATGGAAT----GGCATGGCATGAGATGGGCATGGTATGGT-TGGTTGGTGCG------------------------------------------AC-T--------AAAT-AATGGTTTC----------ATT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................................................................................................................................................................................GCGTGGTATGGT-TGGTGGG.....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................TATCxAGATCGAGGTAAAT................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................AAATGGCAxGTCTGACAAG..................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................GTGAAAACC--------------TTTCGGTTA-GCCAGCCAGCG.........................................................................................................................................................................................................................................................................	29	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................AACGxCTGACATGGAAT----GGC.......................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................AT----GGCATGGGATGGGATGGG........................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droBip1

TTTAAATAGTCTC--GG------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCCGAG-------ACACTT--------------------------------TA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTTTGGCATGTCAT----CCCACCGCATGGCAC-GGCATGGCATGGCATGGTTGGTGCG------------------------------------------GC-A--------AAAT-AATGCTTTC----------ATT

Size

Hit Count

Total Norm

dp4

TTAAAATAGTTGC--AGCCCACAAGTCACATGCCGCCGCCGGCGCATTGGACAT----------------------TGGAGGTGTGAAAACC--------------A-------------AT----------------------------------------------A--TTC-GCTTCAG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TG-GCAAATGACACGTTTTGGACCT--------GC-------------------------------------------------------------------------AATTTCCAG-C------------ATTTACTTTC----------ATT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TTAAAATAGTTGC--AG------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TCTC------------------------------TCCACCAACATAATA--TGG----------------------ACAAGGTGTTAAGGTC------------TCTTTTGGATG-GTAGTC----------------------------------------------A-GTTGCTAGTTAA---CT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AG-CGAAATGACACGTTT----TGTCTTAACCCGCACCGG-------------------------------------------------------------------------CCGG-CCCCCACTTACATAGATATTTTT----------AGT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................................................................................GTGTTAAGGTC------------GCTTTGG.........................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
................................................................................GGTGTTAAGGTC------------GCTTTGG.........................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................TCAAGATCAAGCTGAATT...............................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................ATACTGTCC-----AG-xGAAATGA...............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................CAACATAATC--TGG----------------------ACGAGG......................................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................AGTC----------------------------------------------A-GTTGCTxGTTAA---AT-CA..........................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

TTAAAGCGGCTTC--AA------------------------------------------------------------CAAGGTGTTAAAATC------------G-CAAAGGCCG-TCACAG----------------------------------------------CCACAG-TCCACAG---TC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAG-CCAAATGGCACGTTTTCAATGGGCT----GGCA----------------------------------------GCAGCCCCAAGCCCTCAGCCAGCTTCATCTGCAATTGCGAC-G------------ACTTTCTTTCTGGCCCAACGAAC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................................................................................................................................................................................................................................................................................................CAATTGCGAx-A------------ACTTTCTT...............	18	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................GTATTCGATGGGCT----GGCA----------------------------------------..............................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................GGCACGTTGTCACTGGGC...............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................CGAATCACGTTTTAAGATCGAG......................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

TTGGAATACTTGA---A----------------------------------CA--CTGGTTACAGCGGCTAC---AACAAGGTGTTAAAAACAGAAAAAAGCGAACCAAAGGCCG-GCACAC-----------------------------------------AGC-CACACAG-TCCACAG---TT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAG-CCAAATGGCACGTTTGCCATGGCAT-----CG--------------------------------------------------------------------------------CT-C------------AACAGCTTTA----------AGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................................................TGAAAACAGAAAACAGCGAA...............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

TTTGAATACTTGA---A----------------------------------CA--CTGGTTACACCGACTTCAGCAACTAGGTGTTAAAGCC------------ACCAAAGGCCTTGCAGAC----------------------------------------------A--CAG-TTCACAG---TC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAG-CCAAATGGCACGTTTGCTAAGCATG----GAC--------------------------------AGATCCCCAAGAGCCCCAAGCTCTAA----------------------GC-C-------------AGTTCCATC----------ATC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:57 EDT

dme-mir-4984

chr2L:8141539-8141662 -

Known_mirbase

intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup