dme-mir-982- Best orthologs

dme-mir-982	chrX:4259839-4259931 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 4259894-4259916
   star strand at position 4259855-4259877
   mutations
   read mismatches

Notes: Nothing looks confident at droEug1 and earlier. droEre2 has a large insertion in the miR* region that cause the hairpin structure to disappear

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:4259824-4259946 -		1	TATCAA------GTTAAAA-------A----------------------------A--CGAAATCATGTTAGATC----------------------------------------------------------------------CTGGACAAATATGAAGTAAATTGTTTTTATGCATCAATTAC----------------------------------------TTGATA-TTCATCCTTGAACTAAATGGTTTTA--------------------------------------------------------GAGCTGCAAGA----AAAATTGT
droSim1	chrX:3273907-3274029 -	LASTZ	1	TATGAA------GTTAAAA-------A----------------------------A--CAAAATCATGCTAGATC----------------------------------------------------------------------AAGAACAAATATCATGTAAATTGATTTTTTAAATCAACTAC----------------------------------------ACGATA-TTCGTTCTTGAGCTTAATGGTTCTA--------------------------------------------------------GAGCTGCAAGA----AAAATTGT
droSec1	super_4:2466024-2466146 +	LASTZ	1	TATCAA------GTTAAAA-------A----------------------------A--CGAAATCATGCTAGATC----------------------------------------------------------------------TTGGACAAATATCAAGTAGATTATTTTTATACATCAATTTA----------------------------------------TTGTTA-TTTGTCCTTGAACTTAATTGTTTTA--------------------------------------------------------CAGCTGCAAAA----AAAATTGT
droYak2	chrX:4178368-4178492 +	LASTZ	4	TATCAA------GTTCAGA-------A----------------------------ATATAAAATCATGCTAGATC----------------------------------------------------------------------TTGGAAAAATATCTAATAGATGGTTTTTATACATCAATCAA----------------------------------------TTGATA-TTTTTCCTTGAACTAAATGGGTTTA--------------------------------------------------------GTGCTGCAGCA----AAAATGGT
droEre2	scaffold_4690:1630508-1630651 -	LASTZ	5	TATCAA------GTTAAAA-------A----------------------------ATATAAAAGCAGTCCAGATC----------------------------------------------------------------------ATGGAAAAATATCAAATAGATTGTTTTATTTCA----------------------------------------------------------------------------------GTCCAAACAATACATAATCACGCGAGTCATAGTATCGAAATTTAGCAATTTATGAAGTTAAAAAAATATAAAGCCAT
droEug1	scf7180000409076:259969-260081 -	LASTZ	0	TATTAT------TTTCCGC-------A----------------------------T--TTAAATAATATTAAT------------------------------------------------------------------------------ATATATAATATAAATTCA--CTGCAAATTATCAAT----------------------------------------GGAGTA-TCAGTAATGT-AAAGAATGTTGTTAAAACCA-------------------------------------------------------AAACAA----TAAATAGT
droBia1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000415394:1165261-1165394 +	LASTZ	0	TTTCAACAATCAGTAGATT-------A----------------------------C--CGAAATCATATAAAT-ATATAAAATATAATTAACTTTCGAATTTATCCATCAAAAACACAAGATTCGTCTTTTCATCATTCATGTTTTACGGATG-TT----------------------------------------------------------------------------------------------------------------------------------------------------------------TTCATTAGA----ATGTTTTT
droEle1	scf7180000491011:2115245-2115356 +	LASTZ	0	TATTTG------GTTATTG-TG----A----------------------------T--TGGAATCATAGTTGCT-------------------------------------------------------------------------GTGAATATT----------------TATACAACACT--ATTGTTCTCAATTGAAATGTCAATACA--------------TTTAA----------------AAA--TATATA--------------------------------------------------------GCTTTAC-ATT----AACATTTT
droRho1	scf7180000779334:418263-418387 +	LASTZ	0	TTTCCG-------TGAAATAT-----G----------------------------A--AAAAAGCATTTATGTTT----------------------------------------------------------------------TAAGGTGGATTCTCAGAAGATTGTTTTTAAACATCAATCTT----------------------------------------TTGACAATTCACCCTTAAACAAAATTGTATTA--------------------------------------------------------GTTCTGTAAAA----ATGGATAT
droFic1	scf7180000453901:212756-212888 +	LASTZ	0	AATGGG------CACTAAA------AAAGTGTGTAATTTAAAATTCAATATTTAAACATTAAGTTTTTCGTTTCT----------------------------------------------------------------------TTAGGTTGATTCCTATTCGACTGTATC----------------ATAG---------GCATCAATCCG--------------TTTAGTAT----------------------T---------------------------------------------------------GACTTTTTTAA----AAGATTGT
droKik1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13335:212413-212477 +	LASTZ	0	TTTGTG------GA----------------------------------------------------------------------------------------------------------------------------------------TCGATTTCCAGTA--------------------------------------------------------------------A-TTCTGCAT---------------CAAAATCCGGACAAAAAA----------------------------------------TATTTT--TTG----AAAATTTT
droBip1	scf7180000396360:112225-112332 +	LASTZ	0	TAAGGA------TTTATAA-------A----------------------------A---------GTGTTTAATT----------------------------------------------------------------------TTTTATAAATATATAATAGAAAGATAATATACATTTATTTT----------------------------------------TAAATA-TTCATAAACTAACCAAATGGTCTTG--------------------------------------------------------GATATTCCA------------GA
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:5428540-5428655 -	LASTZ	0	TTGTTG-------TTGGCTGTTAACAA-------------------------------CTTGTTCGATTTGGCCT----------------------------------------------------------------------CTGGGTAGACTCTATATATGT-------------AAATATA--------------------------TATATATCTAATCTCTAATA-TC-------------TCACGTTTTA--------------------------------------------------------CACCTGCAAAA----AAAACTTC
droGri2	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	TATCAAGTTAAAAAA--CGAAATCATGTTAGATCCTGGACAAATATGAAGTAAATTGTTTTTATGCA--TC-----------AATTACTTGATATTCATCCTTGAACTA-AATGGTTT--TAGAGCTGCAAGA----AAAATTGT
droSim1	TATGAAGTTAAAAAA--CAAAATCATGCTAGATCAAGAACAAATATCATGTAAATTGATTTTTTAAA--TC-----------AACTACACGATATTCGTTCTTGAGCTT-AATGGTTC--TAGAGCTGCAAGA----AAAATTGT
droSec1	TATCAAGTTAAAAAA--CGAAATCATGCTAGATCTTGGACAAATATCAAGTAGATTATTTTTATACA--TC-----------AATTTATTGTTATTTGTCCTTGAACTT-AATTGTTT--TACAGCTGCAAAA----AAAATTGT
droYak2	TATCAAGTTCAGAAATATAAAATCATGCTAGATCTTGGAAAAATATCTAATAGATGGTTTTTATACA--TC-----------AATCAATTGATATTTTTCCTTGAACTA-AATGGGTT--TAGTGCTGCAGCA----AAAATGGT
droEre2	TATCAAGTTAAAAAATATAAAAGCAGTCCAGATCATGGAAAAATATCAAATAGATTGTTTTATTTCAGTCCAAACAATACATAATCACGCGAGTCATAGTATCGAAATTTAGCAAT-TTATGAAGTTAAAAAAATATAAAGCCAT

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					None			None	None	None	None		None
UNAFold Image							None					None			None	None	None	None		None

Small RNA-seq read pileup

Species

Alignment

droSim1

TATGAA------GTTAAAA-------A----------------------------A--CAAAATCATGCTAGATC----------------------------------------------------------------------AAGAACAAATATCATGTAAATTGATTTTTTAAATCAACTAC----------------------------------------ACGATA-TTCGTTCTTGAGCTTAATGGTTCTA--------------------------------------------------------GAGCTGCAAGA----AAAATTGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	6044.00	38.00	140.00	4416.00	1450.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTGG..............................................................................................	22	1	169.00	0.00	3.00	119.00	47.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTGT.............................................................................................	23	1	122.00	0.00	5.00	110.00	7.00
.....................................................................................................................................................................................ACTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	21	1	31.00	0.00	0.00	31.00	0.00
...................................................................................................................................................................................CAACTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	23	1	26.00	0.00	2.00	15.00	9.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTGG.............................................................................................	23	1	17.00	0.00	0.00	15.00	2.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTGA.............................................................................................	23	1	9.00	0.00	1.00	8.00	0.00
.....................................................................................................................................................................................ACTAC----------------------------------------ACGATA-TTCGTTCTTGT.............................................................................................	22	1	7.00	0.00	0.00	6.00	1.00
....................................................................................................................................................................................GACTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	7.00	0.00	0.00	6.00	1.00
....................................................................................................................................................................................AGCTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	6.00	0.00	0.00	3.00	3.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTTGTTCTTG..............................................................................................	22	1	5.00	0.00	0.00	3.00	2.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTT...............................................................................................	21	1	4.00	1.00	0.00	3.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTT..............................................................................................	22	1	4.00	1.00	0.00	3.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGACA-TTCGTTCTTG..............................................................................................	22	1	4.00	0.00	0.00	3.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCT................................................................................................	20	1	4.00	1.00	0.00	2.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ATGATA-TTCGTTCTTG..............................................................................................	22	2	2.00	0.00	0.00	1.50	0.50
....................................................................................................................................................................................AACCAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	3.00	0.00	0.00	2.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTCG..............................................................................................	22	1	3.00	1.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCCTG..............................................................................................	22	1	3.00	0.00	0.00	3.00	0.00
......................................................................................................................................................................................CTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	20	1	3.00	0.00	0.00	3.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACAATA-TTCGTTCTTG..............................................................................................	22	1	3.00	0.00	0.00	2.00	1.00
....................................................................................................................................................................................GACTAC----------------------------------------ACGATA-TTCGTTCTGG..............................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTA..............................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTATTG..............................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCTTTCTTG..............................................................................................	22	1	2.00	0.00	0.00	1.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTCCTTG..............................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------GCGATA-TTCGTTCTTG..............................................................................................	22	1	2.00	0.00	0.00	1.00	1.00
....................................................................................................................................................................................AATTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	2	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGGTCTTG..............................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................CACTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	2.00	0.00	0.00	1.00	1.00
.......................................................................................................................................................................................TAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	19	1	2.00	0.00	0.00	1.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCTTGC.............................................................................................	23	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTGC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCATTCTTG..............................................................................................	22	1	2.00	0.00	0.00	1.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------AGGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTCATG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGAGA-TTCGTTCT................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCCTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGxxA-TTCGTTCTTG..............................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACTATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGGTA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................ATCTAC----------------------------------------ACGATA-TTCGTTCTGG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-ATCGTTCTTGT.............................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACAAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACTATA-TTCGTTCTGG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTGGTTTTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGTTTTTG..............................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------AAGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TCCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATG-TTCGTTCTT...............................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATG-TTCGTTCTGG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................ACTAC----------------------------------------ACGATA-TTCGTTCTTGA.............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATC-TTCGTTCTTG..............................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................AACTxC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAT----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGATCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TACGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTTGTTCTGG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGGTA-TTCGTTCTTGT.............................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................ACTAC----------------------------------------ACGATA-TTCGTTCTTGC.............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAA----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................................C----------------------------------------ACGATA-TTCGTTCTTGT.............................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................CAAGTATCATGTAAATTGA........................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-CTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTGC----------------------------------------ACGATA-TTCGTTCTGG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTGGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AAGTAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................AACTAC----------------------------------------ACGATA-TTCGCTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................AAATAC----------------------------------------ACGATA-TTCGTTCTTG..............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

TATCAA------GTTAAAA-------A----------------------------A--CGAAATCATGCTAGATC----------------------------------------------------------------------TTGGACAAATATCAAGTAGATTATTTTTATACATCAATTTA----------------------------------------TTGTTA-TTTGTCCTTGAACTTAATTGTTTTA--------------------------------------------------------CAGCTGCAAAA----AAAATTGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAAC...........................................................................................	22	2	16.50	7.50	5.50	3.50
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAA............................................................................................	21	2	9.00	6.50	0.00	2.50
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAAA...........................................................................................	22	2	3.50	3.00	0.00	0.50
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGA.............................................................................................	20	2	2.50	1.50	0.00	1.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAACT..........................................................................................	23	2	2.00	1.50	0.00	0.50
.........................................................................TC----------------------------------------------------------------------TTGGACAAATATCAAGTAGA............................................................................................................................................................................	22	2	2.00	1.50	0.00	0.50
......................................................................................................................................................................................TTTA----------------------------------------TTGTTA-TTTGTCCTTGAA............................................................................................	22	2	1.00	0.50	0.50	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAACA..........................................................................................	23	2	1.00	0.00	0.50	0.50
.................................................................................................................................................TTGGACAAATATCAAGTAGATT..........................................................................................................................................................................	22	2	1.00	0.50	0.50	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAAT...........................................................................................	22	2	1.00	1.00	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGT.............................................................................................	20	2	1.00	1.00	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAACTA.........................................................................................	24	2	0.50	0.50	0.00	0.00
...................................................................................................................................................................GATTATTTTTGTATATCA............................................................................................................................................................	18	3	0.33	0.00	0.33	0.00
.............................................................................................................................................................CAAGTAGATGATTTATAT..................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00
.........................................................................TC----------------------------------------------------------------------TTxGACAAATATCAAGTAGAT...........................................................................................................................................................................	22	2	0.50	0.50	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGTAT...........................................................................................	22	2	0.50	0.50	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTCGTCCTTGAAC...........................................................................................	22	2	0.50	0.50	0.00	0.00
........................................................................................................................................................................................TA----------------------------------------TTGTTA-TTTGTCCTTGAAC...........................................................................................	21	2	0.50	0.50	0.00	0.00
.................................................................................................................................................TTGGACAAATATCAAGTACAT...........................................................................................................................................................................	21	2	0.50	0.50	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAACC..........................................................................................	23	2	0.50	0.50	0.00	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTGAAAA..........................................................................................	23	2	0.50	0.50	0.00	0.00
...................................................................GCTAGATC----------------------------------------------------------------------TTGAAGAAAT......................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00
.........................................................................................................................................................................................A----------------------------------------TTGTTA-TTTGTCCTTGAAC...........................................................................................	20	2	0.50	0.00	0.50	0.00
.........................................................................TC----------------------------------------------------------------------TTGGACAAATATCAAGT...............................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00
.......................................................................................................................................................................................TTA----------------------------------------TTGTTA-TTTGTCCTTTAAA...........................................................................................	22	2	0.50	0.50	0.00	0.00

droYak2

TATCAA------GTTCAGA-------A----------------------------ATATAAAATCATGCTAGATC----------------------------------------------------------------------TTGGAAAAATATCTAATAGATGGTTTTTATACATCAATCAA----------------------------------------TTGATA-TTTTTCCTTGAACTAAATGGGTTTA--------------------------------------------------------GTGCTGCAGCA----AAAATGGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................................................................................................................................AA----------------------------------------TTGATA-TTTTTCCTTGAAC...........................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

TATCAA------GTTAAAA-------A----------------------------ATATAAAAGCAGTCCAGATC----------------------------------------------------------------------ATGGAAAAATATCAAATAGATTGTTTTATTTCA----------------------------------------------------------------------------------GTCCAAACAATACATAATCACGCGAGTCATAGTATCGAAATTTAGCAATTTATGAAGTTAAAAAAATATAAAGCCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................................................................................................................................................................................................................................................................GAAGTTAAAAAATTTTAA......	18	2	1.00	0.00	0.00	0.00	1.00
..TGAA------GTTAAAA-------A----------------------------ATAAAAA...................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
........................................................................................................................................................................................................................................................................................................................TGAAGTTAAAAAATTTTAA......	19	2	0.50	0.00	0.00	0.00	0.50
TATCAA------GTAAAAA-------A----------------------------ATATT.....................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

TATTAT------TTTCCGC-------A----------------------------T--TTAAATAATATTAAT------------------------------------------------------------------------------ATATATAATATAAATTCA--CTGCAAATTATCAAT----------------------------------------GGAGTA-TCAGTAATGT-AAAGAATGTTGTTAAAACCA-------------------------------------------------------AAACAA----TAAATAGT

Size

Hit Count

Total Norm

droBia1

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droTak1

TTTCAACAATCAGTAGATT-------A----------------------------C--CGAAATCATATAAAT-ATATAAAATATAATTAACTTTCGAATTTATCCATCAAAAACACAAGATTCGTCTTTTCATCATTCATGTTTTACGGATG-TT----------------------------------------------------------------------------------------------------------------------------------------------------------------TTCATTAGA----ATGTTTTT

Size

Hit Count

Total Norm

droEle1

TATTTG------GTTATTG-TG----A----------------------------T--TGGAATCATAGTTGCT-------------------------------------------------------------------------GTGAATATT----------------TATACAACACT--ATTGTTCTCAATTGAAATGTCAATACA--------------TTTAA----------------AAA--TATATA--------------------------------------------------------GCTTTAC-ATT----AACATTTT

Size

Hit Count

Total Norm

droRho1

TTTCCG-------TGAAATAT-----G----------------------------A--AAAAAGCATTTATGTTT----------------------------------------------------------------------TAAGGTGGATTCTCAGAAGATTGTTTTTAAACATCAATCTT----------------------------------------TTGACAATTCACCCTTAAACAAAATTGTATTA--------------------------------------------------------GTTCTGTAAAA----ATGGATAT

Size

Hit Count

Total Norm

droFic1

AATGGG------CACTAAA------AAAGTGTGTAATTTAAAATTCAATATTTAAACATTAAGTTTTTCGTTTCT----------------------------------------------------------------------TTAGGTTGATTCCTATTCGACTGTATC----------------ATAG---------GCATCAATCCG--------------TTTAGTAT----------------------T---------------------------------------------------------GACTTTTTTAA----AAGATTGT

Size

Hit Count

Total Norm

droKik1

Size

Hit Count

Total Norm

droAna3

TTTGTG------GA----------------------------------------------------------------------------------------------------------------------------------------TCGATTTCCAGTA--------------------------------------------------------------------A-TTCTGCAT---------------CAAAATCCGGACAAAAAA----------------------------------------TATTTT--TTG----AAAATTTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
TTTGTG------GA----------------------------------------------------------------------------------------------------------------------------------------TCGATTTCCAGTC--------------------------------------------------------------------G-TTC.....................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00
..TGTG------GA----------------------------------------------------------------------------------------------------------------------------------------ACGATTGCCAGT...............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................................AAAAAA----------------------------------------AAGTTT--TTG----AAAA....	19	7	0.14	0.00	0.00	0.00	0.14
.....................................................................................................................................................................................................................................................................TCTGGACAGAAAA----------------------------------------TATTTT--TTG----AAAAT...	27	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................AAAGA----------------------------------------TxTTTT--GTG----AAAAT...	18	1	1.00	0.00	1.00	0.00	0.00

droBip1

TAAGGA------TTTATAA-------A----------------------------A---------GTGTTTAATT----------------------------------------------------------------------TTTTATAAATATATAATAGAAAGATAATATACATTTATTTT----------------------------------------TAAATA-TTCATAAACTAACCAAATGGTCTTG--------------------------------------------------------GATATTCCA------------GA

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTGTTG-------TTGGCTGTTAACAA-------------------------------CTTGTTCGATTTGGCCT----------------------------------------------------------------------CTGGGTAGACTCTATATATGT-------------AAATATA--------------------------TATATATCTAATCTCTAATA-TC-------------TCACGTTTTA--------------------------------------------------------CACCTGCAAAA----AAAACTTC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:52 EDT

dme-mir-982

chrX:4259839-4259931 -

Known_mirbase

intergenic

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