dme-mir-4955- Best orthologs

dme-mir-4955	chrX:2438772-2438941 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2438797-2438818
   star strand at position 2438893-2438914
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:2438757-2438956 -		1	TT--GCTGATGTCAAA---------------------------TCA---CCGATTTGCTTCCCCT---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTAACGCTTA-----ATTGTTGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCTGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droSim1	chrX:1743323-1743545 -	LASTZ	5	TT--GCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCC---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAAGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-CCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droSec1	super_10:2212704-2212927 -	LASTZ	5	TT-TGCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAACTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droYak2	chrX:5905985-5906183 +	LASTZ	5	TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCCGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTC-------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTTACGCTTAATTTAATTGTCGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAAA-ACCTGCC--------------------------AGCCGTT-CAAAGC
droEre2	scaffold_4644:2389120-2389318 -	LASTZ	5	TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCTGAGAAAAAAATCCCC---------------AGAAA-CCTAAT------------------------ATCAGGATGCTCTCTGTCTC-------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCACGGCAA-----ATTGTTGC-TTAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------GACCGTT-TAAAGC
droEug1	scf7180000409277:126495-126773 -	LASTZ	0	TT--GCTGAAATCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGTTTCCCCC---------TTTATT-TTTTTATTAGTGCACCGAGAAAAAATCGACC---------------ATAG-----AATTCA----------------------------------------------GATTT----------------------------------------------------------------------------------TAAAGTATTTTATAGATTAATTAATGTTAGGAG---------------TTTTTATGCCTAA----------------AGCAGGGGACACATTGT---------------------------------------------------------------------------------------------------------------------------------------------------TTTCTATAGTT--------------TCTATAGTTTTTCAATTAACGTATTAATAAATTATTTCGGG-GCT--TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AGCCGTG-AAAAAC
droBia1	scf7180000301760:4721669-4721893 +	LASTZ	0	TT--GCTGATATCGGG------AAACGTGTCCCGTTTCTGTGCTCT---CCGATTTGTTTACCCT---------TTCC---------TAAGTGCACCGAGAAAAAACGCCCC---------------TAAG-----AATGCTAAA-------------------------------------------------------------------------------------------------AAA----------------------------------------------------AAAGCTAGGAG---------------AAAATATCCTTCAAAGAGAATTTAAATCA-AAA--TG---AAT----------------------------------------------------------------------------------------------------------------------TGCCT----------------------------TTAAT------------------------A-----------------------ACCCATTTCGGG-GAC--TTTTTTCTCTGTGCAGTGCCATAGCCGCA------------------------------------------------------------A----CA-ACCTGCC--------------------------AACCTTT-TGAAAC
droTak1	scf7180000415151:362895-363093 +	LASTZ	0	TT--GCTGGTATCGGG------AAACGTGTCCCGTTTCTGTGCTCTCCACCAAACTGTTTCCCCC---------TTTT---------TTAGTGCACCGAGAAAAAACACCTCCTT------------AGGAA-TAGAAT--------------------------------------------------------------------CCAACTTATTATTGAG---------TAA----------------------------------------------------GAT--------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAT------------------------A-----------------------TCCAATCTTGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AACCGCT-TAAAAC
droEle1	scf7180000491011:764569-764826 -	LASTZ	0	TT--GCCAAATTCAAA-----------------------------A---CCAAA-AATATCCATT---------TT-T---------TAAATATACAAT--------------------------------------------------------------------------------------------AAT-------------TAACTTTAAAGA-AAAAATCTTCGTTAATGTTTTAAAAAA----------------------------------------------------------------------------------------------------------TAA--TAATTTATTATCCTTTGAATAATTTCACCATTATCATGCTATGTTAATTTT---TTAA--------------ACATTTGCCAATGAGCGTTTTACTGAAATACAGAACTAATTGA---------------------------------------------------------------------------------------------------ATTTTTCGTGGGATA-TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAGAC
droRho1	scf7180000779506:556816-557127 -	LASTZ	0	CT--GCTGATGATGGG------AAACGCGTCCCGTTTCTGTGCTCT---CCGATTTGTTGTCTCT---------TTTT---------T--TTAG-ACGAGAAAAAAACAGTT---AAAGAATTTCCAAGAAAGCAT-------------TGAAATCAAACAAAAA---------------CCATATATTATTCTAAAAATAGTCCGTTTACCATAGTGA-AAT---------TAAGGTTTTAAAACC-------------------------------------------------------------------------------------------------------------------TAATTATCCTTTAAGTAATCTCACCA------TGCTATAT-CATTTT---GAAA--------------GCATTTCTTTTTGGGCGTTTTTCTAAAATACCAAAG---------------------------------------------------------------------------------------------------------------------TAT--ATTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCTTT-TAAAAC
droFic1	scf7180000453927:241567-241837 -	LASTZ	0	TT--GCTGATGTCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGCTTCCCCC---------TTTCTT-TT----ATAGTGCACAGAGAAAAAATGCATC---------------AAAAA-CT-----------------------------------------------------AATAAT-------------AAA-------------------------------------T-CCTT----------T-T---------------------TAGAACAAAAAA--AAAAGAA---------------TA--------------------------------------------------------TTCACAATTACTAAG----------------TGAAACATCTTTTCGTAAT-------CAACGATCTTTTTGTT---------------------------------------------------------------------------TTAAGTAATAAGTTTTCA-----------------------ATCTATCTCGGGTGCTA-TTTTTTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-TCCTGCC--------------------------AGCCGTT-TAATAC
droKik1	scf7180000302258:595697-595976 -	LASTZ	0	TT--GTTTACT--------------------------------------TTAATTTTTTTTTTTT---------T--T---------TTGTTGCACAGAGACAAAAATAGTT---T-------TC--T---------TTGCTAAAATATAAAAAATATACGAGAGCAGAAT-TTATATATATATATATTTTTCT-------------A---------------------------------------CTTAAAATGTATGGAATAATGCTTCTGATAAGTAACTTCAGAGATTCC-------------A---------------------------------------------------------------TTAGATAAGAATATTA------TATTAT---------AAA-----------------------------------------------------------------------------------------------------------------GCCGTAAACTAATTTGTCGACA-------------------------TTTTTTCGGTTGATATTTTTATCTCTGTGCAGTGCCATAGCCTTA------------------------------------------------------------A-CCACAAACCTGCC--------------------------AGCCGTT-TAA-AC
droAna3	scaffold_12929:2354513-2354742 -	LASTZ	0	GT--GTTTCTTCCAAATCTTCACTTCTCTTCTCTTTTCTTTTCTTT---CCTT-------CTTCTGTTTTTTTTTTTT----GTTGGTCCCTGCACGGAGAAGAAGTTG-TT---------------AGGAC-AT-----------------------------------------------------TAGAGT-------------GGACCTTAGTGT-GGT---------TAA----------------------------------------------------TAG--------------------------------------------------------------ATCATATGACTCATTGTCCTTGCAATTATTTCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------A-----------------------ACTCG---CTCC--AC--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAAAAA
droBip1	scf7180000396434:346903-347133 -	LASTZ	0	TT--TTA--------------------TTTTTTATTTCCTCTT--------------CTTCCCTC---------TTGTTTTTTTTGGTTCCTGCACAGAGAAAAAGTTC--T---------------AGGAC-CT-----------------------------------------------------TAGAGT-------------GGA-------------------------------------C-CATA----------T-TTGTTGCCTATAAAGTGTTCTATAGATTCT-------------AAGATCCTTGAGGGATTTGTATGA-------------------------------------------------------------------C---------TAA-----------------------------------------------------------------------------------------------------------------TTTTTAGAATAATTATTTTACA-----------------------ACTTG---CTTG-AAT--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAA---
dp4	chrXL_group3a:2134676-2134849 -	LASTZ	0	TTTCGCTGATTCGGGA------ATATATTCTCCACCCCCCCACCCT---CT---------ACCAT---------TT-C---------CTCTTCTGCTGACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACACGATTTTCCCCCTCTCTCTTAACGATCTTAACGCTCC-----ACT---------------------------------------------------------------------CTTTCTGTCT--CTCTCGATTTTTGCAGTGCCATAGCCGTA------------------------------------------------------------AAACACT-GTCTTCC--------------------------TACCGTT-TACCGT
droPer1	super_13:248212-248305 -	LASTZ	0	TC--TCTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCAGGCGTA-----ACAGGTGCGTTGAGTGCATTT----------------------------------------CAA-------TTGTATG-GA--------TAATTGTGCTGTATTGTAATTGAA------------------------------------------------------------ATCCACA-A----------------------------------------------
droWil1	scaffold_181096:12164007-12164188 -	LASTZ	0	TC--GCTGATTTTGGA------AAACATTTCTTATTTGCTCTC-CT---TTAATTTATGTTTTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TCTTTTGTATAT----------------------------------------T----------TTTTAT-G----TTTATTTTGTTTGCAGTGCCATAAC-ATAATAATAGTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAAT---------------------------------------------AT-CAAAAC
droVir3	scaffold_12928:1476007-1476072 -	LASTZ	0	TT--T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTTACTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC----TTTTTCT--TTCTTTATCACGTCTAAACG---------------CAT
droMoj3	scaffold_6473:13536163-13536218 +	LASTZ	0	CG--T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCTCTCTTGCAGTGCCATAAACATC------------------------------------------------------------G-TAATT--TTTTTC--------------------------ATTTATT-TACGTC
droGri2	scaffold_15203:8273975-8274075 +	LASTZ	0	AATAGCTGAA------------------------------------------ATTTGTTTTCCTC---------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC--T-TTTTTCTTTTTTTTTCTTACGTCAAAACGCATCGATCGCATCAGAGG

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	T-TGCTGATGTCAAATCACCGATTTGCTTCCCCTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATCT------------------------CTGTCTCTGTCTAACGCTTA-----ATTGTTGCTCAATTGCGAATTAATGTCTGGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droSim1	T-TGCTGATGTCAAATCACCGATTTGTTTCCCCCTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCCCAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droSec1	TTTGCTGATGTCAAATCACCGATTTGTTTCCCCTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAACTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droYak2	T-TGCTGATGTG--TTCACCGATTTGTTTCCCCTTTTTCCGTGCGCCGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTC----------------------------CCTGTCTCTGTCTTACGCTTAATTTAATTGTCGCTCAATTGCGAATTAATGTCGGGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCAAAACCTGCCAGCCGTTCAAAGC
droEre2	T-TGCTGATGTG--TTCACCGATTTGTTTCCCCTTTTTCCGTGCGCTGAGAAAAAAATCCCCAGAAACCTAATATCAGGATGCTCTCTGTCTC----------------------CCTGTCTCTGTCTCACGGCAA-----ATTGTTGCTTAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCGACCGTTTAAAGC

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
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

TT--GCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCC---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAAGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-CCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................ATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAAGT.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	2.00	0.00	2.00	0.00	0.00
.................................................................................................................................AAT-CATAAT------------------------CTCAGGATG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
....................................................................................................................................................................................ATCTATCTCAGTCT-------------GGG-------------------------------------C-...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCCTG------TCTGACGCTTA-----ATTGTTGC-CC.........................................................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCC..........	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTCGGG-GCT--TTTTTTCTCCG.....................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G------TCTGACGCTTA-----ATTGTTGC-CC.........................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droSec1

TT-TGCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAACTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGC...........	22	1	1.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGT........	20	1	1.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CACA-ACCTGCC--------------------------AGCCGTT-T.....	19	1	1.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCG.........	19	1	1.00	0.00	1.00	0.00

droYak2

TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCCGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTC-------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTTACGCTTAATTTAATTGTCGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAAA-ACCTGCC--------------------------AGCCGTT-CAAAGC

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCTGAGAAAAAAATCCCC---------------AGAAA-CCTAAT------------------------ATCAGGATGCTCTCTGTCTC-------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCACGGCAA-----ATTGTTGC-TTAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------GACCGTT-TAAAGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A------------------------------------------------------------A-CCACA-ACCTGCC--------------------------GACCGTT-......	21	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------GACCGTT-......	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G-GCT--TTTTTTCTCCGTGCAGTT..............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTCTGCATGCAGTGCCA...........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droEug1

TT--GCTGAAATCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGTTTCCCCC---------TTTATT-TTTTTATTAGTGCACCGAGAAAAAATCGACC---------------ATAG-----AATTCA----------------------------------------------GATTT----------------------------------------------------------------------------------TAAAGTATTTTATAGATTAATTAATGTTAGGAG---------------TTTTTATGCCTAA----------------AGCAGGGGACACATTGT---------------------------------------------------------------------------------------------------------------------------------------------------TTTCTATAGTT--------------TCTATAGTTTTTCAATTAACGTATTAATAAATTATTTCGGG-GCT--TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AGCCGTG-AAAAAC

Size

Hit Count

Total Norm

droBia1

TT--GCTGATATCGGG------AAACGTGTCCCGTTTCTGTGCTCT---CCGATTTGTTTACCCT---------TTCC---------TAAGTGCACCGAGAAAAAACGCCCC---------------TAAG-----AATGCTAAA-------------------------------------------------------------------------------------------------AAA----------------------------------------------------AAAGCTAGGAG---------------AAAATATCCTTCAAAGAGAATTTAAATCA-AAA--TG---AAT----------------------------------------------------------------------------------------------------------------------TGCCT----------------------------TTAAT------------------------A-----------------------ACCCATTTCGGG-GAC--TTTTTTCTCTGTGCAGTGCCATAGCCGCA------------------------------------------------------------A----CA-ACCTGCC--------------------------AACCTTT-TGAAAC

Size

Hit Count

Total Norm

droTak1

TT--GCTGGTATCGGG------AAACGTGTCCCGTTTCTGTGCTCTCCACCAAACTGTTTCCCCC---------TTTT---------TTAGTGCACCGAGAAAAAACACCTCCTT------------AGGAA-TAGAAT--------------------------------------------------------------------CCAACTTATTATTGAG---------TAA----------------------------------------------------GAT--------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAT------------------------A-----------------------TCCAATCTTGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AACCGCT-TAAAAC

Size

Hit Count

Total Norm

droEle1

TT--GCCAAATTCAAA-----------------------------A---CCAAA-AATATCCATT---------TT-T---------TAAATATACAAT--------------------------------------------------------------------------------------------AAT-------------TAACTTTAAAGA-AAAAATCTTCGTTAATGTTTTAAAAAA----------------------------------------------------------------------------------------------------------TAA--TAATTTATTATCCTTTGAATAATTTCACCATTATCATGCTATGTTAATTTT---TTAA--------------ACATTTGCCAATGAGCGTTTTACTGAAATACAGAACTAATTGA---------------------------------------------------------------------------------------------------ATTTTTCGTGGGATA-TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAGAC

Size

Hit Count

Total Norm

droRho1

CT--GCTGATGATGGG------AAACGCGTCCCGTTTCTGTGCTCT---CCGATTTGTTGTCTCT---------TTTT---------T--TTAG-ACGAGAAAAAAACAGTT---AAAGAATTTCCAAGAAAGCAT-------------TGAAATCAAACAAAAA---------------CCATATATTATTCTAAAAATAGTCCGTTTACCATAGTGA-AAT---------TAAGGTTTTAAAACC-------------------------------------------------------------------------------------------------------------------TAATTATCCTTTAAGTAATCTCACCA------TGCTATAT-CATTTT---GAAA--------------GCATTTCTTTTTGGGCGTTTTTCTAAAATACCAAAG---------------------------------------------------------------------------------------------------------------------TAT--ATTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCTTT-TAAAAC

Size

Hit Count

Total Norm

droFic1

TT--GCTGATGTCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGCTTCCCCC---------TTTCTT-TT----ATAGTGCACAGAGAAAAAATGCATC---------------AAAAA-CT-----------------------------------------------------AATAAT-------------AAA-------------------------------------T-CCTT----------T-T---------------------TAGAACAAAAAA--AAAAGAA---------------TA--------------------------------------------------------TTCACAATTACTAAG----------------TGAAACATCTTTTCGTAAT-------CAACGATCTTTTTGTT---------------------------------------------------------------------------TTAAGTAATAAGTTTTCA-----------------------ATCTATCTCGGGTGCTA-TTTTTTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-TCCTGCC--------------------------AGCCGTT-TAATAC

Size

Hit Count

Total Norm

droKik1

TT--GTTTACT--------------------------------------TTAATTTTTTTTTTTT---------T--T---------TTGTTGCACAGAGACAAAAATAGTT---T-------TC--T---------TTGCTAAAATATAAAAAATATACGAGAGCAGAAT-TTATATATATATATATTTTTCT-------------A---------------------------------------CTTAAAATGTATGGAATAATGCTTCTGATAAGTAACTTCAGAGATTCC-------------A---------------------------------------------------------------TTAGATAAGAATATTA------TATTAT---------AAA-----------------------------------------------------------------------------------------------------------------GCCGTAAACTAATTTGTCGACA-------------------------TTTTTTCGGTTGATATTTTTATCTCTGTGCAGTGCCATAGCCTTA------------------------------------------------------------A-CCACAAACCTGCC--------------------------AGCCGTT-TAA-AC

Size

Hit Count

Total Norm

droAna3

GT--GTTTCTTCCAAATCTTCACTTCTCTTCTCTTTTCTTTTCTTT---CCTT-------CTTCTGTTTTTTTTTTTT----GTTGGTCCCTGCACGGAGAAGAAGTTG-TT---------------AGGAC-AT-----------------------------------------------------TAGAGT-------------GGACCTTAGTGT-GGT---------TAA----------------------------------------------------TAG--------------------------------------------------------------ATCATATGACTCATTGTCCTTGCAATTATTTCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------A-----------------------ACTCG---CTCC--AC--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAAAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................GTTG-TT---------------AGGAC-AT-----------------------------------------------------TAGAGT-------------G............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.............................................................TTCTGTGTTTTTTTATT----GTT.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................AAGTTG-TT---------------AGGAC-AT-----------------------------------------------------TAGAGT-------------G............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................TT-------CTTTTGTTTTTTTTTTTT----T.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	23	0.04	0.00	0.00	0.00	0.04

droBip1

TT--TTA--------------------TTTTTTATTTCCTCTT--------------CTTCCCTC---------TTGTTTTTTTTGGTTCCTGCACAGAGAAAAAGTTC--T---------------AGGAC-CT-----------------------------------------------------TAGAGT-------------GGA-------------------------------------C-CATA----------T-TTGTTGCCTATAAAGTGTTCTATAGATTCT-------------AAGATCCTTGAGGGATTTGTATGA-------------------------------------------------------------------C---------TAA-----------------------------------------------------------------------------------------------------------------TTTTTAGAATAATTATTTTACA-----------------------ACTTG---CTTG-AAT--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAA---

Size

Hit Count

Total Norm

dp4

TTTCGCTGATTCGGGA------ATATATTCTCCACCCCCCCACCCT---CT---------ACCAT---------TT-C---------CTCTTCTGCTGACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACACGATTTTCCCCCTCTCTCTTAACGATCTTAACGCTCC-----ACT---------------------------------------------------------------------CTTTCTGTCT--CTCTCGATTTTTGCAGTGCCATAGCCGTA------------------------------------------------------------AAACACT-GTCTTCC--------------------------TACCGTT-TACCGT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCCATAGCCGTA------------------------------------------------------------AAACA..................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTGTCT--CTCTCGATTTTTGCAG................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droPer1

TC--TCTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCAGGCGTA-----ACAGGTGCGTTGAGTGCATTT----------------------------------------CAA-------TTGTATG-GA--------TAATTGTGCTGTATTGTAATTGAA------------------------------------------------------------ATCCACA-A----------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....TCTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGACTCTG------GC..................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.C--TCTGTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------CC..................................................................................................................................................................................................................................................	19	11	0.18	0.00	0.00	0.00	0.00	0.18
.....CTGTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCCC................................................................................................................................................................................................................................................	19	4	0.50	0.00	0.00	0.00	0.00	0.50
.C--TCTGTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCT.................................................................................................................................................................................................................................................	20	4	0.50	0.00	0.00	0.00	0.00	0.50
.........CT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCTGCC............................................................................................................................................................................................................................................	19	11	0.18	0.00	0.00	0.00	0.00	0.18
.....CTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGCTCTG------GCT.................................................................................................................................................................................................................................................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
.C--TCTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------GCC.................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTATTGTAATTGAA------------------------------------------------------------AGCCA..................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGAGTGCATTT----------------------------------------Cxx-------TTGTATG-GA--------...........................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
....TCAGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTC------TC..................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00

droWil1

TC--GCTGATTTTGGA------AAACATTTCTTATTTGCTCTC-CT---TTAATTTATGTTTTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TCTTTTGTATAT----------------------------------------T----------TTTTAT-G----TTTATTTTGTTTGCAGTGCCATAAC-ATAATAATAGTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAAT---------------------------------------------AT-CAAAAC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTGTGTTTGAA.................................................................................................................................	18	2	529.50	2.00	511.00	16.00	0.50
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTGTGTTTGCAT................................................................................................................................	19	1	5.00	0.00	5.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAT-G----TTTATTTTGTTTGAA.................................................................................................................................	19	3	1.33	0.00	1.33	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTAG-G----GTTATTTTGTT.....................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTAG-G----GTTATTTTGTTT....................................................................................................................................	18	3	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTGTGTTTGCA.................................................................................................................................	18	3	0.67	0.00	0.67	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAT-G----TTTATTTTGTTTGA..................................................................................................................................	18	3	0.67	0.00	0.67	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTTTGTTTGAAT................................................................................................................................	19	4	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTTTGTTTGAA.................................................................................................................................	18	5	0.40	0.00	0.40	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGTTGATACTTATTATGT............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................ATTTATGTATTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GA..................................................................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
................................................................T---------TTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGTTTTG....................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00
............................................AT---TTAATTTATGTTTTTG---------T.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
..........................................................GTGTGTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-...........................................................................................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTGTTTGCAGTGCCATAAC-......................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................TATGTTGTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTG................................................................................................................................................................................................................................	18	18	0.06	0.00	0.06	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTGTGTTTGGA.................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATAATAGTTAATACTTATTGTGT............................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT----------------------------------------T----------TTTTTT-G----TTTATTTAGT......................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................TTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGGT.......................................................................................................................................................................................................................	20	39	0.03	0.00	0.03	0.00	0.00
..........................................................................GTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGTTTTGT...................................................................................................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00
...........................................................................TTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TCTTTGAT...................................................................................................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00
............................................................TTGTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TTTT.......................................................................................................................................................................................................................	21	12	0.08	0.08	0.00	0.00	0.00
...............................................................TT---------GTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TTTTTT.....................................................................................................................................................................................................................	20	13	0.08	0.00	0.00	0.08	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTAG-G----GTTATTTTGTTT....................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................TTTT---------TTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGT........................................................................................................................................................................................................................	19	43	0.02	0.00	0.00	0.00	0.02
...................................................AATTTGTGTTTTTG---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................................................................................................................................................................................................................................	18	12	0.08	0.00	0.08	0.00	0.00
.............................................................TTTT---------CTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-CC.........................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................TT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TTTCTTGT...................................................................................................................................................................................................................	22	3	0.33	0.33	0.00	0.00	0.00
.....................................................TTTATGTTTTTG---------TTTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT..................................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..........................................................................TTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGTTTTGT...................................................................................................................................................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
.........................................................AGTTTTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGTT..............................................................................................................................................................................................................................	18	10	0.10	0.00	0.00	0.10	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAATACTTATTGTGTT...........................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................TTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TGATT......................................................................................................................................................................................................................	21	9	0.11	0.00	0.11	0.00	0.00
.C--GCTGATTTTGGA------AAACATT...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................TTTTGT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-T..........................................................................................................................................................................................................................	19	471	0.00	0.00	0.00	0.00	0.00
........................................................ATATTATTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-...........................................................................................................................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTxGTTTGTTTGCAG................................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
.............................................T---TTAATATATGTGTTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-G----TTTATTGTGTTTGAAG................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTGGGCCGCCGAATCGAAAACGAAT---------------------------------------------.........	27	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAT-G----TTTATTGTGTTTGCA.................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTGGGCCGCCGAATCGAA.............................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TCTTTTGAAA.................................................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00

droVir3

TT--T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTTACTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC----TTTTTCT--TTCTTTATCACGTCTAAACG---------------CAT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CG--T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCTCTCTTGCAGTGCCATAAACATC------------------------------------------------------------G-TAATT--TTTTTC--------------------------ATTTATT-TACGTC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATxAACAGC------------------------------------------------------------G-TAATT--TTTTT.........................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

AATAGCTGAA------------------------------------------ATTTGTTTTCCTC---------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC--T-TTTTTCTTTTTTTTTCTTACGTCAAAACGCATCGATCGCATCAGAGG	Size	Hit Count	Total Norm	V109 Male body
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGG	19	6	0.17	0.17
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACGCATCGATCGCATCAGAGG	22	1	1.00	1.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TACGTCAAAACGCATCGATC..........	20	1	1.00	1.00

Generated: 04/20/2012 at 05:18:03 EDT

dme-mir-4955

chrX:2438772-2438941 -

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