dme-mir-2535b- Best orthologs

dme-mir-2535b	chrX:21169302-21169372 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 21169306-21169327
   star strand at position 21169348-21169372
   mutations
   read mismatches

Notes: "Interesting case; miRNA lost then reappeared. droFic1 - droBip1 have non-miRNA-like structures. droAna3, droWil1, droVir3, droMoj3 orthologous intron is >400nt long so LASTZ cannot bridge the long ""insertion"" properly and reports two hits. "

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:21169287-21169387 -		1	ACGTACATCACTAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTGAA---CTT------AGC-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droSim1	chrX:12918307-12918407 +	LASTZ	1	ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGC-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droSec1	super_8:3476294-3476394 -	LASTZ	1	ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGA-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droYak2	chrX:20345010-20345110 -	LASTZ	1	ACGTACATCACCAAGGTAAGTGAC--AATGCCG------GGATTGTGGTTATTGAA---AAT------ACC-T-TCTCCACT--CACGGCATTAT--ATTCACTTGCAGTACATCACCGCCGAG
droEre2	scaffold_4690:17698644-17698744 -	LASTZ	1	ACGTACATCACCAAGGTAAGTGAC--AGTGCCG------GGATTGTGGTTATTAAA---AAT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droEug1	scf7180000408193:313028-313128 +	LASTZ	4	ACGTATATCACCAAGGTAAGTGGC--TATGCCG------GGATCGTGGTTGATCTA---TGT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGTAGTACATCACCGCTGAA
droBia1	scf7180000302187:362231-362333 +	LASTZ	4	ACGTACATCACCAAAGTAAGTGGC--CATGCCG------GGATTGTGGTTTAA------CC-AGAGGTTCC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droTak1	scf7180000415158:278082-278185 +	LASTZ	4	ACGTACATCACCAAGGTAAGTGGC--TATGCCG------GGATTGTGGTTTACAATA--GAA---AG-ATC-C-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droEle1	scf7180000490214:747380-747480 +	LASTZ	4	ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGACTGTGGTTCTAAAT---GCC------ATC-A-CCACCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droRho1	scf7180000780082:43771-43867 +	LASTZ	4	ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGATTGTGGTTAAT-------AC------ACC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droFic1	scf7180000454077:620842-620934 -	LASTZ	5	ACGTACATCACCAAGGTAAGTTTA--TATTTATTT-GTGTTGG----------------TGT------ACC-T-CCTCCACT--CACAACATTTC--ATTCACCTGCAGTTCATTACCGCCGAG
droKik1	scf7180000302395:540407-540502 -	LASTZ	5	ACGTACATCACCAAGGTAAGTCTC-------CGAGAACGGGAAC------GAA------TC-GCACA--GATCCATATCTGT--ATC--TGTATC--CTTCTTGTGTAGTACATCACCGCCGAG
droAna3	Unknown	MAF	5	ACTTATATTACAAAGGTAAGT----------------------------------------------------------ATC--CAAGTTATTTC-CTTCAATTTTCAGTTCATAACCGCCGAA
droBip1	scf7180000396733:700642-700737 +	LASTZ	5	ACGTATATAACAAAGGTGAGAGGGACGAGGT-----------CTATAGCTTTCGG---GTTG------TGT-----AATACT--TTAAATATTTT-ATTCCAATTTCAGTATATAACCGCCGAA
dp4	chrXL_group1a:9058690-9058790 +	LASTZ	1	ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG
droPer1	super_15:1452144-1452244 +	LASTZ	1	ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG
droWil1	Unknown	MAF	5	ACTTACATTACCAAGGTGAGT----------------------------------------------------------------------TTTG--TTTTTCTTACAGTACATTACATCGGAG
droVir3	Unknown	MAF	5	ACGTGCATTACCAAGGTAAG------------------------------------------------------CCTCTTCT--CACGACATCCCTTAATCCCTTGCAGTACGTTGCCAACGAA
droMoj3	Unknown	MAF	5	ACATGCATAACCAGGGTAAGTGCTCAGCTGC---------TtTTtTttTttTtgt------------------------tTT--TTttTTtTTTC--GTCGCCTTACAGTACATCTCCAAGGAG
droGri2	scaffold_15203:11132616-11132716 +	LASTZ	5	ACCTACATTACTAAGGTATGTT--------CGA------TGATTTTGGTTTTTTTTGGCTTT------ACT-T-TCACCGTTTACACGACAATTT-CATCCTTTTGCAGTACGTGACCAGTGAG

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	ACGTACATCACTAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTGAA---CTT------AGC-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droSim1	ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGC-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droSec1	ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGA-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droYak2	ACGTACATCACCAAGGTAAGTGAC--AATGCCG------GGATTGTGGTTATTGAA---AAT------ACC-T-TCTCCACT--CACGGCATTAT--ATTCACTTGCAGTACATCACCGCCGAG
droEre2	ACGTACATCACCAAGGTAAGTGAC--AGTGCCG------GGATTGTGGTTATTAAA---AAT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droEug1	ACGTATATCACCAAGGTAAGTGGC--TATGCCG------GGATCGTGGTTGATCTA---TGT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGTAGTACATCACCGCTGAA
droBia1	ACGTACATCACCAAAGTAAGTGGC--CATGCCG------GGATTGTGGTTTAA------CC-AGAGGTTCC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droTak1	ACGTACATCACCAAGGTAAGTGGC--TATGCCG------GGATTGTGGTTTACAATA--GAA---AG-ATC-C-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droEle1	ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGACTGTGGTTCTAAAT---GCC------ATC-A-CCACCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droRho1	ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGATTGTGGTTAAT-------AC------ACC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG
droFic1	ACGTACATCACCAAGGTAAGTTTA--TATTTATTT-GTGTTGG----------------TGT------ACC-T-CCTCCACT--CACAACATTTC--ATTCACCTGCAGTTCATTACCGCCGAG
droKik1	ACGTACATCACCAAGGTAAGTCTC-------CGAGAACGGGAAC------GAA------TC-GCACA--GATCCATATCTGT--ATC--TGTATC--CTTCTTGTGTAGTACATCACCGCCGAG
droAna3	ACTTATATTACAAAGGTAAGT----------------------------------------------------------ATC--CAAGTTATTTC-CTTCAATTTTCAGTTCATAACCGCCGAA
droBip1	ACGTATATAACAAAGGTGAGAGGGACGAGGT-----------CTATAGCTTTCGG---GTTG------TGT-----AATACT--TTAAATATTTT-ATTCCAATTTCAGTATATAACCGCCGAA
dp4	ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG
droPer1	ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG
droWil1	ACTTACATTACCAAGGTGAGT----------------------------------------------------------------------TTTG--TTTTTCTTACAGTACATTACATCGGAG
droVir3	ACGTGCATTACCAAGGTAAG------------------------------------------------------CCTCTTCT--CACGACATCCCTTAATCCCTTGCAGTACGTTGCCAACGAA
droMoj3	ACATGCATAACCAGGGTAAGTGCTCAGCTGC---------TtTTtTttTttTtgt------------------------tTT--TTttTTtTTTC--GTCGCCTTACAGTACATCTCCAAGGAG
droGri2	ACCTACATTACTAAGGTATGTT--------CGA------TGATTTTGGTTTTTTTTGGCTTT------ACT-T-TCACCGTTTACACGACAATTT-CATCCTTTTGCAGTACGTGACCAGTGAG

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

ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGC-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................ACT--CACGGCATTTC--ATTCACTTG..................	23	1	358.00	0.00	294.00	39.00	25.00
...............................................................................ACT--CACGGCATTTC--ATTCACTT...................	22	1	89.00	3.00	79.00	5.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACT....................	21	1	81.00	3.00	73.00	2.00	3.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAG...............	26	1	50.00	2.00	34.00	5.00	9.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCA................	25	1	34.00	3.00	22.00	6.00	3.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGC.................	24	1	34.00	0.00	29.00	5.00	0.00
...............GTAAGTGAC--TATGCCG------GGAT.................................................................................	20	1	31.00	0.00	24.00	6.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTGTGG............................................................................	25	1	29.00	1.00	6.00	4.00	18.00
...............GTAAGTGAC--TATGCCG------GGATT................................................................................	21	1	28.00	0.00	18.00	7.00	3.00
...............GTAAGTGAC--TATGCCG------GGA..................................................................................	19	1	13.00	1.00	8.00	1.00	3.00
...............................................................................ACT--CACGGCATTTC--ATTCAC.....................	20	1	11.00	0.00	10.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGT..............	27	1	8.00	5.00	1.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACTGG..................	23	1	6.00	0.00	4.00	1.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACC....................	21	1	6.00	0.00	5.00	1.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGT..............................................................................	23	1	4.00	0.00	2.00	1.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTG...............................................................................	22	1	4.00	0.00	2.00	0.00	2.00
................TAAGTGAC--TATGCCG------GGATTGT..............................................................................	22	1	3.00	0.00	1.00	2.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTG.............................................................................	24	1	3.00	1.00	1.00	0.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTGTGGTT..........................................................................	27	1	3.00	0.00	0.00	2.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACG....................	21	1	2.00	0.00	2.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTGT............................................................................	25	1	2.00	0.00	0.00	0.00	2.00
................................................TTATTATA---CTT------AGC-G-TCTCC.............................................	20	1	2.00	0.00	2.00	0.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTGC.................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTC.......................	18	1	2.00	0.00	1.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGT.................	24	1	2.00	0.00	0.00	1.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCGG...............	26	1	2.00	0.00	1.00	1.00	0.00
...............................................................................ACT--CACGACATTTC--ATTCACTTG..................	23	1	2.00	0.00	2.00	0.00	0.00
....................................................................................TACGGCATTTC--ATTCACTTG..................	20	1	2.00	0.00	2.00	0.00	0.00
................................................................................CT--CACGGCATTTC--ATTCACTTG..................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGA.................	24	1	2.00	0.00	0.00	2.00	0.00
...............................................................................GCT--CACGGCATTTC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	1.00	0.00
...............GTGAGTGAC--TATGCCG------GGATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTGG..............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGG..............	27	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTAA.................	24	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTTTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTG..................	23	1	1.00	0.00	1.00	0.00	0.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCAGT..............	26	1	1.00	0.00	0.00	0.00	1.00
.................................................................................T--CACGGCATTTC--ATTCACTTGCAGT..............	25	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ACT--GACGGCATTTC--ATTCACTTG..................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGGATTTC--ATTCACTTG..................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCCCTTGCAGT..............	27	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ACT--CATGGCATTTC--ATTCACTT...................	22	1	1.00	0.00	1.00	0.00	0.00
....................................................................................CACGGCATTTC--ATTCACTTGCAG...............	23	1	1.00	0.00	1.00	0.00	0.00
..........................TATGCCG------GGATTGTGGTTATT.......................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGG..................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAC...............	26	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTGGT...........................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--TATGCCG------GGAA.................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCT................	24	1	1.00	0.00	1.00	0.00	0.00
.................AAGTGAC--TATGCCG------GGAT.................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................T--CACGGCATTTC--ATTCAC.....................	18	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTGGAA..........................................................................	27	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTT...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCCG...............	26	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ACT--CACGGAATTTC--ATTCACTTG..................	23	1	1.00	0.00	1.00	0.00	0.00
................................................TTATTATA---CTT------AGC-G-TCTCCACT--........................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CGCGGCATTTC--ATTCACTTGCAG...............	26	1	1.00	1.00	0.00	0.00	0.00
................TAAGTGAC--TATGCCG------GGATTG...............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATG................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--TTTCACC....................	21	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GCATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
.................................................................................T--CACGGCATTTC--ATTCACTTG..................	21	1	1.00	0.00	1.00	0.00	0.00
...........................................................CTT------AGC-G-TCTCCACT--CACGGC..................................	21	1	1.00	0.00	0.00	1.00	0.00

droSec1

ACGTACATCACCAAGGTAAGTGAC--TATGCCG------GGATTGTGGTTATTATA---CTT------AGA-G-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGT..............	27	1	53.00	5.00	30.00	18.00
...............................................................................ACT--CACGGCATTTC--ATTCACTT...................	22	1	50.00	0.00	3.00	47.00
...............................................................................ACT--CACGGCATTTC--ATTCACT....................	21	1	47.00	1.00	0.00	46.00
.................................................................................T--CACGGCATTTC--ATTCACTTGCAGT..............	25	1	21.00	1.00	15.00	5.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAG...............	26	1	14.00	1.00	5.00	8.00
...............GTAAGTGAC--TATGCCG------GGATTGTGG............................................................................	25	1	11.00	0.00	8.00	3.00
...............GTAAGTGAC--TATGCCG------GGATTGT..............................................................................	23	1	6.00	3.00	1.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCA................	25	1	4.00	2.00	1.00	1.00
.................AAGTGAC--TATGCCG------GGATTGTGGTT..........................................................................	25	1	4.00	3.00	0.00	1.00
................TAAGTGAC--TATGCCG------GGATTG...............................................................................	21	1	4.00	2.00	2.00	0.00
...............GTAAGTGAC--TATGCCG------GGAT.................................................................................	20	1	3.00	1.00	1.00	1.00
...............GTAAGTGAC--TATGCCG------GGATTG...............................................................................	22	1	3.00	2.00	0.00	1.00
................TAAGTGAC--TATGCCG------GGATTGT..............................................................................	22	1	3.00	1.00	1.00	1.00
..........................................................................................ATTTC--ATTCACTTGCAGT..............	18	1	2.00	0.00	2.00	0.00
.....................GAC--TATGCCG------GGATTGTGGTT..........................................................................	21	1	2.00	2.00	0.00	0.00
.....................GAC--TATGCCG------GGATTGTGGTTATT.......................................................................	24	1	2.00	0.00	2.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTGC.................	22	1	2.00	0.00	0.00	2.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCAGT..............	26	1	2.00	0.00	2.00	0.00
.....................GAC--TATGCCG------GGATTGTGGTTA.........................................................................	22	1	2.00	0.00	2.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTGCAGA..............	25	1	2.00	0.00	2.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTG.............................................................................	24	1	2.00	0.00	2.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTGGTT..........................................................................	27	1	2.00	1.00	1.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTGCAG...............	24	1	2.00	0.00	0.00	2.00
...............GTAAGTGAC--TATGCCG------GGATT................................................................................	21	1	2.00	2.00	0.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTG..................	21	1	2.00	0.00	0.00	2.00
.................................................................................T--CACGGTATTTC--ATTCACTTGCAG...............	24	1	1.00	0.00	1.00	0.00
...............GTAAGTGAC--TATGCCG------GG...................................................................................	18	1	1.00	0.00	0.00	1.00
.....................GAC--TATGCCG------GGATTGTGGTTAT........................................................................	23	1	1.00	1.00	0.00	0.00
.......................C--TATGCCG------GGATTGTGGTTATTA......................................................................	23	1	1.00	1.00	0.00	0.00
...................GTGAC--TATGCCG------GGATTGTGGTTA.........................................................................	24	1	1.00	1.00	0.00	0.00
.................AAGTGAC--TATGCCG------GGATTGTGT............................................................................	23	1	1.00	0.00	0.00	1.00
....................................................TATA---CTT------AGA-G-TCTCCACT--CACGGCA.................................	26	1	1.00	0.00	1.00	0.00
...............TTAAGTGAC--TATGCCG------GGATT................................................................................	21	1	1.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAT...............	26	1	1.00	0.00	1.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTTGCA................	23	1	1.00	0.00	0.00	1.00
...............................................................................ACT--CTCGGCATTTC--ATTCACTTGCA................	25	1	1.00	0.00	0.00	1.00
..........................TAAGCCG------GGATTGTGGGT..........................................................................	18	1	1.00	0.00	1.00	0.00
.......................C--TATGCCG------GGATTGTGGTTATT.......................................................................	22	1	1.00	1.00	0.00	0.00
.................AAGTGAC--TATGCCG------GGATTG...............................................................................	20	1	1.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGA..............	27	1	1.00	0.00	1.00	0.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCA................	24	1	1.00	0.00	0.00	1.00
................................................................................CT--CACGGCATTTC--ATTCACTTGT.................	23	1	1.00	0.00	0.00	1.00
...................GTGAC--TATGCCG------GGATTGTGGTT..........................................................................	23	1	1.00	1.00	0.00	0.00
.........................................................................................CATTTC--ATTCACTTGCAGTT.............	20	1	1.00	1.00	0.00	0.00
....................................................................AGA-G-TCTCCACA--AACGGC..................................	18	1	1.00	0.00	1.00	0.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTGCAGT..............	27	1	1.00	0.00	1.00	0.00
...................GTGAC--TATGCCG------GGATGCTG.............................................................................	20	1	1.00	1.00	0.00	0.00
...............GTAAGTGAC--TATGCCG------GGATTGTGGT...........................................................................	26	1	1.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTA..................	23	1	1.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGC.................	24	1	1.00	0.00	0.00	1.00
...........................................................................CTCCACT--CACGGCATTTC--ATTCACTT...................	26	1	1.00	0.00	1.00	0.00
.................................................................................T--CACGGCATTTC--ATTCACTT...................	20	1	1.00	0.00	0.00	1.00
..................................................ATTATA---CTT------AGA-G-TCTCCACT--CACGGCA.................................	28	1	1.00	0.00	0.00	1.00
.....................................................ATA---CTT------AGA-G-TCTCCACT--CACGGCA.................................	25	1	1.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCA......................	19	1	1.00	0.00	1.00	0.00
..................................................ATTATA---CTT------AGA-G-TCTCCACT--........................................	21	1	1.00	0.00	1.00	0.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCAG...............	25	1	1.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTG..................	23	1	1.00	0.00	0.00	1.00
.............................................................T------AGA-G-TCTCCACT--CACGGCATTTC--ATT........................	27	1	1.00	1.00	0.00	0.00
...............................................................................ACT--CACTGCATTTC--ATTCACTTGCA................	25	1	1.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCAC.....................	20	1	1.00	0.00	0.00	1.00

droYak2

ACGTACATCACCAAGGTAAGTGAC--AATGCCG------GGATTGTGGTTATTGAA---AAT------ACC-T-TCTCCACT--CACGGCATTAT--ATTCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............................................................................ACT--CACGGCATTAT--ATTCACTTG..................	23	1	162.00	0.00	0.00	0.00	1.00	161.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCA................	25	1	33.00	0.00	0.00	1.00	0.00	32.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGC.................	24	1	29.00	0.00	0.00	0.00	0.00	29.00
...............................................................................ACT--CACGGCATTAT--ATTCACTT...................	22	1	20.00	0.00	3.00	0.00	4.00	13.00
...............................................................................ACT--CACGGCATTAT--ATTCACT....................	21	1	19.00	0.00	0.00	0.00	3.00	16.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCAG...............	26	1	18.00	1.00	2.00	0.00	3.00	12.00
...............GTAAGTGAC--AATGCCG------GGATTGT..............................................................................	23	1	9.00	0.00	0.00	7.00	0.00	2.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCAGT..............	27	1	8.00	3.00	2.00	0.00	1.00	2.00
...............GTAAGTGAC--AATGCCG------GGATTGTGG............................................................................	25	1	8.00	0.00	0.00	1.00	0.00	7.00
......................AT--AATGCCG------GGGTTGTG.............................................................................	17	1	6.00	0.00	0.00	0.00	6.00	0.00
...............GTAAGTGAC--AATGCCG------GGATTGTGGTT..........................................................................	27	1	6.00	0.00	0.00	2.00	0.00	4.00
...............GTAAGTGAC--AATGCCG------GGATTGTGGT...........................................................................	26	1	5.00	0.00	0.00	3.00	0.00	2.00
.................AAGTGAG--AATGCCG------GTAT.................................................................................	18	1	3.00	0.00	1.00	1.00	1.00	0.00
...............GTAAGTGAC--AATGCCG------GGATTGTGGTTAT........................................................................	29	1	3.00	0.00	0.00	0.00	0.00	3.00
...............GTAAGTGAC--AATGCCG------GGATTG...............................................................................	22	1	3.00	1.00	0.00	2.00	0.00	0.00
.....................GAC--AATGCCG------GGATTGTGGTT..........................................................................	21	1	2.00	0.00	0.00	2.00	0.00	0.00
...............GTAAGTGAC--AATGCCG------GGATTTGG.............................................................................	24	1	2.00	0.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCG................	25	1	2.00	0.00	0.00	0.00	0.00	2.00
.................AAGTGAC--AATGCCG------GGATTGTGGTTATTG......................................................................	29	1	2.00	0.00	0.00	2.00	0.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCACC....................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
...............GTAAGTGAC--AATGCCG------GGATTGTG.............................................................................	24	1	2.00	0.00	0.00	2.00	0.00	0.00
.......................C--AATGCCG------GGATTGTGGTT..........................................................................	19	1	2.00	0.00	0.00	2.00	0.00	0.00
...............................................................................ACG--CACGGCATTAT--ATTCACTTGCAG...............	26	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCT................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CCCGGCATTTT--ATTCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTGAC--AATGCCG------GGAT.................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--AATGCCG------GGA..................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--AATGCCG------GGATTGG..............................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGACATTAT--ATTCACTTGCAGT..............	27	1	1.00	0.00	0.00	0.00	1.00	0.00
..................AGTGAC--AATGCCG------GGATTGT..............................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................T--CACGGCATTAT--ATTCACTTGCAGT..............	25	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................AAT--CACGGCATTAT--ATTCACT....................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................ACT--CACGGCATTAT--GTTCACTTGCAGT..............	27	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................AATGCCG------GGATTGTGGTTA.........................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGTATTAT--ATTCACTTG..................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................CACGGCATTAT--ATTCACTTTCAGT..............	24	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................................................CACGGCATTAT--ATTCACTTGCA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTTCA................	25	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGG.................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCCG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTAT--ATCCACTTGCAGT..............	27	1	1.00	0.00	1.00	0.00	0.00	0.00
..........................AATGCGG------GGATCGTGG............................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGCCATTAT--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCCCTGG..................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTACAGT..............	27	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................ATGCCG------GGATTGTGGTTATT.......................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................AAGTGAC--AATGCCG------GGATTG...............................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................CACGGCATTAT--ATTCACTTGCAGT..............	24	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................T--AATGCCG------GGGTTGTG.............................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
.................AAGTGAC--CATGCCG------GGATTGTGG............................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..................AGTGAC--AATGCCG------GGCTTGTGGTTA.........................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
.................AAGTGAC--AATGCCG------GGATTGTGGT...........................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................CATTAT--ATTCACTTGCAGTT.............	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................ACT--TACGGCATTAT--ATTCACTTGC.................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTAT--xTTCACT....................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.................AAGTGAC--AATGCCG------GGATTGT..............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................C--AATGCCG------GGATTGTGGTTATTG......................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................GAC--AAGGCCG------GGAATGTGG............................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...............GTAAGTGAC--AATTCCG------GGATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
..................AGTGAC--AATGCCG------GGATTG...............................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................GAC--AAGGCCG------GGAATGTGGT...........................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................CT--CACGGCATTAT--ATTCACTTGCAG...............	25	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................................................CACGGCATTAT--ATTCACTTGC.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................CT--CCCGGCATTAT--ATTCACGTGCAG...............	25	1	1.00	0.00	0.00	0.00	1.00	0.00
....................TTAC--AATGCCG------GTATTGTG.............................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCACTTGCAGTT.............	28	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTAT--ATTCACTGG..................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.................AAGTGAC--AATGCCG------GGATTGTG.............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGCCATTAT--ATTCACTTT..................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................GAC--AATGCCG------GGATTGTGGTTAT........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ACGTACATCACCAAGGTAAGTGAC--AGTGCCG------GGATTGTGGTTATTAAA---AAT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................ACT--CACGGCATTTC--ATTCACT....................	21	1	113.00	0.00	1.00	0.00	112.00
...............................................................................ACT--CACGGCATTTC--ATTCACTT...................	22	1	109.00	0.00	3.00	0.00	106.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAG...............	26	1	25.00	1.00	0.00	0.00	24.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGT..............	27	1	18.00	1.00	0.00	0.00	17.00
...............GTAAGTGAC--AGTGCCG------GGATTGTGG............................................................................	25	1	17.00	0.00	0.00	0.00	17.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCA................	25	1	14.00	0.00	3.00	0.00	11.00
................TAAGTGAC--AGTGCCG------GGATTGT..............................................................................	22	1	5.00	0.00	0.00	0.00	5.00
...............GTAAGTGAC--AGTGCCG------GGA..................................................................................	19	1	4.00	0.00	0.00	0.00	4.00
...............................................................................ACT--CACGGCACTTC--ATTCACTT...................	22	1	3.00	0.00	0.00	0.00	3.00
...............GTAAGTGAC--AGTGCCG------GGATT................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
................TAAGTGAC--AGTGCCG------GGATTGTGG............................................................................	24	1	3.00	0.00	0.00	0.00	3.00
...............GTAAGTGAC--AGTGCCG------GGAT.................................................................................	20	1	3.00	0.00	0.00	0.00	3.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGC.................	24	1	3.00	0.00	2.00	0.00	1.00
...............................................................................AAT--CACGGCATTTC--ATTCACT....................	21	1	3.00	0.00	0.00	0.00	3.00
..........................................................................................ATTTC--ATTCACTTGCAGT..............	18	1	2.00	0.00	0.00	0.00	2.00
................................................................................CT--CACGGCATTTC--ATTCACT....................	20	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CATGGCATTTC--ATTCACT....................	21	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTACA................	25	1	2.00	0.00	0.00	0.00	2.00
...............GTAAGTGAC--AGTGCCG------GGATTG...............................................................................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAGA..............	27	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CATGGCATTTC--ATTCACTT...................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--CTTCACTT...................	22	1	2.00	0.00	1.00	0.00	1.00
...............GTAAGTGAC--AGTGCCG------GGATTGT..............................................................................	23	1	2.00	0.00	0.00	0.00	2.00
...............GTAAGTGAC--AGTGCCG------GGATTGTG.............................................................................	24	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTG..................	23	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACTGCATTTC--ATTCACTT...................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ACT--CACGGCATTTC--ATTCAC.....................	20	1	2.00	0.00	1.00	0.00	1.00
...............GTAAGTGAC--AGTGCCG------GAATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--AGTGCCT------GGATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
....................................................................................CACGGCATTTC--ATTCACTTGCA................	22	1	1.00	0.00	0.00	0.00	1.00
................TAAGTGAC--AGTGCCG------GGATTGTG.............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATCTC--ATTCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGCAT...............	26	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CGCGGCATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTAACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTGCA................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--AACGGCATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................AAT--CACGGAATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
..........................AGTGCCG------GGATTGTGGTT..........................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGAATTTC--ATTCCCTT...................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTACAG...............	26	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--AGTGCCG------GGATTGAGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGAATTTC--ATTAACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--AAAGGCATTTC--ATTCACTTGCA................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGTA................	25	1	1.00	0.00	0.00	0.00	1.00
................................................................................CT--CACGGCATTTC--ATTCACTTGCAGT..............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--CACGGCATTTC--ATTCACTTGT.................	24	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--CTTCACTTGA.................	24	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTAACTT...................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGACATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...................GTGAC--AGTGCCG------GGATTGTGGTTAT........................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ATT--AACGGCATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATCTC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00
.....................GAC--AGTGCCG------GGATTGTGGTTATT.......................................................................	24	1	1.00	0.00	0.00	0.00	1.00
....................................................................................CACGGCATTTC--ATTCACTTGCAG...............	23	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--AACGGCATTTC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTGCAGT..............	27	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACTGCATTTC--ATTCA......................	19	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--AGTGCCG------GGATTGGGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
....................................................................................CACGGCATTTC--ATTCACTTGCAGT..............	24	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTA--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............GTACGTGAC--AGTGCCG------GGATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
.....................GAC--AGTGCCG------GGATTGTGGT...........................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............TTAAGTGAC--AGTGCCG------GGATTGTGG............................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACTGCATTTC--ATTCACTTGCAGT..............	27	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCAAT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTGC.................	24	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTGAC--AGTGCCG------GG...................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--ATTCA......................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACT--AACGTCATTTC--ATTCACT....................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGGCATTTC--CTTCCCT....................	21	1	1.00	0.00	1.00	0.00	0.00
....................TGAC--AGTGCCG------GGATTGT..............................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGTCATTTC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACGACATTTC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00
................................................................................TT--CACGGCATTTC--ATTCACTT...................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................ACT--CACTGCATTTC--ATTCACTTGCA................	25	1	1.00	0.00	0.00	0.00	1.00

droEug1

ACGTATATCACCAAGGTAAGTGGC--TATGCCG------GGATCGTGGTTGATCTA---TGT------ACC-T-TCTCCACT--CACGGCATTTC--ATTCACTTGTAGTACATCACCGCTGAA

Size

Hit Count

Total Norm

droBia1

ACGTACATCACCAAAGTAAGTGGC--CATGCCG------GGATTGTGGTTTAA------CC-AGAGGTTCC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG

Size

Hit Count

Total Norm

droTak1

ACGTACATCACCAAGGTAAGTGGC--TATGCCG------GGATTGTGGTTTACAATA--GAA---AG-ATC-C-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG

Size

Hit Count

Total Norm

droEle1

ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGACTGTGGTTCTAAAT---GCC------ATC-A-CCACCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG

Size

Hit Count

Total Norm

droRho1

ACGTACATCACCAAGGTAAGTGGG--TATGCCG------GGATTGTGGTTAAT-------AC------ACC-T-CCTCCACT--CACGGCATTTC--ATTCACTTGCAGTACATCACCGCCGAG

Size

Hit Count

Total Norm

droFic1

ACGTACATCACCAAGGTAAGTTTA--TATTTATTT-GTGTTGG----------------TGT------ACC-T-CCTCCACT--CACAACATTTC--ATTCACCTGCAGTTCATTACCGCCGAG

Size

Hit Count

Total Norm

droKik1

ACGTACATCACCAAGGTAAGTCTC-------CGAGAACGGGAAC------GAA------TC-GCACA--GATCCATATCTGT--ATC--TGTATC--CTTCTTGTGTAGTACATCACCGCCGAG

Size

Hit Count

Total Norm

droAna3

ACTTATATTACAAAGGTAAGT----------------------------------------------------------ATC--CAAGTTATTTC-CTTCAATTTTCAGTTCATAACCGCCGAA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

ACGTATATAACAAAGGTGAGAGGGACGAGGT-----------CTATAGCTTTCGG---GTTG------TGT-----AATACT--TTAAATATTTT-ATTCCAATTTCAGTATATAACCGCCGAA

Size

Hit Count

Total Norm

dp4

ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................TCT--CACGGCATATC--AATCACTTGCA................	25	1	52.00	4.00	28.00	19.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAG...............	26	1	41.00	9.00	19.00	12.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTT...................	22	1	26.00	4.00	1.00	20.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACT....................	21	1	19.00	5.00	1.00	12.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTTGC.................	24	1	14.00	2.00	4.00	7.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAGT..............	27	1	14.00	9.00	1.00	4.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTG..................	23	1	7.00	1.00	1.00	4.00	1.00
...............GTAAGTGGC--TATGCCGCG-ACGGGT..................................................................................	24	1	5.00	3.00	2.00	0.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGGG..................................................................................	24	1	3.00	0.00	3.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--GATCACTTGC.................	24	1	2.00	0.00	1.00	1.00	0.00
.................................................................................T--CACGGCATATC--AATCACTTGCA................	23	1	2.00	0.00	2.00	0.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGG...................................................................................	23	1	2.00	0.00	1.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAA...............	26	1	2.00	0.00	1.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAC...............	26	1	1.00	0.00	0.00	1.00	0.00
.................AAGTGGC--TATGCCGCG-ACGGGA..................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--AATCCCTT...................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCC................	25	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATACC--AATCACTT...................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................GCT--AACGGCATATC--AATCACT....................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--ACTCACTTGCAG...............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCC--CACGGCATATC--AATCACTTGCA................	25	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCG--GACGGCATATC--AATCACTT...................	22	1	1.00	0.00	0.00	1.00	0.00
...............GTAAGTGGC--TATGCCGCC-ACCGG...................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--CATCACTTGCA................	25	1	1.00	0.00	1.00	0.00	0.00
.................AAGTGGC--TATGCCGCG-GCGGGG..................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCATCTC--AATCACTTGCCG...............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCC--CACGGCATATC--AATCACTTGCAGT..............	27	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--GATCACTTGCAG...............	26	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................ACGGCATATC--AATCACTTGCAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................CCT--CACGGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCT--TACGGCATATC--AATCACTTGCAG...............	26	1	1.00	1.00	0.00	0.00	0.00
...............................................................................TCT--CACGGAATATC--AATCACTTGCAG...............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--CATCACTTG..................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAGTT.............	28	1	1.00	1.00	0.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--TATCACTTGCAG...............	26	1	1.00	0.00	1.00	0.00	0.00
...............................................................................TCA--CACGGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	1.00	0.00
.................AAGTGGC--TATGCCGCG-ACGGGT..................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGGATT------G.........................................................................	27	1	1.00	1.00	0.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGT.................	24	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGTCATATC--AATCAGTT...................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--AACGGCATATC--AATCACTTGCA................	25	1	1.00	0.00	1.00	0.00	0.00
......................................................................................CGGCATATC--AATCACTTGC.................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTTGA.................	24	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCGCTTGCA................	25	1	1.00	0.00	0.00	1.00	0.00

droPer1

ACGTACATCACAAAGGTAAGTGGC--TATGCCGCG-ACGGGATT------GAA------CC-TCTCA--TCTC-TCACCTCT--CACGGCATATC--AATCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................................................................TCT--CACGGCATATC--AATCACTTGCAG...............	26	1	64.00	0.00	10.00	16.00	27.00	11.00
...............................................................................TCT--CACGGCATATC--AATCACTT...................	22	1	39.00	1.00	2.00	12.00	17.00	7.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCA................	25	1	37.00	0.00	4.00	10.00	13.00	10.00
...............................................................................TCT--CACGGCATATC--AATCACT....................	21	1	12.00	0.00	0.00	5.00	6.00	1.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAGT..............	27	1	12.00	1.00	0.00	4.00	7.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTG..................	23	1	10.00	0.00	0.00	1.00	9.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGGT..................................................................................	24	1	7.00	3.00	0.00	2.00	2.00	0.00
...............................................................................TCT--CACGGCATATC--AATC.......................	18	1	7.00	0.00	0.00	0.00	0.00	7.00
................TAAGTGGC--TATGCCGCG-ACGGGT..................................................................................	23	1	5.00	2.00	0.00	1.00	2.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAGA..............	27	1	4.00	0.00	0.00	0.00	2.00	2.00
...............................................................................TCT--CACGGCATATC--AATCACTTGC.................	24	1	4.00	0.00	0.00	1.00	3.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGG...................................................................................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
...............GTAAGTGGC--TATGCCGCG-ACGGGG..................................................................................	24	1	2.00	0.00	0.00	1.00	1.00	0.00
................TAAGTGGC--TATGCCGCG-ACGGGA..................................................................................	23	1	2.00	0.00	1.00	0.00	1.00	0.00
.................................................................................T--CTCGGCATATC--AATCACTTGCAGT..............	25	1	2.00	2.00	0.00	0.00	0.00	0.00
................................................................................CT--CACGGCATATC--AATCACTT...................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
...............................................................................TAT--CACGGCATATC--AATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACTGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACCTCCA................	25	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCT................	25	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................TCT--CAAGGCATATC--CATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACAGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AGTCACTTGCT................	25	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGAATATC--AATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................CCT--CACGGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--ACTCACTT...................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTCC.................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTGGC--TATGCCCCG-ACGGGT..................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................CTCT--CACCGCATATC--AATCACTT...................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTGGC--TATGTCGCG-ACGGGT..................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGTCATATC--AATCACTTGCA................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................TCT--CACGGCTTATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................T--CACGGCATATC--AATCACTT...................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATGACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAC...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCAGATC--AATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--ATTCACTTGT.................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................T--CACGGCATATC--AATCACTTGCAG...............	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCG--CACGGCATATC--AAGCACT....................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCAT...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCG--CACGGCATATA--AATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................A--CACGGCATATC--AATCACTTGCAGA..............	25	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCTCTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGCCG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTGGC--TATGCCCCG-ACGGG...................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................GCT--CACTGCATATC--AATCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCG--CACGGCATATC--AATCACT....................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTTCAG...............	26	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................TCG--CACGGCATATC--AATCACTT...................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--ATTCACTTGCAG...............	26	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TCT--CACGGCATATC--AATCACTTGA.................	24	1	1.00	0.00	0.00	1.00	0.00	0.00

droWil1

ACTTACATTACCAAGGTGAGT----------------------------------------------------------------------TTTG--TTTTTCTTACAGTACATTACATCGGAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................GxTT----------------------------------------------------------------------TTTG--TTCTTCTTACAG...............	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

ACGTGCATTACCAAGGTAAG------------------------------------------------------CCTCTTCT--CACGACATCCCTTAATCCCTTGCAGTACGTTGCCAACGAA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ACATGCATAACCAGGGTAAGTGCTCAGCTGC---------TtTTtTttTttTtgt------------------------tTT--TTttTTtTTTC--GTCGCCTTACAGTACATCTCCAAGGAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................TTTTTTTGT------------------------TTT--TTGTTTGTT...............................	21	12	0.08	0.08	0.00	0.00	0.00
.............................................TTGTTTTTGT------------------------TGT--TTTTTTTT................................	21	12	0.08	0.08	0.00	0.00	0.00
..........................................TTGTTTTTGTTGT------------------------TTT--TTTTT...................................	21	12	0.08	0.08	0.00	0.00	0.00
..............................................TTTTTTTTT------------------------TTT--TTTTTTTTTT..............................	22	51	0.02	0.02	0.00	0.00	0.00
..........................................TTTTTTTTTTTTT------------------------TTT--TTTTTT..................................	22	51	0.02	0.02	0.00	0.00	0.00
.............................................ATTTTTTTTT------------------------TTT--TTTTTTTT................................	21	74	0.01	0.00	0.00	0.00	0.01
............................................TTTTTTTTTTT------------------------TTT--TTTTTTTT................................	22	51	0.02	0.02	0.00	0.00	0.00
...........................................TTTTTTTTTTTT------------------------TTT--TTTTTTT.................................	22	51	0.02	0.02	0.00	0.00	0.00
...............................................TTTTTTGT------------------------TTT--TTTCTTTTGT..............................	21	6	0.17	0.17	0.00	0.00	0.00
....................................................TxT------------------------TTT--TTTTTTTTTGC--GTTGCC.....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................C---------CGTTTTTTTTTTTGT------------------------TTT--T.......................................	20	2	0.50	0.00	0.00	0.50	0.00
.........................................TTTTTTTTTTTTTT------------------------TTT--TTTTT...................................	22	51	0.02	0.02	0.00	0.00	0.00
.............................................TTTTTTTTTT------------------------TTT--TTTTTTTTT...............................	22	51	0.02	0.02	0.00	0.00	0.00
.....................GTTCAGCGGC---------TTTTTTTT............................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........................................TTTTTTTTTTTTTTT------------------------TTT--TTTT....................................	22	51	0.02	0.02	0.00	0.00	0.00

droGri2

ACCTACATTACTAAGGTATGTT--------CGA------TGATTTTGGTTTTTTTTGGCTTT------ACT-T-TCACCGTTTACACGACAATTT-CATCCTTTTGCAGTACGTGACCAGTGAG	Size	Hit Count	Total Norm	V109 Male body
....................TT--------CAA------TGATTTTTGTTTTT.......................................................................	19	2	0.50	0.50
......ATTACTCAGGTATGAT--------CGA------.....................................................................................	19	1	1.00	1.00

Generated: 04/20/2012 at 05:18:57 EDT

dme-mir-2535b

chrX:21169302-21169372 -

Known_mirbase

mirtron

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