dme-mir-965- Best orthologs

dme-mir-965	chr2L:243035-243141 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 243055-243076
   star strand at position 243096-243118
   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	chr2L:243020-243156 -		1	TAATTGTACA------ATCTG------------------------------------GACA------ATATTGCTCAAC-ATTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCT-GTGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA---------AAA----------GTGT--------------TTTT---------C
droSim1	chr2L:248245-248381 -	LASTZ	1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droSec1	super_14:240987-241123 -	LASTZ	1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droYak2	chr2L:236040-236180 -	LASTZ	1	TAATTGTACAATCACCATC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTTT-GT-AAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA---------ATA----------GTGT--------------ATTT---------C
droEre2	scaffold_4929:289337-289472 -	LASTZ	1	TACTTGTAGA------ACC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCT-GTAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA---------AAA----------GTGA--------------ATCT---------T
droEug1	scf7180000409461:574432-574571 +	LASTZ	4	TAATTTTTTT--GAGAACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCTATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAAAGCAACAGCAGCAA---------AAA----------GTGT--------------TTTT---------A
droBia1	scf7180000301547:14040-14201 +	LASTZ	4	CACTTGTGCC------ATC---------------------------------------ACG------ATATTGCCCGAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAGAAGTTGGTGCAACAGCAACGACCGT-GTGA---TAAATTGTAG----GAGTA------TATGTTCTTTTATGATC
droTak1	scf7180000413017:293129-293264 +	LASTZ	4	TACTTTTACA------ATC-------------------------------------TGACA------ATATTGCTTAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAAAAGCAACAG---------AAA----------GTAT--------------GATT---------A
droEle1	scf7180000490454:128315-128470 +	LASTZ	4	TAGTTTTACA------ACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAATAAATTGTAA----GAGTAAAACAATGCGTTC---------T
droRho1	scf7180000779252:273002-273136 -	LASTZ	4	TCCTTTTACA------ACC-------------------------------------TGAGA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTGTATGTGTCATTCT-TTAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAA----------GGA---------------TGAT---------A
droFic1	scf7180000453904:509771-509921 -	LASTZ	4	ACGGTGTAAA------AGC-------------------------------------CAAAG-ATT--TTATTGCTCAAC-ATTTTGAGGGGTGAAACTGTACGTTGTATGTGCCCTATT-ATAAAAACCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACACCAACAA---------AAA----------GTGACCGATAAATAAT--CTCT---------A
droKik1	scf7180000302401:552944-553112 -	LASTZ	4	TAGTC---CA------AAT-TGCAGCTAATGTGTTATGATATATAAATAGAATGAATAATA------TTATTGCTCATC-ATTTTGGGGGGTCAAACTGTACGTTATATGTGCCAATCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACAACAACGA---------AAA--------A-GTGT--------------A-AT---------A
droAna3	scaffold_12943:4147952-4148086 +	LASTZ	1	TGGGTTTTCT----------G------------------------------------GA------------AGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCT-TAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAA----------GTGT----------------TT---------T
droBip1	scf7180000395973:371238-371378 +	LASTZ	4	ATACTATATA------GTCTA-------------------------GTAGTATTAATGACA------ATATTGCTCAAC-CATTTGGGGGGTCAAACTGTACGTTGTATGTGCCAAACT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGCCAGCAA----------------------------------------TTGT---------C
dp4	chr4_group1:4362148-4362281 +	LASTZ	1	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droPer1	super_5:848159-848292 -	LASTZ	1	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droWil1	scaffold_180764:130106-130233 -	LASTZ	1	TATGT--AATA--AA-TT----------------------------------------AAAGAATCAATTCTACACAAC-AT-TTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA------------------------------------------------------
droVir3	scaffold_12963:8856389-8856513 +	LASTZ	1	TTAGTGTAGA------AAA-------------------------------------AGAAAAAAAC--ACACACACAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAAT-G-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC--------------------------------------------------------
droMoj3	scaffold_6500:2474475-2474605 -	LASTZ	1	AATGTGAACA------A----------------------------------------------------AACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGTAA-ACA-ATGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG---------CAA----TTTAA-GCAT--------------AGCT---------A
droGri2	scaffold_15252:12933990-12934109 -	LASTZ	1	G--------------------------------------------------------GAAA------ATAACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTATATGTGTAAAT-G-AAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT---------AAA----------AAG----------------TCT---------T

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	TAATTGTACA------ATCTG------------------------------------GACA------ATATTGCTCAAC-ATTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCT-GTGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA---------AAA----------GTGT--------------TTTT---------C
droSim1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droSec1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droYak2	TAATTGTACAATCACCATC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTTT-GT-AAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA---------ATA----------GTGT--------------ATTT---------C
droEre2	TACTTGTAGA------ACC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCT-GTAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA---------AAA----------GTGA--------------ATCT---------T
droEug1	TAATTTTTTT--GAGAACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCTATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAAAGCAACAGCAGCAA---------AAA----------GTGT--------------TTTT---------A
droBia1	CACTTGTGCC------ATC---------------------------------------ACG------ATATTGCCCGAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAGAAGTTGGTGCAACAGCAACGACCGT-GTGA---TAAATTGTAG----GAGTA------TATGTTCTTTTATGATC
droTak1	TACTTTTACA------ATC-------------------------------------TGACA------ATATTGCTTAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAAAAGCAACAG---------AAA----------GTAT--------------GATT---------A
droEle1	TAGTTTTACA------ACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAATAAATTGTAA----GAGTAAAACAATGCGTTC---------T
droRho1	TCCTTTTACA------ACC-------------------------------------TGAGA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTGTATGTGTCATTCT-TTAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAA----------GGA---------------TGAT---------A
droFic1	ACGGTGTAAA------AGC-------------------------------------CAAAG-ATT--TTATTGCTCAAC-ATTTTGAGGGGTGAAACTGTACGTTGTATGTGCCCTATT-ATAAAAACCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACACCAACAA---------AAA----------GTGACCGATAAATAAT--CTCT---------A
droKik1	TAGTC---CA------AAT-TGCAGCTAATGTGTTATGATATATAAATAGAATGAATAATA------TTATTGCTCATC-ATTTTGGGGGGTCAAACTGTACGTTATATGTGCCAATCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACAACAACGA---------AAA--------A-GTGT--------------A-AT---------A
droAna3	TGGGTTTTCT----------G------------------------------------GA------------AGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCT-TAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAA----------GTGT----------------TT---------T
droBip1	ATACTATATA------GTCTA-------------------------GTAGTATTAATGACA------ATATTGCTCAAC-CATTTGGGGGGTCAAACTGTACGTTGTATGTGCCAAACT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGCCAGCAA----------------------------------------TTGT---------C
dp4	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droPer1	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droWil1	TATGT--AATA--AA-TT----------------------------------------AAAGAATCAATTCTACACAAC-AT-TTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA------------------------------------------------------
droVir3	TTAGTGTAGA------AAA-------------------------------------AGAAAAAAAC--ACACACACAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAAT-G-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC--------------------------------------------------------
droMoj3	AATGTGAACA------A----------------------------------------------------AACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGTAA-ACA-ATGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG---------CAA----TTTAA-GCAT--------------AGCT---------A
droGri2	G--------------------------------------------------------GAAA------ATAACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTATATGTGTAAAT-G-AAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT---------AAA----------AAG----------------TCT---------T

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

TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	929.00	364.00	253.00	46.00	266.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	355.00	263.00	11.00	74.00	7.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	262.00	25.00	181.00	32.00	24.00
.......................................................................................GGGGTGAAACTGTACGTTATA.........................................................................................................................	21	1	38.00	15.00	10.00	2.00	11.00
.......................................................................................GGGGTGAAACTGTACGTTATAT........................................................................................................................	22	1	34.00	18.00	6.00	3.00	7.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCT..............................................................................	21	1	25.00	0.00	19.00	1.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCC..............................................................................	21	1	24.00	0.00	22.00	2.00	0.00
..................................................................................................................................TAACCGTATAGCTTTTCCCCT..............................................................................	21	1	21.00	0.00	19.00	0.00	2.00
............................................................................................GAAACTGTACGTTATATG.......................................................................................................................	18	1	16.00	0.00	4.00	2.00	10.00
..............................................................................................................TGCCCTTCT-GTGAAATTC....................................................................................................	18	1	14.00	0.00	9.00	0.00	5.00
..............................................................................................................TGCCCTTCT-GTGAAATTCA...................................................................................................	19	1	12.00	2.00	4.00	0.00	6.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	11.00	0.00	6.00	5.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATATT.......................................................................................................................	23	1	9.00	8.00	0.00	0.00	1.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCTT.............................................................................	22	1	9.00	0.00	6.00	0.00	3.00
......................................................................................GGGGGTGAAACTGTACGTTATATG.......................................................................................................................	24	1	7.00	2.00	1.00	0.00	4.00
.......................................................................................GGGGAGAAACTGTACGTTATATG.......................................................................................................................	23	1	7.00	6.00	0.00	0.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	6.00	6.00	0.00	0.00	0.00
...........................................................................................TGAAACTGTACGTTATATG.......................................................................................................................	19	1	6.00	0.00	2.00	1.00	3.00
........................................................................................GGGTGAAACTGTACGTTATATG.......................................................................................................................	22	1	6.00	0.00	0.00	0.00	6.00
.......................................................................................GGGGGGAAACTGTACGTTATATG.......................................................................................................................	23	1	5.00	3.00	0.00	0.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCG..............................................................................	21	1	5.00	0.00	4.00	1.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATATGA......................................................................................................................	24	1	5.00	3.00	1.00	0.00	1.00
.......................................................................................GGGGTGAAACTGTACGCTATATG.......................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTCTATG.......................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATCTG.......................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	4.00	3.00	0.00	1.00	0.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCC..............................................................................	21	1	3.00	0.00	3.00	0.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTTTATG.......................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00
..................................................................................................................................................TCCCTTAAAAGTTGGAGC.................................................................	18	1	3.00	0.00	0.00	3.00	0.00
.......................................................................................GGTGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	2.00	0.00	1.00
.......................................................................................GGGGTGAAACTGTACGTTA...........................................................................................................................	19	1	3.00	2.00	0.00	0.00	1.00
..................................................................................................................................TAAGTGTATAGCTTTTCCCCT..............................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	3.00	0.00	0.00	0.00

droSec1

TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	892.00	99.00	485.00	308.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	855.00	138.00	385.00	332.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	213.00	25.00	49.00	139.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	47.00	7.00	16.00	24.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCTTT.............................................................................	22	1	28.00	0.00	27.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	21.00	0.00	7.00	14.00
.......................................................................................GGGGTGAAACTGTACGTTATAT........................................................................................................................	22	1	18.00	2.00	11.00	5.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTT.............................................................................	21	1	9.00	0.00	2.00	7.00
..................................................................................................................................TAAGCGTATAGTTTTTCCCCTT.............................................................................	22	1	6.00	0.00	6.00	0.00
......................................................................................GGGGGTGAAACTGTACGTTATATG.......................................................................................................................	24	1	5.00	0.00	3.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	5.00	1.00	3.00	1.00
.......................................................................................GGGGTGAAGCTGTACGTTATATG.......................................................................................................................	23	1	4.00	0.00	3.00	1.00
.......................................................................................GGGGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	4.00	0.00	0.00	4.00
....................................................................................................................................AGCGTATAGCTTTTCCCCTT.............................................................................	20	1	4.00	0.00	3.00	1.00
.......................................................................................GGGGTGAAACTxTACGTTATATG.......................................................................................................................	22	1	4.00	0.00	3.00	1.00
.......................................................................................GGGGTGAAATTGTACGTTATATG.......................................................................................................................	23	1	4.00	0.00	4.00	0.00
..................................................................................................................................TAAGCCTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	0.00	2.00	2.00
.......................................................................................GGGGTGAAACTGTACGTTATA.........................................................................................................................	21	1	4.00	1.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTC.............................................................................	22	1	4.00	0.00	4.00	0.00
.......................................................................................GGGGCGAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	2.00	1.00
.......................................................................................GGGGTAAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	1.00	1.00	1.00
..................................................................................................................................TAAGCGTATAGCTCTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATATGA......................................................................................................................	24	1	3.00	1.00	2.00	0.00
........................................................................................GGGTGAAACTGTACGTTATATG.......................................................................................................................	22	1	3.00	0.00	2.00	1.00
..................................................................................................................................TAAGTGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00

droYak2

TAATTGTACAATCACCATC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTTT-GT-AAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA---------ATA----------GTGT--------------ATTT---------C	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	1047.00	211.00	262.00	45.00	525.00	4.00
.......................................................................................GGGGTTAAACTGTACGTTATATG.......................................................................................................................	23	1	174.00	100.00	5.00	12.00	14.00	43.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	169.00	16.00	42.00	13.00	84.00	14.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	32.00	8.00	7.00	2.00	15.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTATA.........................................................................................................................	21	1	20.00	11.00	0.00	0.00	0.00	9.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	18.00	1.00	4.00	0.00	12.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	12.00	5.00	3.00	0.00	4.00	0.00
..................................................................................................................................TAAGCGTATAACTTTTCCCCTT.............................................................................	22	1	6.00	1.00	2.00	0.00	3.00	0.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	6.00	2.00	0.00	0.00	4.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTATATT.......................................................................................................................	23	1	5.00	4.00	1.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTGTAGCTTTTCCCCTT.............................................................................	22	1	4.00	1.00	1.00	0.00	2.00	0.00
..................................................................................................................................TAAGCGTATACCTTTTCCCCTT.............................................................................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCCT.............................................................................	22	1	4.00	1.00	0.00	0.00	3.00	0.00
..................................................................................................................................TAGGCGTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	1.00	2.00	0.00	1.00	0.00
..................................................................................................................................TAAGCGTATCGCTTTTCCCCTT.............................................................................	22	1	4.00	1.00	1.00	0.00	2.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	4.00	3.00	0.00	0.00	1.00	0.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCT..............................................................................	21	1	3.00	0.00	0.00	0.00	0.00	3.00
..................................................................................................................................TCAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
..................................................................................................................................TAAGCGTGTAGCTTTTCCCCT..............................................................................	21	1	3.00	0.00	0.00	0.00	3.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTATATGTGCC...................................................................................................................	27	1	3.00	0.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTATATGT......................................................................................................................	24	1	3.00	1.00	0.00	1.00	0.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTACCCTT.............................................................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
..................................................................................................................................TAACAGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	1.00	0.00	0.00	2.00	0.00
......................................................................................GGGGGTTAAACTGTACGTTATATG.......................................................................................................................	24	1	3.00	2.00	0.00	0.00	0.00	1.00
..................................................................................................................................TAAGCGTATTGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	1.00	0.00	2.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTT...........................................................................	24	1	3.00	1.00	0.00	0.00	2.00	0.00

droEre2

TACTTGTAGA------ACC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCT-GTAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA---------AAA----------GTGA--------------ATCT---------T	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	1327.00	172.00	20.00	0.00	1135.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	702.00	213.00	139.00	0.00	350.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	169.00	19.00	13.00	0.00	137.00
.......................................................................................GGGGTGAAACTGTACGTTATATT.......................................................................................................................	23	1	43.00	28.00	0.00	0.00	15.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	34.00	5.00	14.00	0.00	15.00
.......................................................................................GGGGTGAAACTGTACGTTATAT........................................................................................................................	22	1	28.00	12.00	0.00	0.00	16.00
.......................................................................................TGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	25.00	1.00	0.00	0.00	24.00
.......................................................................................GTGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	21.00	0.00	0.00	0.00	21.00
.......................................................................................GGGGTGAAACTGTACGTTATATA.......................................................................................................................	23	1	16.00	1.00	0.00	0.00	15.00
.......................................................................................GGTGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	15.00	0.00	0.00	0.00	15.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	12.00	0.00	1.00	0.00	11.00
.......................................................................................GGGGTGAAACTGTACGTTATA.........................................................................................................................	21	1	11.00	5.00	0.00	0.00	6.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCATT.............................................................................	22	1	11.00	0.00	0.00	0.00	11.00
.......................................................................................GGGGTTAAACTGTACGTTATATG.......................................................................................................................	23	1	10.00	1.00	0.00	0.00	9.00
.......................................................................................GGGGTGAAACTGTACGTTATATC.......................................................................................................................	23	1	10.00	0.00	0.00	0.00	10.00
.......................................................................................GGGGTGAAACTTTACGTTATATG.......................................................................................................................	23	1	9.00	0.00	0.00	0.00	9.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTG............................................................................	23	1	7.00	0.00	1.00	0.00	6.00
.......................................................................................GGGGCGAAACTGTACGTTATATG.......................................................................................................................	23	1	7.00	2.00	0.00	0.00	5.00
.......................................................................................GGGGTGAAAATGTACGTTATATG.......................................................................................................................	23	1	7.00	0.00	0.00	0.00	7.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	6.00	1.00	1.00	0.00	4.00
.......................................................................................GGGTTGAAACTGTACGTTATATG.......................................................................................................................	23	1	6.00	0.00	0.00	0.00	6.00
.......................................................................................GGGGTGAAACTGTACTTTATATG.......................................................................................................................	23	1	6.00	0.00	0.00	0.00	6.00
.......................................................................................GGGGTGAAACTGTACGTTATCTG.......................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCC................................................................................	19	1	5.00	0.00	1.00	0.00	4.00
..................................................................................................................................TAAGCGTATAGATTTTCCCCTT.............................................................................	22	1	4.00	0.00	0.00	0.00	4.00
..................................................................................................................................TAAGCGTATAGCTTTTCCACT..............................................................................	21	1	4.00	0.00	0.00	0.00	4.00
.......................................................................................GGGGTGAAACTGTATGTTATATG.......................................................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
.......................................................................................GGGGAGAAACTGTACGTTATATG.......................................................................................................................	23	1	4.00	1.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	4.00	4.00	0.00	0.00	0.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTT.............................................................................	21	1	3.00	1.00	1.00	0.00	1.00
.......................................................................................GGGGTGAGACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................GGGGTGAAACTGTACGCTATATG.......................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
......................................................................................GGGGGTGAAACTGTACGTTATATG.......................................................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	3.00	3.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTACCCTT.............................................................................	22	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................GGGGTGAAACTGTAAGTTATATG.......................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCAT..............................................................................	21	1	3.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGTATAGCTTTTCCACTT.............................................................................	22	1	3.00	0.00	0.00	0.00	3.00
........................................................................................GGGTGAAACTGTACGTTATATG.......................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................AGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
..............................................................................................................TGTCCTTCT-GTAAAATTCA...................................................................................................	19	1	3.00	0.00	1.00	0.00	2.00
......................................................................................CGGGGTGAAACTGTACGTTATATG.......................................................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	1.00	0.00	0.00	2.00
.......................................................................................GGGGTGAAACTGTACGTTA...........................................................................................................................	19	1	3.00	2.00	0.00	0.00	1.00

droEug1

TAATTTTTTT--GAGAACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCTATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAAAGCAACAGCAGCAA---------AAA----------GTGT--------------TTTT---------A

Size

Hit Count

Total Norm

droBia1

CACTTGTGCC------ATC---------------------------------------ACG------ATATTGCCCGAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAGAAGTTGGTGCAACAGCAACGACCGT-GTGA---TAAATTGTAG----GAGTA------TATGTTCTTTTATGATC

Size

Hit Count

Total Norm

droTak1

TACTTTTACA------ATC-------------------------------------TGACA------ATATTGCTTAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAAAAGCAACAG---------AAA----------GTAT--------------GATT---------A

Size

Hit Count

Total Norm

droEle1

TAGTTTTACA------ACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAATAAATTGTAA----GAGTAAAACAATGCGTTC---------T

Size

Hit Count

Total Norm

droRho1

TCCTTTTACA------ACC-------------------------------------TGAGA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTGTATGTGTCATTCT-TTAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAA----------GGA---------------TGAT---------A

Size

Hit Count

Total Norm

droFic1

ACGGTGTAAA------AGC-------------------------------------CAAAG-ATT--TTATTGCTCAAC-ATTTTGAGGGGTGAAACTGTACGTTGTATGTGCCCTATT-ATAAAAACCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACACCAACAA---------AAA----------GTGACCGATAAATAAT--CTCT---------A

Size

Hit Count

Total Norm

droKik1

TAGTC---CA------AAT-TGCAGCTAATGTGTTATGATATATAAATAGAATGAATAATA------TTATTGCTCATC-ATTTTGGGGGGTCAAACTGTACGTTATATGTGCCAATCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACAACAACGA---------AAA--------A-GTGT--------------A-AT---------A

Size

Hit Count

Total Norm

droAna3

TGGGTTTTCT----------G------------------------------------GA------------AGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCT-TAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAA----------GTGT----------------TT---------T	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	785.00	76.00	161.00	351.00	197.00
.......................................................................................GGGGTCAAACTGTACGTTCTATG.......................................................................................................................	23	1	662.00	3.00	632.00	11.00	16.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	296.00	30.00	122.00	81.00	63.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	81.00	15.00	16.00	39.00	11.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	35.00	0.00	17.00	13.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	18.00	0.00	2.00	6.00	10.00
.......................................................................................GGTGTCAAACTGTACGTTCTATG.......................................................................................................................	23	1	15.00	0.00	15.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTG............................................................................	23	1	12.00	1.00	6.00	4.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTT...........................................................................	24	1	11.00	2.00	1.00	8.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCTATT.......................................................................................................................	23	1	9.00	0.00	6.00	0.00	3.00
.......................................................................................GGGGTCAAACTGTACGTTCTATGT......................................................................................................................	24	1	8.00	0.00	7.00	0.00	1.00
..............................................................................................................TGGCAATCT-TAGAAATTCA...................................................................................................	19	1	6.00	0.00	3.00	0.00	3.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCTT.............................................................................	22	1	6.00	1.00	3.00	0.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	6.00	0.00	0.00	0.00	6.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	6.00	0.00	0.00	2.00	4.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	6.00	0.00	0.00	5.00	1.00
.......................................................................................GGGGTCAAACTGTACGTTCTAT........................................................................................................................	22	1	5.00	0.00	5.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTA.............................................................................	22	1	5.00	0.00	0.00	0.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCAT.............................................................................	22	1	4.00	2.00	2.00	0.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTATATG.......................................................................................................................	23	1	4.00	0.00	4.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCA..............................................................................	21	1	4.00	0.00	4.00	0.00	0.00
.......................................................................................GGGGTCAAACTGCACGTTCTATG.......................................................................................................................	23	1	4.00	0.00	3.00	1.00	0.00
.......................................................................................GGGGTCAAGCTGTACGTTCTATG.......................................................................................................................	23	1	4.00	0.00	3.00	1.00	0.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTT.............................................................................	21	1	4.00	2.00	1.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCC................................................................................	19	1	3.00	2.00	0.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTG.............................................................................	22	1	3.00	0.00	0.00	2.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCTTT.............................................................................	22	1	3.00	1.00	0.00	1.00	1.00
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	1.00	0.00	2.00
.......................................................................................GGGGTCAAACTGTACGTTCTATGTG.....................................................................................................................	25	1	3.00	0.00	2.00	0.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAAA..........................................................................	25	1	3.00	1.00	0.00	0.00	2.00
.......................................................................................GGGGTCAAACTGTACGTTCTGTG.......................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.......................................................................................GTGGTCAAACTGTACGTTCTATG.......................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTTCCCTT.............................................................................	22	1	3.00	0.00	0.00	1.00	2.00
..................................................................................................................................TAAGCGTAGAGCTTTTCCCCTT.............................................................................	22	1	3.00	1.00	0.00	2.00	0.00
..................................................................................................................................TAAGCGTATATCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	1.00	1.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCACT..............................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATACCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	0.00	2.00	1.00
..................................................................................................................................GAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	0.00	2.00	1.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCT..............................................................................	21	1	3.00	0.00	0.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGATTTTCCCCT..............................................................................	21	1	3.00	1.00	2.00	0.00	0.00
..................................................................................................................................TAAGCGTACAGCTTTTCCCCTT.............................................................................	22	1	3.00	1.00	1.00	0.00	1.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTTT............................................................................	22	1	3.00	0.00	1.00	2.00	0.00

droBip1

ATACTATATA------GTCTA-------------------------GTAGTATTAATGACA------ATATTGCTCAAC-CATTTGGGGGGTCAAACTGTACGTTGTATGTGCCAAACT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGCCAGCAA----------------------------------------TTGT---------C

Size

Hit Count

Total Norm

dp4

TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	642.00	62.00	379.00	201.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCTATG.......................................................................................................................	23	1	104.00	13.00	87.00	4.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	103.00	20.00	61.00	22.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	42.00	7.00	27.00	8.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	16.00	0.00	15.00	1.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTGTATG.......................................................................................................................	23	1	8.00	0.00	8.00	0.00	0.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	7.00	0.00	6.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	6.00	0.00	2.00	4.00	0.00
..............................................................................................................TGACAATAT-TCGAAATTCA...................................................................................................	19	1	6.00	0.00	5.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	5.00	0.00	5.00	0.00	0.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTT.............................................................................	21	1	5.00	1.00	1.00	3.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	4.00	0.00	4.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCCT.............................................................................	22	1	4.00	0.00	3.00	1.00	0.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	0.00	4.00	0.00	0.00
..................................................................................................................................TAAGCGTGTAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	1.00	2.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTT...........................................................................	24	1	3.00	0.00	2.00	1.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCTAT........................................................................................................................	22	1	3.00	1.00	2.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCTTT.............................................................................	22	1	3.00	0.00	1.00	2.00	0.00

droPer1

TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	740.00	28.00	192.00	123.00	397.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	114.00	10.00	31.00	8.00	60.00	5.00
.......................................................................................GGGGTCAAACTGTACGTTCTATG.......................................................................................................................	23	1	105.00	8.00	34.00	6.00	6.00	51.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	52.00	2.00	9.00	15.00	26.00	0.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	16.00	0.00	1.00	0.00	15.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCTA.........................................................................................................................	21	1	12.00	0.00	0.00	0.00	0.00	12.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	6.00	0.00	4.00	0.00	2.00	0.00
..................................................................................................................................TAAACGTATAGCTTTTCCCCTT.............................................................................	22	1	5.00	0.00	3.00	1.00	1.00	0.00
..................................................................................................................................TAAGCGTGTAGCTTTTCCCCTT.............................................................................	22	1	5.00	0.00	1.00	1.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	5.00	0.00	0.00	2.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGCCTTTCCCCTT.............................................................................	22	1	5.00	0.00	0.00	0.00	5.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCT..........................................................................................................................	20	1	4.00	0.00	0.00	0.00	0.00	4.00
.......................................................................................GGGGTCAAACTGTACGTTC...........................................................................................................................	19	1	4.00	0.00	0.00	0.00	0.00	4.00
..............................................................................................................TGACAATAT-TCGAAATTCA...................................................................................................	19	1	4.00	0.00	3.00	0.00	1.00	0.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	0.00	0.00	1.00	3.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTCTATGA......................................................................................................................	24	1	3.00	0.00	0.00	0.00	0.00	3.00
.........................................................................................................................................................................CAACATTCGG-AACA---ACAA......................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGTGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	1.00	0.00	2.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCCT.............................................................................	22	1	3.00	0.00	0.00	1.00	2.00	0.00

droWil1

TATGT--AATA--AA-TT----------------------------------------AAAGAATCAATTCTACACAAC-AT-TTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA------------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................GGGGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	1768.00	19.00	784.00	484.00	481.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	948.00	76.00	618.00	249.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	410.00	15.00	211.00	139.00	45.00
.......................................................................................GGGGTTAAACTGTACGTTGTAT........................................................................................................................	22	1	149.00	2.00	104.00	33.00	10.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	78.00	2.00	39.00	36.00	1.00
.......................................................................................GGGGTTAAACTGTACGTTGTA.........................................................................................................................	21	1	62.00	1.00	37.00	15.00	9.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	31.00	5.00	17.00	9.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTGTATGT......................................................................................................................	24	1	29.00	0.00	9.00	7.00	13.00
.......................................................................................GGGGTTAAACTGTACGTTGTATGA......................................................................................................................	24	1	19.00	0.00	15.00	2.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	18.00	1.00	17.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	17.00	0.00	17.00	0.00	0.00
..............................................................................................................TGCAAATCTTAAGAAATCCA...................................................................................................	20	1	14.00	1.00	10.00	3.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTGCATG.......................................................................................................................	23	1	9.00	0.00	5.00	2.00	2.00
.......................................................................................GGGGTTAAACTGTACGTTGT..........................................................................................................................	20	1	9.00	1.00	7.00	1.00	0.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCT..............................................................................	21	1	8.00	0.00	0.00	1.00	7.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTA.............................................................................	22	1	6.00	0.00	5.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAAA..........................................................................	25	1	6.00	0.00	6.00	0.00	0.00
.......................................................................................GGGGTGAAACTGTACGTTATATG.......................................................................................................................	23	1	6.00	0.00	1.00	5.00	0.00
.......................................................................................TGGGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	5.00	0.00	1.00	3.00	1.00
.......................................................................................GGGGTTAAACTGTACGTTGGATG.......................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
..................................................................................................................................TAATCGTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	0.00	2.00	1.00	1.00
........................................................................................GGGTTAAACTGTACGTTGTATG.......................................................................................................................	22	1	4.00	0.00	3.00	1.00	0.00
..................................................................................................................................TACGCGTATAGCTTTTCCCCTT.............................................................................	22	1	4.00	1.00	2.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCATT.............................................................................	22	1	4.00	0.00	4.00	0.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTGTATA.......................................................................................................................	23	1	4.00	0.00	1.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTG............................................................................	23	1	4.00	1.00	1.00	2.00	0.00
.......................................................................................GGGGTTAAAATGTACGTTGTATG.......................................................................................................................	23	1	3.00	0.00	1.00	2.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTGTATGG......................................................................................................................	24	1	3.00	0.00	0.00	1.00	2.00
.......................................................................................GGGGTTAAACTGTAAGTTGTATG.......................................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTCCCCTT..............................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCC................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
.......................................................................................GGAGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCACTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATAACTTTTCCCCT..............................................................................	21	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................GCGGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	3.00	0.00	1.00	2.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCC..............................................................................	21	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................GGGGTTAAACTGTACGTTATATG.......................................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
.......................................................................................GGGGTTAAACTGTACGTTTTATG.......................................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
.......................................................................................GGTGTTAAACTGTACGTTGTATG.......................................................................................................................	23	1	3.00	0.00	1.00	0.00	2.00

droVir3

TTAGTGTAGA------AAA-------------------------------------AGAAAAAAAC--ACACACACAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAAT-G-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC--------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	1173.00	143.00	956.00	72.00	0.00	2.00
.......................................................................................GGGGTCAAACTGTACGTTGTATG.......................................................................................................................	23	1	312.00	54.00	60.00	114.00	40.00	44.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	248.00	44.00	174.00	12.00	1.00	17.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	114.00	20.00	86.00	8.00	0.00	0.00
..................................................................................................................................TAAGCGAATAGCTTTTCCCCTT.............................................................................	22	1	18.00	0.00	18.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTC............................................................................	23	1	13.00	1.00	11.00	1.00	0.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTGTATT.......................................................................................................................	23	1	12.00	0.00	1.00	11.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	10.00	3.00	7.00	0.00	0.00	0.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	7.00	0.00	7.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	7.00	0.00	3.00	4.00	0.00	0.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	7.00	0.00	7.00	0.00	0.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTGTAT........................................................................................................................	22	1	7.00	1.00	1.00	4.00	1.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCCT.............................................................................	22	1	6.00	1.00	4.00	1.00	0.00	0.00
........................................................................................GGGTCAAACTGTACGTTGTATG.......................................................................................................................	22	1	6.00	0.00	0.00	3.00	1.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	6.00	0.00	4.00	2.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTA...........................................................................	24	1	5.00	0.00	5.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCT..............................................................................	21	1	5.00	0.00	4.00	0.00	0.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTT...........................................................................	24	1	5.00	0.00	5.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGAATAGCTTTTCCCCT..............................................................................	21	1	4.00	0.00	4.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTC.............................................................................	22	1	4.00	1.00	3.00	0.00	0.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTGTA.........................................................................................................................	21	1	4.00	0.00	0.00	3.00	0.00	1.00
.......................................................................................GGGGTCAAACTGTACGTTTTATG.......................................................................................................................	23	1	4.00	0.00	1.00	3.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCTCCTT.............................................................................	22	1	4.00	0.00	4.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAT...........................................................................	24	1	4.00	0.00	0.00	4.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCG..............................................................................	21	1	4.00	0.00	0.00	0.00	0.00	4.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTC...........................................................................	24	1	3.00	0.00	3.00	0.00	0.00	0.00
..................................................................................................................................CAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGCATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
.......................................................................................GGGGTCAAACTGTACGTTGTATGT......................................................................................................................	24	1	3.00	0.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGTATAACTTTTCCCCTT.............................................................................	22	1	3.00	0.00	2.00	1.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTG............................................................................	23	1	3.00	0.00	2.00	1.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTCTTCCCCTT.............................................................................	22	1	3.00	0.00	2.00	1.00	0.00	0.00
.......................................................................................GGGGTCAAATTGTACGTTGTATG.......................................................................................................................	23	1	3.00	1.00	1.00	1.00	0.00	0.00
............................................................................................CAAACTGTACGTTGTATG.......................................................................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
..................................................................................................................................TAAGCCAATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
..................................................................................................................................TAACCGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
...................................................................................................................................AAGCGTATAGCTTTTCCCCTT.............................................................................	21	1	3.00	0.00	3.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTCCCCCTT.............................................................................	22	1	3.00	1.00	2.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATGGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCTT..............................................................................	21	1	3.00	0.00	3.00	0.00	0.00	0.00

droMoj3

AATGTGAACA------A----------------------------------------------------AACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGTAA-ACA-ATGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG---------CAA----TTTAA-GCAT--------------AGCT---------A	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	1023.00	112.00	153.00	115.00	643.00
.......................................................................................GGGGTCAAACTGTACGTTGTATG.......................................................................................................................	23	1	772.00	86.00	27.00	20.00	639.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	205.00	46.00	49.00	48.00	62.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	86.00	10.00	6.00	8.00	62.00
.......................................................................................GGGGTCAAACTGTACGTTGTAT........................................................................................................................	22	1	44.00	4.00	0.00	0.00	40.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAA...........................................................................	24	1	31.00	0.00	0.00	0.00	31.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTA............................................................................	23	1	23.00	1.00	3.00	2.00	17.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCC...............................................................................	20	1	16.00	1.00	5.00	3.00	7.00
.......................................................................................GGGGTCAAACTGTACGTTGTATT.......................................................................................................................	23	1	13.00	0.00	0.00	1.00	12.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTC............................................................................	23	1	12.00	4.00	2.00	1.00	5.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTG............................................................................	23	1	8.00	0.00	5.00	1.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAT...........................................................................	24	1	7.00	1.00	0.00	0.00	6.00
..................................................................................................................................TAAGCGGATAGCTTTTCCCCTT.............................................................................	22	1	7.00	0.00	2.00	1.00	4.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTAAA..........................................................................	25	1	6.00	1.00	1.00	0.00	4.00
.......................................................................................GGGGTCAAACTGTACGTTGT..........................................................................................................................	20	1	6.00	0.00	2.00	0.00	4.00
.......................................................................................GGGGTCAAACTGTACGTTGTATGA......................................................................................................................	24	1	6.00	0.00	0.00	0.00	6.00
..................................................................................................................................TAAGCGTATAGCCTTTCCCCTT.............................................................................	22	1	5.00	3.00	1.00	0.00	1.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTC.............................................................................	22	1	5.00	1.00	2.00	0.00	2.00
.......................................................................................GGGGTCAAACTGTACGTTGTCTG.......................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
..................................................................................................................................TAAGAGTATAGCTTTTCCCCTT.............................................................................	22	1	5.00	0.00	0.00	0.00	5.00
.......................................................................................GGGGTCAAACTGTACGCTGTATG.......................................................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTA.............................................................................	22	1	4.00	1.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTT...........................................................................	24	1	4.00	0.00	2.00	0.00	2.00
..................................................................................................................................TAAGCGTATAGCTTTTACCCTT.............................................................................	22	1	4.00	0.00	0.00	1.00	3.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTTAT..........................................................................	25	1	4.00	1.00	0.00	0.00	3.00
..................................................................................................................................TAAGCGCATAGCTTTTCCCCTT.............................................................................	22	1	3.00	1.00	0.00	0.00	2.00
..................................................................................................................................TAAGTGTATAGCTTTTCCCCTT.............................................................................	22	1	3.00	0.00	1.00	0.00	2.00
.......................................................................................GGGGTCAAACTGTACGGTGTATG.......................................................................................................................	23	1	3.00	0.00	0.00	1.00	2.00

droGri2

G--------------------------------------------------------GAAA------ATAACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTATATGTGTAAAT-G-AAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT---------AAA----------AAG----------------TCT---------T	Size	Hit Count	Total Norm	V109 Male body
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTT.............................................................................	22	1	33.00	33.00
.......................................................................................GGGGTCAAACTGTACGTTATATG.......................................................................................................................	23	1	6.00	6.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCT..............................................................................	21	1	6.00	6.00
..................................................................................................................................TAAGCGTATAGCTTTTCCCCTTT............................................................................	23	1	4.00	4.00
...........................................................................................................ATGTCAAAAT-G-AAGAAATT.....................................................................................................	19	1	3.00	3.00
...........................................................................................................ATGTCAAAAT-G-AAGAAATTCA...................................................................................................	21	1	2.00	2.00
...........................................................................................................ATGTCTAAGT-G-AAGAAATT.....................................................................................................	19	1	1.00	1.00
..................................................................................................................................TAAGCGxxTAGCTTTTCCCCTT.............................................................................	20	1	1.00	1.00
.................................................................................................................AAGT-G-AAGAAATTCATAAGCGC............................................................................................	22	1	1.00	1.00
....................................................................................................................................AGCGTATAGCTTTTCCCCTTT............................................................................	21	1	1.00	1.00
..................................................................................................................................TAAGCGTATAGGTTTTCCCCTT.............................................................................	22	1	1.00	1.00
..................................................................................................................................TAAGCGTCTAGCTTTTCCCCT..............................................................................	21	1	1.00	1.00

Generated: 04/20/2012 at 05:31:49 EDT

dme-mir-965

chr2L:243035-243141 -

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