dme-mir-318- Best orthologs

dme-mir-318	chr3R:6234024-6234091 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 6234066-6234087
   star strand at position 6234030-6234051
   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	chr3R:6234009-6234106 +		1	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSim1	chr3R:15159142-15159239 -	LASTZ	1	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--TAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSec1	super_0:15709308-15709405 -	LASTZ	1	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droYak2	chr3R:10262524-10262621 +	LASTZ	1	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCACTA--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEre2	scaffold_4770:15383893-15383990 -	LASTZ	1	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEug1	scf7180000409692:710233-710330 +	LASTZ	4	G-------ACCCC-----------TGGTTTCAGTTTATGGGATACACACAGCTCAGTCTTGTCACATGT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droBia1	scf7180000302402:8322956-8323053 +	LASTZ	4	G-------TCCCC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTCGTGTCGCATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droTak1	scf7180000415380:1406001-1406136 -	LASTZ	4	G-------TCCAGTTTAAGAAAAAGGATTTCAGTTTATGGGATATACACAGTTCAGTCTTGTCGCCTTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCAACAAGGGATATTTATTCAAACCCAAAA
droEle1	scf7180000490995:508430-508525 -	LASTZ	4	G-------ACTCT-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTCTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGA--GAAATTTGTTCA---------------------------
droRho1	scf7180000777158:16332-16429 -	LASTZ	4	G-------GACCC-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droFic1	scf7180000453800:2313678-2313775 +	LASTZ	4	G-------ATCCA-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTC--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droKik1	scf7180000302475:1425888-1425985 +	LASTZ	4	T-------GCCCC-----------CGATTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTTTTCGATCCTCATCACTGGGCTTTGTTTATCTCATAAAAGCGAAATTT--------------------------------
droAna3	scaffold_13340:867198-867296 -	LASTZ	1	G-------TCCTC-----------CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT-GCGA---GCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
droBip1	scf7180000394085:131950-132048 +	LASTZ	4	G-------TCCTC-----------CGGTTTCAAATTATGGGATACACACAGTTCAGTTTTGTCACTTTT-GCGA---ACATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
dp4	chr2:7233334-7233438 -	LASTZ	1	CGTGTGCCTCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droPer1	super_0:1094016-1094113 -	LASTZ	1	C-------TCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droWil1	scaffold_181108:652-751 +	LASTZ	1	G-------TCAGA-----------CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCATTCCACGA---GCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA---------------------------
droVir3	scaffold_13047:1194317-1194415 +	LASTZ	1	T-------GATTT-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA---------------------------
droMoj3	scaffold_6540:5225327-5225427 +	LASTZ	1	G-------TGATT---------AAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA---------------------------
droGri2	scaffold_14906:5077291-5077389 -	LASTZ	1	G-------ATTTC-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA---------------------------

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	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSim1	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--TAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSec1	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droYak2	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCACTA--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEre2	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEug1	G-------ACCCC-----------TGGTTTCAGTTTATGGGATACACACAGCTCAGTCTTGTCACATGT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droBia1	G-------TCCCC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTCGTGTCGCATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droTak1	G-------TCCAGTTTAAGAAAAAGGATTTCAGTTTATGGGATATACACAGTTCAGTCTTGTCGCCTTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCAACAAGGGATATTTATTCAAACCCAAAA
droEle1	G-------ACTCT-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTCTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGA--GAAATTTGTTCA---------------------------
droRho1	G-------GACCC-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droFic1	G-------ATCCA-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTC--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droKik1	T-------GCCCC-----------CGATTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTTTTCGATCCTCATCACTGGGCTTTGTTTATCTCATAAAAGCGAAATTT--------------------------------
droAna3	G-------TCCTC-----------CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT-GCGA---GCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
droBip1	G-------TCCTC-----------CGGTTTCAAATTATGGGATACACACAGTTCAGTTTTGTCACTTTT-GCGA---ACATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
dp4	CGTGTGCCTCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droPer1	C-------TCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droWil1	G-------TCAGA-----------CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCATTCCACGA---GCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA---------------------------
droVir3	T-------GATTT-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA---------------------------
droMoj3	G-------TGATT---------AAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA---------------------------
droGri2	G-------ATTTC-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA---------------------------

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

G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--TAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	255.00	6.00	129.00	33.00	87.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	219.00	1.00	145.00	43.00	30.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	21.00	1.00	14.00	2.00	4.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	1	8.00	0.00	5.00	3.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	1	8.00	0.00	6.00	0.00	2.00
................................................................................TCGCTGGGCTTTGTTTATCTC...............................................	21	1	2.00	0.00	1.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	2.00	0.00	0.00	0.00	2.00
................................................................................TCACTGGGCTCTGTTTATCTCT..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTCTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTATTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTAGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................................CACTGGGCTTTGTTTATCTC...............................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCCCTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTCATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAAAA...........................................	25	1	1.00	1.00	0.00	0.00	0.00
..................................................................................CCTGGGCTTTGTTTATCTC...............................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ATCACTGGGCTTTGTTTATC.................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTGTGTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGACTTTGTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCCTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	1.00

droSec1

G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	5745.00	1084.00	7.00	4654.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	659.00	151.00	0.00	508.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	161.00	38.00	0.00	123.00
..................................................................................ACTGGGCTTTGTTTATCTCA..............................................	20	1	32.00	4.00	0.00	28.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	23.00	5.00	0.00	18.00
................................................................................TCACTGGGCTTTGTTTATTTCA..............................................	22	1	12.00	8.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATATCA..............................................	22	1	10.00	9.00	0.00	1.00
................................................................................TCACTGGGCTTTGTCTATCTCA..............................................	22	1	9.00	0.00	0.00	9.00
................................................................................TCACTGGGCTTTGTTTATCCCA..............................................	22	1	9.00	3.00	0.00	6.00
................................................................................TCAATGGGCTTTGTTTATCTCA..............................................	22	1	8.00	1.00	0.00	7.00
.................................................................................CACTGGGCTTTGTTTATCTCA..............................................	21	1	8.00	2.00	0.00	6.00
................................................................................TCACTGGCCTTTGTTTATCTCA..............................................	22	1	7.00	1.00	0.00	6.00
................................................................................TCACTGGTCTTTGTTTATCTCA..............................................	22	1	7.00	1.00	0.00	6.00
................................................................................TCACTGGGCTTTGTTTGTCTCA..............................................	22	1	7.00	1.00	0.00	6.00
................................................................................TCGCTGGGCTTTGTTTATCTCA..............................................	22	1	6.00	0.00	0.00	6.00
................................................................................TAACTGGGCTTTGTTTATCTCA..............................................	22	1	6.00	0.00	0.00	6.00
................................................................................TCACAGGGCTTTGTTTATCTCA..............................................	22	1	6.00	0.00	0.00	6.00
................................................................................TCACTGGGCTTTGTTTCTCTCA..............................................	22	1	6.00	1.00	0.00	5.00
................................................................................TCACTGGGCTTTTTTTATCTCA..............................................	22	1	6.00	0.00	0.00	6.00
................................................................................TCACTGGGCTTTGCTTATCTCA..............................................	22	1	6.00	1.00	0.00	5.00
................................................................................TCACTGGGCCTTGTTTATCTCA..............................................	22	1	6.00	1.00	0.00	5.00
................................................................................TCACTGGGCTTTGxTTATCTCA..............................................	21	1	5.00	0.00	0.00	5.00
................................................................................TCACTGGACTTTGTTTATCTCA..............................................	22	1	5.00	1.00	0.00	4.00
................................................................................TCACTGGGCTTTCTTTATCTCA..............................................	22	1	5.00	1.00	0.00	4.00
................................................................................CCACTGGGCTTTGTTTATCTCA..............................................	22	1	5.00	1.00	0.00	4.00
................................................................................TCACTGAGCTTTGTTTATCTCA..............................................	22	1	5.00	1.00	0.00	4.00
................................................................................TCACTTGGCTTTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATGTCA..............................................	22	1	4.00	3.00	0.00	1.00
................................................................................TCACTAGGCTTTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGATTTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATCTAA..............................................	22	1	4.00	2.00	0.00	2.00
................................................................................TCACTGGGCTTTGTTTACCTCA..............................................	22	1	4.00	1.00	0.00	3.00
................................................................................TCACTGGGTTTTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGCATTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATATC...............................................	21	1	4.00	4.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATCACA..............................................	22	1	4.00	0.00	0.00	4.00
................................................................................TCACTGCGCTTTGTTTATCTCA..............................................	22	1	3.00	1.00	0.00	2.00
................................................................................ACACTGGGCTTTGTTTATCTCA..............................................	22	1	3.00	1.00	0.00	2.00
................................................................................TCACTxGGCTTTGTTTATCTCA..............................................	21	1	3.00	0.00	0.00	3.00
................................................................................TCATTGGGCTTTGTTTATCTCA..............................................	22	1	3.00	1.00	0.00	2.00
................................................................................TCACTGGGCTTTGTTCATCTCA..............................................	22	1	3.00	2.00	0.00	1.00
..................................................................................ACTGGGCTTTGTTTATCTC...............................................	19	1	3.00	1.00	0.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	1	3.00	0.00	0.00	3.00
................................................................................TCACTGGGCTTTGTTTATCTCC..............................................	22	1	3.00	1.00	0.00	2.00
................................................................................TCCCTGGGCTTTGTTTATCTCA..............................................	22	1	3.00	3.00	0.00	0.00
................................................................................GCACTGGGCTTTGTTTATCTCA..............................................	22	1	3.00	0.00	0.00	3.00
................................................................................TCACTGAGCTTTGTTTATCTC...............................................	21	1	3.00	0.00	0.00	3.00
................................................................................TCACTGTGCTTTGTTTATCTCA..............................................	22	1	3.00	0.00	0.00	3.00
...............................................................................CTCACTGGGCTTTGTTTATCTCA..............................................	23	1	3.00	1.00	0.00	2.00

droYak2

G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCACTA--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	2538.00	1.00	208.00	328.00	297.00	1704.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	1004.00	0.00	21.00	37.00	36.00	910.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	46.00	0.00	8.00	7.00	4.00	27.00
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	1	24.00	0.00	0.00	0.00	0.00	24.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	1	11.00	0.00	0.00	0.00	0.00	11.00
..................................................................................ACTGGGCTTTGTTTATCTCA..............................................	20	1	10.00	0.00	3.00	2.00	3.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTCC..............................................	22	1	9.00	0.00	2.00	0.00	7.00	0.00
................................................................................TCACTGGGCTTTGTTTCTCTCA..............................................	22	1	7.00	0.00	4.00	0.00	3.00	0.00
................................................................................TCACTGGGCTTTGTTTATCC................................................	20	1	6.00	0.00	0.00	0.00	0.00	6.00
................................................................................TCACTGGGCTTTGTTTACCTCA..............................................	22	1	4.00	0.00	1.00	1.00	2.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAT.............................................	23	1	4.00	0.00	0.00	0.00	0.00	4.00
................................................................................TCACGGGGCTTTGTTTATCTCA..............................................	22	1	4.00	0.00	0.00	0.00	3.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
................................................................................CCACTGGGCTTTGTTTATCTC...............................................	21	1	3.00	0.00	0.00	0.00	0.00	3.00
................................................................................TCACTGGACTTTGTTTATCTCA..............................................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	3.00	0.00	0.00	1.00	2.00	0.00
................................................................................TCACTGGGCTTTGGTTATCTC...............................................	21	1	3.00	0.00	0.00	0.00	1.00	2.00
................................................................................TCACCGGGCTTTGTTTATCTCA..............................................	22	1	3.00	0.00	0.00	1.00	0.00	2.00

droEre2

G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	23.00	2.00	2.00	0.00	19.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	5.00	0.00	2.00	0.00	3.00
................................................................................TCACTTGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTAA..............................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTAGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGGTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00

droEug1

G-------ACCCC-----------TGGTTTCAGTTTATGGGATACACACAGCTCAGTCTTGTCACATGT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------

Size

Hit Count

Total Norm

droBia1

G-------TCCCC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTCGTGTCGCATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------

Size

Hit Count

Total Norm

droTak1

G-------TCCAGTTTAAGAAAAAGGATTTCAGTTTATGGGATATACACAGTTCAGTCTTGTCGCCTTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCAACAAGGGATATTTATTCAAACCCAAAA

Size

Hit Count

Total Norm

droEle1

G-------ACTCT-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTCTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGA--GAAATTTGTTCA---------------------------

Size

Hit Count

Total Norm

droRho1

G-------GACCC-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------

Size

Hit Count

Total Norm

droFic1

G-------ATCCA-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTC--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------

Size

Hit Count

Total Norm

droKik1

T-------GCCCC-----------CGATTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTTTTCGATCCTCATCACTGGGCTTTGTTTATCTCATAAAAGCGAAATTT--------------------------------

Size

Hit Count

Total Norm

droAna3

G-------TCCTC-----------CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT-GCGA---GCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	17.00	4.00	8.00	3.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	7.00	2.00	4.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	7.00	3.00	4.00	0.00	0.00
................................................................................TCACTGGGCTTCGTTTATCT................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGCTTATCT................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGCGCTTTGTTTATCTGA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGTTTTTGTTTATCT................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGAGCTTTGTTTATCT................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGATTTGTTTATCT................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTAA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCGCTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTCTCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00

droBip1

G-------TCCTC-----------CGGTTTCAAATTATGGGATACACACAGTTCAGTTTTGTCACTTTT-GCGA---ACATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------

Size

Hit Count

Total Norm

dp4

CGTGTGCCTCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	106.00	67.00	10.00	12.00	17.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	36.00	16.00	1.00	4.00	15.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	21.00	17.00	0.00	2.00	2.00
..................................................................................ACTGGGCTTTGTTTATCTCA..............................................	20	1	2.00	1.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................TCTCTGGGCTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCTCTGGGCTTTGTTTATCTCT..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTCTCA................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCGCTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
.................................................................................CACTGGGCTTTGTTTATCTCA..............................................	21	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCxTTGTTTATCTCA..............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGTTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................CTCACTGGGCTTTGTTTATCTC...............................................	22	1	1.00	0.00	0.00	0.00	1.00

droPer1

C-------TCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	74.00	6.00	0.00	14.00	15.00	39.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	33.00	8.00	0.00	5.00	8.00	12.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	15.00	5.00	0.00	6.00	4.00	0.00
................................................................................TAACTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTCTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................GTTCAGTTTTGTCGCTTTT--.............................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTAACTCA..............................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGTTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................TCACTGGGCGTTGTTTTTCTC...............................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................ACGCTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

G-------TCAGA-----------CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCATTCCACGA---GCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA---------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	2	3551.50	90.00	23.50	10.50	3427.50
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	2	1126.50	18.00	1.00	7.00	1100.50
................................................................................TCACTGGGCTTTGTTTATCTCAT.............................................	23	2	49.50	0.00	0.00	0.00	49.50
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	2	37.00	0.00	0.00	0.00	37.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	2	17.50	6.50	0.00	2.00	9.00
................................................................................TCACTGGGCTTTATTTATCTCA..............................................	22	2	6.00	0.00	0.00	0.00	6.00
................................................................................TCACTGGGCTTTCTTTATCTCA..............................................	22	2	4.50	0.00	0.00	0.00	4.50
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	2	4.50	0.00	0.50	0.00	4.00
................................................................................TCACTGGGCTTTATTTATCTC...............................................	21	2	4.00	0.00	0.00	0.00	4.00
................................................................................TCACTGGGCCTTGTTTATCTCA..............................................	22	2	4.00	0.00	0.00	0.00	4.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	2	4.00	0.00	0.00	0.00	4.00
..................................................................................ACTGGGCTTTGTTTATCTCA..............................................	20	2	4.00	1.00	0.00	0.50	2.50
................................................................................TCACTGGGCTTTGGTTATCTCA..............................................	22	2	3.50	0.00	0.00	0.00	3.50
................................................................................TCACTGGGCTTTTTTTATCTC...............................................	21	2	3.50	0.00	0.00	0.00	3.50
................................................................................TCACTGGGCTTTGTTTATCCCA..............................................	22	2	3.00	0.50	0.00	0.00	2.50
................................................................................TCACTGGGCTTTGTTTATCTCAC.............................................	23	2	2.50	0.00	0.00	0.00	2.50
................................................................................TCACTGGGCTTTGCTTATCTCA..............................................	22	2	2.50	0.00	0.00	0.00	2.50
................................................................................TCACTGGGCCTTGTTTATCTC...............................................	21	2	2.00	0.00	0.00	0.00	2.00
................................................................................TCACTGGGCTTTGTCTATCTCA..............................................	22	2	2.00	0.00	0.00	0.00	2.00
................................................................................TCACTGGGCTTTGTTTACCTCA..............................................	22	2	2.00	0.50	0.00	0.00	1.50
................................................................................TCACTGGGGTTTGTTTATCTCA..............................................	22	2	2.00	0.00	0.00	0.00	2.00
................................................................................TCACTGGGCTTTTTTTATCTCA..............................................	22	2	1.50	0.00	0.00	0.00	1.50
................................................................................CCACTGGGCTTTGTTTATCTCA..............................................	22	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	2	1.50	0.00	0.00	0.00	1.50
..................................................................................ACTGGGCTTTGTTTATCTCATT............................................	22	2	1.50	0.00	0.50	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCCC...............................................	21	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCACTGGGCTCTGTTTATCTCA..............................................	22	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCACTGGGCTTTGTTTATCTCATT............................................	24	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCCCTGGGCTTTGTTTATCTCA..............................................	22	2	1.50	1.50	0.00	0.00	0.00
................................................................................TCACCGGGCTTTGTTTATCTC...............................................	21	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCACTGGGCTTTGCTTATCTC...............................................	21	2	1.50	0.00	0.00	0.00	1.50
................................................................................TCACTGGGTTTTGTTTATCTCA..............................................	22	2	1.50	0.00	0.50	0.00	1.00
................................................................................TCACTGGGCGTTGTTTATCTCA..............................................	22	2	1.50	0.00	0.00	0.00	1.50
..................................................................................ACTGGGCTTTGTTTATCTC...............................................	19	2	1.50	0.00	0.00	0.00	1.50
................................................................................TTACTGGGCTTTGTTTATCTC...............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTGTCTCA..............................................	22	2	1.00	0.00	0.50	0.00	0.50
................................................................................TCACTGGGCTTTxTTTATCTCA..............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTTGGCTTTGTTTATCTC...............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACAGGGCTTTGTTTATCTCA..............................................	22	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTTA..............................................	22	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCGCTGGGCTTTGTTTATCTCA..............................................	22	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTxTTTATCTC...............................................	20	2	1.00	0.00	0.00	0.00	1.00
................................................................................ACACTGGGCTTTGTTTATCTCA..............................................	22	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCGCTGGGCTTTGTTTATCTC...............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTCGTTTATCTCA..............................................	22	2	1.00	0.00	0.00	0.00	1.00
.................................................................................CACTGGGCTTTGTTTATCTCA..............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACCGGGCTTTGTTTATCTCA..............................................	22	2	1.00	0.50	0.00	0.00	0.50
................................................................................TCACTCGGCTTTGTTTATCTC...............................................	21	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCC..............................................	22	2	1.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTCTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTGATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGTCTTTGTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTAGGCTTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTATTTATCAC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATTTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGAGCTTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGTTTTGTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGATTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACGGGGCTTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTGGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATTTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTTGGCCTTGTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTCATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTAACTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATCTCACT............................................	24	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATCTCACC............................................	24	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGACTTTGTTTATCT................................................	20	2	0.50	0.00	0.00	0.50	0.00
................................................................................TCACTGGGATTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATCACA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
...............................................................................CTCACTGGGCTTTGTTTATCTCA..............................................	23	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCATTGGGCTTTGTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCCTTTTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATGTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTATATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTCGGCTTTGTTTATCTCAT.............................................	23	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGGTTTGTTTATC.................................................	19	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGTTTTGTTTATCTT...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCATTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCTCTGGGCTTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TTACTGGGCTTTGTTTATCTCA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGxTTATCTC...............................................	20	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCATTGTTTATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCxTTGTTTATCTCA..............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTATCTGA..............................................	22	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTxGGCTTTGTTTATCTC...............................................	20	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTCATCTC...............................................	21	2	0.50	0.00	0.00	0.00	0.50
................................................................................TCACTGGGCTTTGTTTxTCT................................................	19	4	0.25	0.25	0.00	0.00	0.00
...............................AATTTAGGGGGTACACCA...................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

T-------GATTT-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA---------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	653.00	11.00	93.00	4.00	43.00	502.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	545.00	2.00	17.00	0.00	41.00	485.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	41.00	3.00	11.00	1.00	4.00	22.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	1	16.00	0.00	2.00	0.00	1.00	13.00
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	1	13.00	0.00	0.00	0.00	0.00	13.00
................................................................................TCACTGGGCTTTGTTTATCTCAT.............................................	23	1	6.00	0.00	0.00	0.00	0.00	6.00
................................................................................CCACTGGGCTTTGTTTATCTC...............................................	21	1	3.00	0.00	1.00	0.00	0.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	3.00	0.00	0.00	0.00	1.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	3.00	2.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCTCC..............................................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
................................................................................TCACTGGGCTTTGCTTATCTCA..............................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
................................................................................TCACTGGGCCTTGTTTATCTCA..............................................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTAA..............................................	22	1	2.00	0.00	1.00	0.00	0.00	1.00
..................................................................................ACTGGGCTTTGTTTATCTC...............................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................CTCACTGGGCTTTGTTTATCTCA..............................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTGTTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGCGCTTTGATTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTTTCTC...............................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCGATGTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACCGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................TCTCACTGGGCTTTGTTTATCTCA..............................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTTTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCC................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCGTTGTTTAGCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGCTTATCT................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTATCG................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGCTTATCTC...............................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGCGCTTTGTTTCTCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTT...............................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTAGGCTTTGTTTATC.................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGGTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGTTTTGTTTATCTC...............................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTGTTTCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................CCACTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTATTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCCCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCGTTGTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

G-------TGATT---------AAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA---------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	1063.00	901.00	88.00	67.00	7.00
................................................................................TCACTGGGCTTTGTTTATCTC...............................................	21	1	208.00	157.00	23.00	28.00	0.00
................................................................................TCACTGGGCTTTGTTTATCT................................................	20	1	163.00	97.00	29.00	37.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAT.............................................	23	1	22.00	17.00	2.00	3.00	0.00
................................................................................TCACTGGGCTTTGTTTATC.................................................	19	1	7.00	3.00	3.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	6.00	4.00	1.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAA.............................................	23	1	5.00	4.00	1.00	0.00	0.00
................................................................................TCACTGGGATTTGTTTATCTCA..............................................	22	1	3.00	1.00	1.00	1.00	0.00
................................................................................TCACTGGGCTTTGTCTATCTCA..............................................	22	1	2.00	1.00	0.00	0.00	1.00
................................................................................TCACTGGGCTTTGTTTGTCTCA..............................................	22	1	2.00	1.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGCTTATCTCA..............................................	22	1	2.00	2.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTACCTCA..............................................	22	1	2.00	1.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCC..............................................	22	1	2.00	0.00	0.00	1.00	1.00
................................................................................TCACTGTGCTTTGTTTATCTCA..............................................	22	1	2.00	1.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCG..............................................	22	1	2.00	2.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTAT..................................................	18	1	2.00	1.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGCTTATCT................................................	20	1	2.00	0.00	1.00	1.00	0.00
................................................................................TCGCTGGGCTTTGTTTATCTCA..............................................	22	1	2.00	1.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTCTCT................................................	20	1	2.00	0.00	0.00	2.00	0.00
................................................................................TCACTAGGCTTTGTTTATCAC...............................................	21	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATATC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTTTCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGAGCTTTGTTTCTCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTTTCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................GCACTGGGCTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCAGTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCAATGGGCTTAGTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTCGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGTGCTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TTACTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................CTCACTGGGCTTTGTTTATCTCA..............................................	23	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGxTTATCTC...............................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................ACACTGGGCTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCATT............................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTxTTTATC.................................................	18	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACCGGGCTTTGTTTATCTC...............................................	21	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCGTTGTTTAGCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATAT................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAAA............................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCCCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGTCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCCTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACGGGGCTTTGTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................CCACTGGGCTTTGTTTATCT................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATATCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTCGGCTTTGTTTATCT................................................	20	1	1.00	0.00	0.00	1.00	0.00
..................................................................................ACTGGGCTTTGTTTATCTCA..............................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCCA...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGATTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGGGCTCTGTTTATCT................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTTGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTCGGCTGTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTTTTTATCTC...............................................	21	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTCGTTTGTCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCAATGGGCTTTGTTTATCT................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................TAACTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TCACTGCCCTTTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTTA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................CCACTGGGCTTTGTTTATCTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTTTTTATCTTA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................GCACTGGGCTTTGTTTATCT................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTCTCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
..................................................................................ACTGGGCTTTGTTTATCTCATT............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTAA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTCTGTTTATCTCA..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATGTCA..............................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTCGGCTTTGTTTATCTC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................TCAGATGT-CCAA---GCATCACTGGGC...........................................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCxTTGTTTATCTCA..............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCAATGGGCTTTGTTTATCTC...............................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCTTTGCTTATCTCC..............................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCACTGGGCTTTGTTTATCTCAAT............................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCACTGGGCGTTGTTTATCT................................................	20	1	1.00	0.00	0.00	1.00	0.00

droGri2

G-------ATTTC-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA---------------------------	Size	Hit Count	Total Norm	V109 Male body
................................................................................TCACTGGGCTTTGTTTATCTCA..............................................	22	1	2.00	2.00
................................................................................TCACTGGGCTTTGTTTATCTCT..............................................	22	1	1.00	1.00

Generated: 04/20/2012 at 05:33:20 EDT

dme-mir-318

chr3R:6234024-6234091 +

Known_mirbase

intergenic

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup