dme-mir-276a-as- Best orthologs

dme-mir-276a-as	chr3L:10358328-10358425 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 10358379-10358400
   star strand at position 10358342-10358363
   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	chr3L:10358313-10358440 -		1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droSim1	chr3L:9747980-9748107 -	LASTZ	1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droSec1	super_0:2571151-2571278 -	LASTZ	1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droYak2	chr3L:10348871-10348998 -	LASTZ	1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC
droEre2	scaffold_4784:10353122-10353248 -	LASTZ	1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAA-AA-------TATCT----------T-GC
droEug1	scf7180000409711:2221453-2221580 -	LASTZ	4	G-GA---TTTTT-----------------------GCAT-------------TTAGTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC
droBia1	scf7180000302428:7389635-7389762 +	LASTZ	4	G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG
droTak1	scf7180000415515:147698-147825 +	LASTZ	4	G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droEle1	scf7180000490564:1195760-1195887 -	LASTZ	4	A-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droRho1	scf7180000778277:12893-13020 -	LASTZ	4	G-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droFic1	scf7180000453841:693857-693984 +	LASTZ	4	G-GA---TTTTA-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droKik1	scf7180000302334:36986-37129 +	LASTZ	4	GGGA---ACTTT-----------------------GCATTATTTTCTTAAATTTTCTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG
droAna3	scaffold_13337:15274238-15274391 -	LASTZ	1	G-AT---TTTTT-GGTTGAAGGGGAAACCAACTCCGCTTTA------------TGTTTT-----CGTTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAGAAA-------TATCT----------T-GG
droBip1	scf7180000395933:129274-129384 -	LASTZ	4	------------------------------------------------------------------TTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
dp4	chrXR_group6:8756376-8756506 -	LASTZ	1	---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG
droPer1	super_27:1191188-1191318 -	LASTZ	1	---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG
droWil1	scaffold_181024:222598-222734 +	LASTZ	1	G-TT---TTTTCTTGTT------------------GC----------------TGTTTTCGTAACGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATTAAATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGCATA-------T--TT----------TCAG
droVir3	scaffold_13049:16143973-16144088 -	LASTZ	1	C-----------------------------------------------------ACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATATAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-CA
droMoj3	scaffold_6680:20621809-20621940 +	LASTZ	1	C-GCTCGTTTTC-----------------------GTTT-------------TTGTTTG-----AGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATTTAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TACTT----------T-GG
droGri2	scaffold_15110:12521926-12522042 +	LASTZ	4	G-T--------------------------------------------------TTCTT------TGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTATGAGTATTTAAATTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-TG

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-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droSim1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droSec1	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droYak2	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC
droEre2	G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAA-AA-------TATCT----------T-GC
droEug1	G-GA---TTTTT-----------------------GCAT-------------TTAGTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC
droBia1	G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG
droTak1	G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droEle1	A-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droRho1	G-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droFic1	G-GA---TTTTA-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
droKik1	GGGA---ACTTT-----------------------GCATTATTTTCTTAAATTTTCTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG
droAna3	G-AT---TTTTT-GGTTGAAGGGGAAACCAACTCCGCTTTA------------TGTTTT-----CGTTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAGAAA-------TATCT----------T-GG
droBip1	------------------------------------------------------------------TTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG
dp4	---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG
droPer1	---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG
droWil1	G-TT---TTTTCTTGTT------------------GC----------------TGTTTTCGTAACGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATTAAATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGCATA-------T--TT----------TCAG
droVir3	C-----------------------------------------------------ACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATATAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-CA
droMoj3	C-GCTCGTTTTC-----------------------GTTT-------------TTGTTTG-----AGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATTTAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TACTT----------T-GG
droGri2	G-T--------------------------------------------------TTCTT------TGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTATGAGTATTTAAATTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-TG

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-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................................................TAGGAACTTCATACCTCG...................................................	18	12	0.17	0.00	0.17	0.00	0.00
.............................................................................................................................TAAGAACTCTATACCTAG...................................................	18	8	0.13	0.00	0.13	0.00	0.00
....................................................................GTTTTTTGGTCTTTCGAG............................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droSec1

G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.31	0.19	0.00	0.13
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	12	0.17	0.00	0.08	0.08
......................................................................................AGCAAGGTATAAAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.00	0.06
...................................................................................................................................CTCTATACCTCGCTGATGGCA..........................................	21	8	0.13	0.00	0.00	0.13
......................................................................................AGCAAGGTATGGAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.08
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.00	0.06
......................................................................................AGCGCGGTATCAAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.13

droYak2

G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.25	0.19	0.00	0.00	0.06	0.00
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	12	0.25	0.08	0.00	0.00	0.17	0.00
......................................................................................AGCAAGGTATAAAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.00	0.00	0.06	0.00
.............................................................................................................................TAGGAACTTTATACCGCGCT.................................................	20	16	0.06	0.00	0.00	0.00	0.06	0.00
.............................................................................................................................TAGGAACTTCATACCTCG...................................................	18	12	0.08	0.00	0.00	0.00	0.08	0.00
......................................................................................AGCAAGGTATGGAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.00	0.08	0.00
.............................................................................................................................TAGGAACTTCATACCTCGCT.................................................	20	12	0.08	0.00	0.00	0.00	0.08	0.00
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.00	0.00	0.06	0.00
......................................................................................AGCGCGGTATTAAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.00	0.13	0.00
......................................................................................AGCGAGGTATGAAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.00	0.08	0.00
......................................................................................AGCGCGGTATGCAGTTCCTACG......................................................................................	22	4	0.25	0.25	0.00	0.00	0.00	0.00
.............................................................................................................................TAGGAACTGTATACCGCGCT.................................................	20	8	0.13	0.00	0.13	0.00	0.00	0.00

droEre2

G-GA---TTTTT-----------------------GCAT-------------TCACTT------GGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAA-AA-------TATCT----------T-GC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................AGCACGGTATAAAGTTCCTCCG......................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
.............................................................................................................................TAGGAACTTCATACCTCGCTG................................................	21	8	0.13	0.00	0.13	0.00	0.00
.............................................................................................................................TAGGAACTTTATACCTCGCTCA...............................................	22	8	0.13	0.00	0.13	0.00	0.00
......................................................................................AGCGCGGTATCAAGTTCCTACG......................................................................................	22	8	0.13	0.13	0.00	0.00	0.00

droEug1

G-GA---TTTTT-----------------------GCAT-------------TTAGTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GC

Size

Hit Count

Total Norm

droBia1

G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG

Size

Hit Count

Total Norm

droTak1

G-GA---TTTTT-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG

Size

Hit Count

Total Norm

droEle1

A-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG

Size

Hit Count

Total Norm

droRho1

G-GA---TTTTT-----------------------GCAT-------------TTACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG

Size

Hit Count

Total Norm

droFic1

G-GA---TTTTA-----------------------GCAT-------------TTACTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAA--TGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG

Size

Hit Count

Total Norm

droKik1

GGGA---ACTTT-----------------------GCATTATTTTCTTAAATTTTCTT------TGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------C-GG

Size

Hit Count

Total Norm

droAna3

G-AT---TTTTT-GGTTGAAGGGGAAACCAACTCCGCTTTA------------TGTTTT-----CGTTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAGAAA-------TATCT----------T-GG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.25	0.00	0.00	0.25	0.00
......................................................................................AGCGAGGTATGAAGTTCCTACG......................................................................................	22	12	0.17	0.00	0.17	0.00	0.00
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	16	0.13	0.00	0.06	0.06	0.00
.......................................................................................................................................................AAAAACCAGGTxAGCAA-------TA.................	18	2	0.50	0.00	0.00	0.50	0.00
......................................................................................AGCACGGTATAAAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
......................................................................................AGCATGGTATAAAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
.............................................................................................................................TAGGAACTCCATACCTCGCTC................................................	21	8	0.13	0.00	0.00	0.13	0.00
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.08	0.00
......................................................................................AGCGTGGTATGAAGTTCCTACG......................................................................................	22	4	0.25	0.00	0.00	0.25	0.00
.............................................................................................................................TAGGAACTTAATACCTCGCT.................................................	20	12	0.08	0.00	0.00	0.08	0.00
......................................................................................AGCACGGTATACAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
.............................................................................................................................TAGGAACTTTATACCGCGCT.................................................	20	16	0.06	0.00	0.00	0.06	0.00

droBip1

------------------------------------------------------------------TTGATTTTAGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATGTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAA-------TATCT----------T-GG

Size

Hit Count

Total Norm

dp4

---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.........................................................................................................ACGAGTTTATTATATAAAC......................................................................	19	4	0.25	0.00	0.00	0.25	0.00
.............................................................................................................................TTGAAACTCTATACCTCGCTGA...............................................	22	8	0.13	0.00	0.13	0.00	0.00

droPer1

---------------------------------------------------------T------CGTTGTCTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATAATATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAAAAAAATACACACATCTTCTCCTCCGTT-CG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	16	0.19	0.00	0.00	0.00	0.19	0.00
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.13	0.00	0.00	0.00	0.13	0.00
.............................................................................................................................TAGGAACTCCATACCTCGCTC................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
.............................................................................................................................TAGGAACTTCATACCTCGCT.................................................	20	12	0.08	0.00	0.00	0.00	0.08	0.00
.............................................................................................................................AAGGAGCTCTATACCTCGCTG................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
......................................................................................AGCACGGTATAAAGTTCCT.........................................................................................	19	8	0.13	0.00	0.00	0.00	0.13	0.00
......................................................................................AGCGAGGTATGAAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.00	0.08	0.00
......................................................................................................................................................CAAAATCCAGGTAAAAAAC.........................	19	2	0.50	0.00	0.50	0.00	0.00	0.00
.............................................................................................................................TAGGAACTATATACCGCGCTG................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
......................................................................................AGCACGGTATAGAGTTCCT.........................................................................................	19	16	0.06	0.00	0.00	0.00	0.06	0.00
.............................................................................................................................TAGGAACTTTAGACCTCGCTGA...............................................	22	8	0.13	0.00	0.00	0.13	0.00	0.00
......................................................................................AGCACGGTATCGAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.00	0.13	0.00
.............................................................................................................................TAGGAACTTTATACCTCGCTC................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.08	0.00	0.00

droWil1

G-TT---TTTTCTTGTT------------------GC----------------TGTTTTCGTAACGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTTTATTAAATGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGCATA-------T--TT----------TCAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	12	0.83	0.00	0.08	0.75	0.00
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	12	0.42	0.00	0.00	0.42	0.00
......................................................................................AGCAAGGTATAAAGTTCCTACG......................................................................................	22	12	0.17	0.00	0.00	0.17	0.00
......................................................................................AGCGAGGTATGAAGTTCCTACG......................................................................................	22	8	0.25	0.00	0.00	0.25	0.00
......................................................................................AGCAAGGTATGGAGTTCCTACG......................................................................................	22	8	0.25	0.00	0.00	0.25	0.00
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
..TT---TTTTTTTGTT------------------GC----------------TGTTTTCG.....................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................................................TAGGAACTTAATACCTCG...................................................	18	10	0.10	0.00	0.00	0.00	0.10

droVir3

C-----------------------------------------------------ACTT------CGTTGTTTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATATAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-CA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................AGCACGGTATAGAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.06	0.00	0.00	0.00
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.06	0.00	0.06	0.00	0.00	0.00
.............................................................................................................................TAGGAACTTTATACCTxGCTGAT..............................................	22	8	0.13	0.00	0.13	0.00	0.00	0.00

droMoj3

C-GCTCGTTTTC-----------------------GTTT-------------TTGTTTG-----AGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTACGAGTATTTAAATTGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TACTT----------T-GG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................................AGCGCGGTATAAAGTTCCTACG......................................................................................	22	16	0.31	0.00	0.19	0.13	0.00
.............................................................................................................................TAGGAACTTCATACCTCGCT.................................................	20	12	0.17	0.00	0.17	0.00	0.00
......................................................................................AGCGCGGTATGGAGTTCCTACG......................................................................................	22	12	0.08	0.00	0.00	0.08	0.00
.............................................................................................................................TAGGAACTCCATACCGCGCTG................................................	21	8	0.13	0.00	0.00	0.13	0.00
..........................................................G-----AGTTGTGTTTTGGCATT.................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
......................................T-------------TTGTTTx-----AGTTGTGTTTTGC.....................................................................................................................	20	4	0.25	0.25	0.00	0.00	0.00
......................................................................................AGCACGGTTTAAAGTTCCT.........................................................................................	19	8	0.13	0.00	0.00	0.00	0.13
.......................................................................................GCGCGGTATGGAGTTCCTACG......................................................................................	21	12	0.08	0.00	0.00	0.08	0.00
......................................................................................AGCAAGGTATAAAGTTCCT.........................................................................................	19	16	0.06	0.00	0.06	0.00	0.00
........TTTT-----------------------GTTT-------------TTATTTG-----AGTT..............................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00
......................................................................................AGCGAGGTATGAAGTTCCTAC.......................................................................................	21	12	0.08	0.00	0.00	0.08	0.00

droGri2

G-T--------------------------------------------------TTCTT------TGTTGTGTTTTGGTCTTCCAAGAGCACGGTATGAAGTTCCTATGAGTATTTAAATTTAACGTAGGAACTCTATACCTCGCTGATGGCAAAAACCAGGTAGC--A-------TATTT----------T-TG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:14:49 EDT

dme-mir-276a-as

chr3L:10358328-10358425 -

Novel

antisense_to_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