sblock53072- Best orthologs

sblock53072	chr2R:20896404-20896491 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 20896418-20896439
   star strand at position 20896466-20896484
   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	chr2R:20896389-20896506 -		1	AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGT-GGTCCGT----CA---------------------------------GATTGTCTAAAGGCTAAAATTTCTT--------TGCGACTGACGAACGGCACATGAGAC--------GGGTGGAAATAGTTA----AGAAATTT
droSim1	chr2R:19348259-19348395 -	LASTZ	4	AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGT-GGTCCGT----CGGACGGTGGCA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGAC--------GGGTGGGAATAGTTA-----AAAATTT
droSec1	super_23:753669-753783 -	LASTZ	3	AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGT---------------------------GGCC---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGAC--------GGGTGGGAATAGTTA-----AAAATTT
droYak2	chr2R:20861288-20861417 -	LASTZ	3	AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGC-GGTCCGT----CGGACGGTGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTT--------TGCGGCTGACGAACGGCACATGGGAC--------GGGCGGGAATAGTTA----AGAAATTT
droEre2	scaffold_4845:22271655-22271786 -	LASTZ	3	AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGT-GGTCCGCCCGTCGGACGGCGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCT----------GCGAATGACGAACGGCACATGAGAC--------GGGCGGGAATAGTTA----GGAAATTT
droEug1	scf7180000409464:1425212-1425305 +	LASTZ	5	AC-AAGAAAAT--AACGACA-CGAGCG----------T--------------------------------------------AAGCGC------------------------------------GCGGGA---------------------CAGACCGTCG--------AATAGTCTT--------A--------GGGCCGACTCATGAGAC--------AAT--AGAAACTTTG----AGAGATTT
droBia1	scf7180000301754:5870493-5870638 -	LASTZ	4	AACACGAAAAT--AACGAAA-CGAACG----------C-------------------------------------GAAC-GCGAACGCTCGA---TTGTCATGAGT-TGTCCGT----CGGACGGTGGGG---------------------CGGACCGTCTGAAAGTCGGACAGTCTT--------AGGGACCGACGG-CGACACATGAGAC--------GGGCGAGAGACGTAC----AGAAATTT
droTak1	scf7180000415805:314121-314283 +	LASTZ	5	AACACGAAAAT--AACGAAA-CGAACG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGTTTGTCCGT----CGAACGGCGGGACGGACGGACAGACGGACAGAACAGACCGTCTTAAAGTCAGAGAGTCTT--------AGGGACTGACGGCCGACACATGAGAC--------AGGCGAGAAACGTAA----AGAAATTT
droEle1	scf7180000491107:285842-285979 +	LASTZ	5	AACACGAAAAT--AACGAAA-CGAACG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGC-AGTCCGT----TGGACAGTGGGACTAG-----------------CGAACAGCCTCAGAGACGAAAAGTCTG--------AGAGACT-------GACACATAAGAC--------AGGCGAGAAACGTAA----AGAAATTT
droRho1	scf7180000778233:36343-36477 -	LASTZ	5	AACACGAAAAT--AACGAAA-----------------------------------------------------------------CGAACGA---TTGTCATGAGC-TGTCCGT----CGGACAGTGGGACTAA-----------------CGGACCGCCTTACAGACGGAAAGTCTG--------AGGGACTGACGACCGACACATGAGAG--------GGGCAAGAAACGTAA----AGATATTT
droFic1	scf7180000453858:596758-596859 +	LASTZ	4	AACATGAAAAT--AACGAAA-CAAGCG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGT-TGTTTGT----CTTACGCTGGGA---------------------CACA----------------------------------------------CCACATGAGAC--------GGCCGAGAAGCGTAG----AG-AATTT
droKik1	scf7180000302366:1044859-1045012 -	LASTZ	4	AAAACACAAAA--TACGAAA-C----------------------------------------------GGCACGGCTTC-GCAAACGCTCT-CGATTGTCATGAGT-TGTCAGT----CGGC----GGGTCGGTTGGTCGGTTGGT-----GGTACCGCCAGCCAGACGAAAAGGCTG--------AGGGACT-------GACACATGAGAC--------AGGC-AGAAATGTAA----AGAAATTT
droAna3	scaffold_13266:12188779-12188871 -	LASTZ	5	AA-GAGACAAAGTAACGAAA-C----------------------------------------------------------------GAGCGG---CG-----------------------GACGGACGGACGAA-----------------CGGAC--------------------------------GGACTGACGG-CGACACATGAGAC--------TGGCGAGAAATGTAA----AGAAATTT
droBip1	scf7180000396547:292755-292809 +	LASTZ	5	CT-GAA-AGAT--AAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCAAGAGACACATGAGAC--------TGGCGAGAAATGTAA----AGAAATTT
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_2:2188699-2188812 -	LASTZ	1	TA-AAATAAAG--AACGAGC-CGAA------------------------------------------TGGCACGGCTTC-GCAAACGGTCGA---TTGTCATGACT-TGTCTGT----CAGTCATTCAGACGAA-----------------CGA-------------------------------------------------ACAGACGAC--------GGCAAAGAAATGTTA----AGAAATTT
droWil1	scaffold_180697:1942494-1942595 -	LASTZ	0	GA-AGGAAAAT--AAAAAA--CAAA---------------------------------------AAACGGCA-------------CGGTCGA---TTGTCA-----------------------GAGAGA---------------------CAGACTTTGG-----------------------------AGAGACAGCCACAGCAACAAAC--------TGTCAAGATATGTAA----AGAAATTT
droVir3	scaffold_12875:17133808-17133943 +	LASTZ	0	AG-AAGAAGAA--GGAGAAA--------------------------------------------AAACGGCACGACTTT-G----CAAACGA---TTGTCATGAGT-TGTCAGG----CAGACAG---------------------------------ACAGAGAGCGAGAGAGAGAG--------------AGGGGGAGAGAGAGAGAGACGGACAGTTGGACAGATAATGTAA----AGAAATTT
droMoj3	scaffold_6496:10865763-10865924 -	LASTZ	0	GA-GAGAGAGA--GAGAGAGAGAAAGAGAGTAAAGAGTAGAACTGCGGGAGGGAGTGTGGAAGAAAACGGCACGACTTT-GCG-ACAGACGA---TTGTCAGG-------------------CAGAGTGG---------------------CAGAG------------------------TGACAGAGACAGCGACAGACGGCGAGACAGTT--------GGACAGATAATGTA-----AGAAATTT
droGri2	scaffold_15245:16666095-16666207 +	LASTZ	0	AA-ACG---------------------------------------------------------------GCACGACTTTTGCG-ACTGACGA---TTGTCATGAGT-TGTCAGG----CAGGCAAACAGACAGA-----------------CAG------------------------------------ACAGGCGAACAGACAGACAGAC--------GGGCAGATAATGTAAAGAAAGAAATTT

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	AA-ACGAAA-ATAACGAAA---------------------CG--CTCGATTGTCATGAGTGG----TCCGTC---------------------------------AGATTGTCTAAAGGCTAAAATTTCTT--------TGCGACTGACGAACGGCACATGAGACGGGTGGAAATAGTTAAGAAATTT
droSim1	AA-ACGAAA-ATAACGAAA---------------------CG--CTCGATTGTCATGAGTGG----TCCGTCGGACGGTGGCA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGACGGGTGGGAATAGTTAA-AAATTT
droSec1	AA-ACGAAA-ATAACGAAA---------------------CG--CTCGATTGT--------------------------GGCC---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGACGGGTGGGAATAGTTAA-AAATTT
droYak2	AA-ACGAAA-ATAACGAAA---------------------CG--CTCGATTGTCATGAGCGG----TCCGTCGGACGGTGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTT--------TGCGGCTGACGAACGGCACATGGGACGGGCGGGAATAGTTAAGAAATTT
droEre2	AA-ACGAAA-ATAACGAAA---------------------CG--CTCGATTGTCATGAGTGGTCCGCCCGTCGGACGGCGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCT----------GCGAATGACGAACGGCACATGAGACGGGCGGGAATAGTTAGGAAATTT
droEug1	AC-AAGAAA-ATAACGACACGAGCG-----TAA------GCG--C--------------------------------GCGGGA---------------------CAGACCGTCG--------AATAGTCTT--------A--------GGGCCGACTCATGAGACAAT--AGAAACTTTGAGAGATTT
droBia1	AACACGAAA-ATAACGAAACGAACG-----CGAACGCGAACG--CTCGATTGTCATGAGTTG----TCCGTCGGACGGTGGGG---------------------CGGACCGTCTGAAAGTCGGACAGTCTT--------AGGGACCGACGG-CGACACATGAGACGGGCGAGAGACGTACAGAAATTT
droTak1	AACACGAAA-ATAACGAAACGAACG-----CAA------ACG--CTCGATTGTCATGAGTT---TGTCCGTCGAACGGCGGGACGGACGGACAGACGGACAGAACAGACCGTCTTAAAGTCAGAGAGTCTT--------AGGGACTGACGGCCGACACATGAGACAGGCGAGAAACGTAAAGAAATTT
droEle1	AACACGAAA-ATAACGAAACGAACG-----CAA------ACG--CTCGATTGTCATGAGCAG----TCCGTTGGACAGTGGGACTAG-----------------CGAACAGCCTCAGAGACGAAAAGTCTG--------AGAGACT-------GACACATAAGACAGGCGAGAAACGTAAAGAAATTT
droRho1	AACACGAAA-ATAACGAAACG-----------------------AACGATTGTCATGAGCTG----TCCGTCGGACAGTGGGACTAA-----------------CGGACCGCCTTACAGACGGAAAGTCTG--------AGGGACTGACGACCGACACATGAGAGGGGCAAGAAACGTAAAGATATTT
droFic1	AACATGAAA-ATAACGAAACAAGCG-----CAA------ACG--CTCGATTGTCATGAGTTG----TTTGTCTTACGCTGGGA---------------------CACAC----------------------------------------------CACATGAGACGGCCGAGAAGCGTAGAG-AATTT
droKik1	AAAACACAA-AATACGAAACGG----CACGGCTTCGCAAACGCTCTCGATTGTCATGAGTTG----TCAGTCGGC----GGGTCGGTTGGTCGGTTGGT-GGTACCGCCAG----CCAGACGAAAAGGCTG--------AGGGACT-------GACACATGAGACAGGC-AGAAATGTAAAGAAATTT
droAna3	AAGAGACAAAGTAACGAAACGAGC-----------------------GG----------------------CGGACGGACGGACGAA-----------------CGGAC--------------------------------GGACTGACGG-CGACACATGAGACTGGCGAGAAATGTAAAGAAATTT
droBip1	CT-GA-AAG-ATAAA-----------------------------------------------------------------------------------------------------------------------------------GTCAAGAGACACATGAGACTGGCGAGAAATGTAAAGAAATTT
droPer1	TA-AAATAA-AGAACGAGCCGAATGGCACGGCTTCGCAAACG--GTCGATTGTCATGACTTG----TCTGTCAGTCATTCAGACGAA-----------------CGA-------------------------------------------------ACAGACGACGGCAAAGAAATGTTAAGAAATTT

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															None
UNAFold Image															None

Small RNA-seq read pileup

Species

Alignment

droSim1

AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGT-GGTCCGT----CGGACGGTGGCA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGAC--------GGGTGGGAATAGTTA-----AAAATTT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................................................................................................GATAAAAAGTCGTTGCGA................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..................AA-----------------------------------------------------------------CGCTCGA---TTGTCATGA...............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................ACTGAGCGACTGACGAACGG.............................................	20	1	1.00	0.00	0.00	1.00	0.00

droSec1

AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGT---------------------------GGCC---------------------CAGACTGTCTAAAGGCTAAAAAGTCTTTGCGACTGAGCGACTGACGAACGGCACATGAGAC--------GGGTGGGAATAGTTA-----AAAATTT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................GAAA-----------------------------------------------------------------CGATCGA---TTGT---------------------------TGC......................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGC-GGTCCGT----CGGACGGTGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCTT--------TGCGGCTGACGAACGGCACATGGGAC--------GGGCGGGAATAGTTA----AGAAATTT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................CGGACGGTGGGA---------------------CAGACTGT........................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AA-ACGAAAAT--AACGAAA-----------------------------------------------------------------CGCTCGA---TTGTCATGAGT-GGTCCGCCCGTCGGACGGCGGGA---------------------CAGACTGTCTAAAGGCTAAAAAGTCT----------GCGAATGACGAACGGCACATGAGAC--------GGGCGGGAATAGTTA----GGAAATTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................................................TGTCTAAAGGCTAAAAAGTC.......................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droEug1

AC-AAGAAAAT--AACGACA-CGAGCG----------T--------------------------------------------AAGCGC------------------------------------GCGGGA---------------------CAGACCGTCG--------AATAGTCTT--------A--------GGGCCGACTCATGAGAC--------AAT--AGAAACTTTG----AGAGATTT

Size

Hit Count

Total Norm

droBia1

AACACGAAAAT--AACGAAA-CGAACG----------C-------------------------------------GAAC-GCGAACGCTCGA---TTGTCATGAGT-TGTCCGT----CGGACGGTGGGG---------------------CGGACCGTCTGAAAGTCGGACAGTCTT--------AGGGACCGACGG-CGACACATGAGAC--------GGGCGAGAGACGTAC----AGAAATTT

Size

Hit Count

Total Norm

droTak1

AACACGAAAAT--AACGAAA-CGAACG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGTTTGTCCGT----CGAACGGCGGGACGGACGGACAGACGGACAGAACAGACCGTCTTAAAGTCAGAGAGTCTT--------AGGGACTGACGGCCGACACATGAGAC--------AGGCGAGAAACGTAA----AGAAATTT

Size

Hit Count

Total Norm

droEle1

AACACGAAAAT--AACGAAA-CGAACG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGC-AGTCCGT----TGGACAGTGGGACTAG-----------------CGAACAGCCTCAGAGACGAAAAGTCTG--------AGAGACT-------GACACATAAGAC--------AGGCGAGAAACGTAA----AGAAATTT

Size

Hit Count

Total Norm

droRho1

AACACGAAAAT--AACGAAA-----------------------------------------------------------------CGAACGA---TTGTCATGAGC-TGTCCGT----CGGACAGTGGGACTAA-----------------CGGACCGCCTTACAGACGGAAAGTCTG--------AGGGACTGACGACCGACACATGAGAG--------GGGCAAGAAACGTAA----AGATATTT

Size

Hit Count

Total Norm

droFic1

AACATGAAAAT--AACGAAA-CAAGCG----------C--------------------------------------------AAACGCTCGA---TTGTCATGAGT-TGTTTGT----CTTACGCTGGGA---------------------CACA----------------------------------------------CCACATGAGAC--------GGCCGAGAAGCGTAG----AG-AATTT

Size

Hit Count

Total Norm

droKik1

AAAACACAAAA--TACGAAA-C----------------------------------------------GGCACGGCTTC-GCAAACGCTCT-CGATTGTCATGAGT-TGTCAGT----CGGC----GGGTCGGTTGGTCGGTTGGT-----GGTACCGCCAGCCAGACGAAAAGGCTG--------AGGGACT-------GACACATGAGAC--------AGGC-AGAAATGTAA----AGAAATTT

Size

Hit Count

Total Norm

droAna3

AA-GAGACAAAGTAACGAAA-C----------------------------------------------------------------GAGCGG---CG-----------------------GACGGACGGACGAA-----------------CGGAC--------------------------------GGACTGACGG-CGACACATGAGAC--------TGGCGAGAAATGTAA----AGAAATTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................................................................................GA-----------------CTGAC--------------------------------GGACTGACGG-C...............................................	18	2	4.00	0.00	4.00	0.00	0.00
............................................................................................................................GACGGACGGA-----------------CGGAC--------------------------------GGC........................................................	18	4	0.75	0.00	0.75	0.00	0.00
........................................................................................................................GACGGACGGACGGA-----------------CGGC............................................................................................	18	4	0.75	0.00	0.75	0.00	0.00
....................................................................................................................................GA-----------------CGGAC--------------------------------GGACGGACGG-C...............................................	18	4	0.75	0.00	0.75	0.00	0.00
................................................................................................................................GACGxA-----------------CGGAC--------------------------------GGACGGACG..................................................	19	2	1.00	1.00	0.00	0.00	0.00
........................................................................................................................GACxGACGGACGGA-----------------CGGAC--------------------------------G..........................................................	19	2	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................GGACGGACGGA-----------------CCGAC--------------------------------GGAC.......................................................	20	8	0.13	0.00	0.13	0.00	0.00
............................................................................................................................GACAGACGGA-----------------CGGAC--------------------------------GGA........................................................	18	51	0.02	0.00	0.02	0.00	0.00
.........................................................................................................................ACAGACGGACGGA-----------------CGGAC--------------------------------GGA........................................................	21	8	0.13	0.13	0.00	0.00	0.00
........................................................................................................................GACAGACGGACAAA-----------------CGGAC--------------------------------...........................................................	19	41	0.02	0.00	0.02	0.00	0.00
........................................................................................................................GACAGACGGACGAT-----------------CGGAC--------------------------------GG.........................................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................................G-----------------------GACGGACCGACGGA-----------------CGGAC--------------------------------GGA........................................................	23	2	0.50	0.00	0.50	0.00	0.00
................................................................................................G-----------------------GACGGACGGACGGA-----------------CGGAC--------------------------------GT.........................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................GACGGACGGACGGA-----------------CGGAC--------------------------------...........................................................	19	21	0.05	0.00	0.05	0.00	0.00
....................................................................................................................................GA-----------------CTGAC--------------------------------GGACTGACGG-................................................	17	17	0.06	0.00	0.00	0.06	0.00
........................................................................................................................GACAGACGGACGGA-----------------CGGA............................................................................................	18	51	0.02	0.00	0.02	0.00	0.00
................................................................................................................................GACGGA-----------------CGGAC--------------------------------GGACGGAC...................................................	19	21	0.05	0.00	0.05	0.00	0.00
............................................................................................................................GACGGACGGA-----------------CGGAC--------------------------------GGAC.......................................................	19	21	0.05	0.00	0.05	0.00	0.00
...................................................................................................................................GGA-----------------CTGAC--------------------------------GGACTGACGG-................................................	18	7	0.14	0.00	0.14	0.00	0.00
..............ATGAAG-C----------------------------------------------------------------GAGCGG---CG-----------------------GAC............................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................AAG---CG-----------------------GACGGACGGACGA..................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................GGACAGACGGA-----------------CGGAC--------------------------------GGAC.......................................................	20	21	0.05	0.00	0.05	0.00	0.00
...........................................................................................................................GGACCGACGAA-----------------CAGAC--------------------------------GGAC.......................................................	20	8	0.13	0.00	0.13	0.00	0.00
...........................................................................................................................GGACAGACGAA-----------------CAGAC--------------------------------GGAC.......................................................	20	20	0.05	0.00	0.05	0.00	0.00
................................................................................................G-----------------------GACGGACGGACCGA-----------------CGGAC--------------------------------...........................................................	20	8	0.13	0.00	0.13	0.00	0.00
................................................................................................G-----------------------GACAGACGGACGGA-----------------CGGAC--------------------------------...........................................................	20	21	0.05	0.00	0.05	0.00	0.00
..........................................................................................GA---CG-----------------------GACGGACGGACGGA-----------------C...............................................................................................	19	21	0.05	0.00	0.05	0.00	0.00

droBip1

CT-GAA-AGAT--AAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCAAGAGACACATGAGAC--------TGGCGAGAAATGTAA----AGAAATTT

Size

Hit Count

Total Norm

dp4

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TA-AAATAAAG--AACGAGC-CGAA------------------------------------------TGGCACGGCTTC-GCAAACGGTCGA---TTGTCATGACT-TGTCTGT----CAGTCATTCAGACGAA-----------------CGA-------------------------------------------------ACAGACGAC--------GGCAAAGAAATGTTA----AGAAATTT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................................................................................................................GACGAA-----------------CGA-------------------------------------------------ACAGCCGCC--------...........................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
..........................................................................................................................CATTCAGACGAA-----------------CGA-------------------------------------------------ACAGAC......................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................CGA---TTATCATCACT-TGTCTGT----.................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

GA-AGGAAAAT--AAAAAA--CAAA---------------------------------------AAACGGCA-------------CGGTCGA---TTGTCA-----------------------GAGAGA---------------------CAGACTTTGG-----------------------------AGAGACAGCCACAGCAACAAAC--------TGTCAAGATATGTAA----AGAAATTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........A--AAAAAA--CAAA---------------------------------------AAACGGAA-------------C.................................................................................................................................................................	20	2	1.50	0.00	0.00	0.00	1.50
.............................................................................................................................CGAGA---------------------CAGAGTTTGG-----------------------------AGA......................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................GA---------------------CAGACTTTGG-----------------------------AGAGACAGCCACAGC..........................................	27	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................AGAGACAGCCACAGCAAC.......................................	18	1	1.00	0.00	1.00	0.00	0.00
......AAGAC--AAAAAA--CAAA---------------------------------------AAA....................................................................................................................................................................................	18	39	0.03	0.00	0.03	0.00	0.00
.A-AGGAAAAT--AAAAAA--AAAC---------------------------------------.......................................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00
......AAAAG--AAAAAA--CAAG---------------------------------------AAA....................................................................................................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
...........................................................................................................................................................CTTTGG-----------------------------AGAGACAGCCACAGC..........................................	21	1	1.00	1.00	0.00	0.00	0.00
...............AAAA--CAAA---------------------------------------AAACGGAA-------------CT................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.............AAAAAA--CAAA---------------------------------------AGACGGCG-------------..................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................GACAGTGACAGCAACAAAC--------T..........................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................................................GGTCGA---TTGTCA-----------------------GAGAGA---------------------CA..............................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................AA----AAAAGTTT	21	3	0.33	0.00	0.33	0.00	0.00

droVir3

AG-AAGAAGAA--GGAGAAA--------------------------------------------AAACGGCACGACTTT-G----CAAACGA---TTGTCATGAGT-TGTCAGG----CAGACAG---------------------------------ACAGAGAGCGAGAGAGAGAG--------------AGGGGGAGAGAGAGAGAGACGGACAGTTGGACAGATAATGTAA----AGAAATTT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................................................GG----CAGACAG---------------------------------ACAGTGGG.................................................................................	17	2	2.50	0.00	2.50	0.00	0.00	0.00
AG-AAGAAGAA--GAAGAAG--------------------------------------------AA.....................................................................................................................................................................................	19	16	0.13	0.13	0.00	0.00	0.00	0.00
................................................................................................................GG----CAGACAG---------------------------------ACAGTGGGC................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
......................................................................................................................CAGCCAG---------------------------------ACAGAGAGAGAGAG...........................................................................	21	9	0.11	0.11	0.00	0.00	0.00	0.00
............................................................................................................................................................................AGAGAG--------------GGCGGGAGAGAGAGAGAG.....................................	24	25	0.04	0.00	0.00	0.04	0.00	0.00
...AAGAAGAA--GGAGAAG--------------------------------------------AAG....................................................................................................................................................................................	18	11	0.09	0.00	0.00	0.09	0.00	0.00
......................................................................................................................................................................GGGGAGAGAGAG--------------AGGGGGA................................................	19	12	0.08	0.08	0.00	0.00	0.00	0.00
............................................................................................................................G---------------------------------ACAGAGAGCGAGAGAGAGAG--------------AGC....................................................	24	47	0.02	0.00	0.00	0.02	0.00	0.00
.........................................................................................................................................................................GAGGGAGGG--------------AGGGGGAG...............................................	17	19	0.05	0.00	0.05	0.00	0.00	0.00
.G-AAGAAGAA--GAAGAAA--------------------------------------------AGA....................................................................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
......................................................................................................................CAGACAG---------------------------------ACAGAGAGGGAC.............................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................AGACAG--------------AGGGGCAGAGAGAGAG.......................................	22	9	0.11	0.11	0.00	0.00	0.00	0.00
..................................................................................................................................................................AGAGCGCGAGAGAGAG--------------AG.....................................................	18	41	0.02	0.00	0.02	0.00	0.00	0.00
................................................................................................................................................................AGAGAGCGAGATAGCGAG--------------A......................................................	19	48	0.02	0.02	0.00	0.00	0.00	0.00
...........................................................................................................................AG---------------------------------ACAAAGAGCGAGAGAGTGA......................................................................	21	6	0.17	0.17	0.00	0.00	0.00	0.00
..............................................................................................................CTGG----CAGACAG---------------------------------ACAGT....................................................................................	16	4	0.25	0.00	0.25	0.00	0.00	0.00
..............................................................................................................CTGG----CAGACAG---------------------------------ACAGTG...................................................................................	17	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................AGAGAA--------------AGCGGGAGAGAGAGA........................................	21	38	0.03	0.03	0.00	0.00	0.00	0.00
............................................................................................................................................................................AGAGAG--------------AGTGGGAGAGAGAGTG.......................................	22	38	0.03	0.03	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GAGAGAGAGAG--------------AGGGGGG................................................	18	20	0.05	0.05	0.00	0.00	0.00	0.00
................................................................................................................GG----CAGACAG---------------------------------ACAGCGGGC................................................................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
......................................................................................................................................................................CGAGAGAGAGCG--------------TGGG...................................................	16	20	0.05	0.00	0.05	0.00	0.00	0.00
..............................................................................................................CTGG----CAGACAG---------------------------------ACAGTGA..................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................AGAGAGAGAG--------------AGTGGGAGAGAGAGA........................................	25	9	0.11	0.11	0.00	0.00	0.00	0.00
...........................................................................................................................................................................GAGAGTG--------------AGCGGGAGAGAGA..........................................	20	36	0.03	0.03	0.00	0.00	0.00	0.00
............................................................................................................................................................................AGAGTG--------------AGCGGGAGAGAGAGAGA......................................	23	26	0.04	0.04	0.00	0.00	0.00	0.00
......................................................................................................................................................................TGAGATAGAGAG--------------AGGGGGAGA..............................................	21	6	0.17	0.17	0.00	0.00	0.00	0.00
................................................................................................................................................................AGAGCGCGAGAGAGAGAG--------------.......................................................	18	41	0.02	0.00	0.02	0.00	0.00	0.00

droMoj3

GA-GAGAGAGA--GAGAGAGAGAAAGAGAGTAAAGAGTAGAACTGCGGGAGGGAGTGTGGAAGAAAACGGCACGACTTT-GCG-ACAGACGA---TTGTCAGG-------------------CAGAGTGG---------------------CAGAG------------------------TGACAGAGACAGCGACAGACGGCGAGACAGTT--------GGACAGATAATGTA-----AGAAATTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......GAGA--GAGAGAGAGAAAGA............................................................................................................................................................................................................................	18	46	0.04	0.02	0.00	0.02	0.00
.........GA--GAGAGAGAGAAAGAGA..........................................................................................................................................................................................................................	18	40	0.05	0.05	0.00	0.00	0.00
.....GAGAGA--TAGAGAGAGAAAGA............................................................................................................................................................................................................................	20	49	0.02	0.00	0.00	0.00	0.02
.........................................................................................................................................................GAG------------------------GGACAGAGGCAGCGA....................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....GAGAGA--GAGAGAGAGAAAGA............................................................................................................................................................................................................................	20	36	0.03	0.03	0.00	0.00	0.00
...GAGAGAGC--GAGAGAGAGAAAG.............................................................................................................................................................................................................................	21	52	0.02	0.00	0.00	0.00	0.02
....AGAGAGC--GAGAGAGAGAAAGA............................................................................................................................................................................................................................	21	45	0.02	0.02	0.00	0.00	0.00
.....................................................................................................................................................................................GACAGACACAGCGATAGA................................................	18	5	0.20	0.00	0.00	0.20	0.00
....AGAGAGA--GGGAGAGAGAAAGCGAGT........................................................................................................................................................................................................................	25	4	0.25	0.25	0.00	0.00	0.00
.....GAGAGA--GTGAGAGAGAAAGAGA..........................................................................................................................................................................................................................	22	37	0.03	0.00	0.00	0.03	0.00
...........................................................................................................................AGAGTGA---------------------CAGAG------------------------TGACAGAGTCA........................................................	23	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................GA-------------------CAGAGTGA---------------------CAGAG------------------------TGACAGA............................................................	22	1	1.00	1.00	0.00	0.00	0.00
............................................GCGGGAGGGAGTGTGGAAG........................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...GAGAGAGA--GAGAGGGAGAAAGA............................................................................................................................................................................................................................	22	48	0.02	0.02	0.00	0.00	0.00

droGri2

AA-ACG---------------------------------------------------------------GCACGACTTTTGCG-ACTGACGA---TTGTCATGAGT-TGTCAGG----CAGGCAAACAGACAGA-----------------CAG------------------------------------ACAGGCGAACAGACAGACAGAC--------GGGCAGATAATGTAAAGAAAGAAATTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:35 EDT

sblock53072

chr2R:20896404-20896491 -

Candidate

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