sblock222077- Best orthologs

sblock222077	chr3RHet:576709-576818 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 576781-576802
   star strand at position 576728-576746
   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	chr3RHet:576694-576833 +		1	ATTTGTTTTCGGTTGTT-TT------CTTATTTTCGTATATAAAATTATAAATGGGTT-------------------------------------------------------ACAT--------AAT--GTTA-------------------------------------------------TATAATGC-----------TAC---------ATAAATGTATAAT-----------------------------ATGTAA----CCCATTTATAATTTTAT------ATACGAAA--ATACTTAT--C-CTCTGAGG-GAGTGA
droSim1	chrU:9556601-9556718 -	LASTZ	0	ATTTGTTTTCGGTTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTGC-------------GATGATA---------------------------------------------------------------------------------------------------------------------------
droSec1	super_7722:503-638 -	LASTZ	0	ATTTGTTTTCGATTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTAC-------------TATAATATAAAAT-----ATGG------------------------TATTATTT----------------------------------------------------------------------------
droYak2	chr3R:6981890-6982030 -	LASTZ	0	ATTATTTTTTGCTTGTT-TT------CTGAATTTTTTATATAAAACAGTTAGTGGATT-------------------------------------------------------TAGTGTAA-AAATTT--TTGATAGGACAAGAAAAATTATAAGAACA-------ATAACTAAAATTATTAT-------------AGTTGCATAAAAT-----GTGG------------------------TATTATTT-----------------------------------------------------------TC---T---------GA
droEre2	scaffold_4684:13326-13445 +	LASTZ	0	ATTTGTTTTCGGTTGTT-TT------CTTTTTTTCGTATATAAAATTATAAATGGGTT-------------------------------------------------------ACAT--------ATT--TTGATAATCCGTATAGTATAATAAG----------------------TTTTAT-------------GATAATATAAAAT-----ATGA------------------------TATTATTT-----------------------------------------------------------T-----------TTTGA
droEug1	scf7180000409434:14602-14733 +	LASTZ	0	ATTATTTTTTGATTGTT-TT------CTAAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTATAA-ACAATT--TT-A--------------TAATATGATCATTTTATGATAACTACTAATATTAT-------TAT---TATATTTTAAAAT-----GTC--------------------------ATTATGT-----------------------------------------------------------TC---T-----------
droBia1	scf7180000300680:23-161 -	LASTZ	0	ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGATAAGTGGATT-------------------------------------------------------AAGTGAGAAACAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTA---T-------------AATCACTTAA-GT-----GTAGA-----------------------TTTTATTT-----------------------------------------------------------TC---T---------GA
droTak1	scf7180000415873:9535-9670 +	LASTZ	0	TTCTGTACTCTTTTGTG-TATCTTCCTTTGGTTTTACATATTTTACAATAAGTTTTCT-------------------------------------------------------TGGTATGC-TCTT-AAATTTAT---------------------ACA-------ATAACAAAGGTTGTTAA-------AGT---GATTATTTGGAATACATTATAA------------------------TATTTTGT----------------------------------------------------------------------GTGTGA
droEle1	scf7180000491055:5756-5897 +	LASTZ	0	ATTATTTTTTGCTTGTC-TT------CTTAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTGATA-AAATTG--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTATAATTATTAT-------------AATTACGTAAAGA-----GTGG------------------------TATTATCA-----------------------------------------------------------G-----------ATGAA
droRho1	scf7180000762627:316-437 -	LASTZ	0	ATTATTTTTTGCTTGTT-TT------TTAAATTTTGTATATGAAAAGGTAAGTGGGTT-------------------------------------------------------TAGTGTAC-ACATTT--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTACAATTATTAT-------------AATTACAAAA-----------------------------------------------------------------------------------------------------------------------A
droFic1	scf7180000454094:3746-3886 -	LASTZ	0	ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGGTGAGTGGATT-------------------------------------------------------TAGTGTAA-AAAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTATTAT-------------AATTACGTAAAGT-----GTAG------------------------TGTTATTT-----------------------------------------------------------TC---T---------GA
droKik1	scf7180000301889:2472-2603 -	LASTZ	0	ATAATGTTTTGATTGTT-TT------CTGAATTTTGTATATAAAAGAGTAAGTGGCTT-------------------------------------------------------TTTTTTTA-TTTATTTATTTAT------------TTATTAAGAA---------------------------------T-----------AGC---------AAATATCTGCCAT-----------------------------TTTAAATCCATATCCT-----------------------------------TTC-CTCAGACC-GGATAA
droAna3	scaffold_13079:304244-304384 -	LASTZ	0	ATTGTCTTTTACTTGTT-TT------CTTAGTTTTTTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAAAGTAA-AGAATT--TTGAAAGGACAAATAAAATAATAATAACA-------ATAACTAAAATTATTAT-------------AATTATATAATTT-----GTGG------------------------AATTATTT-----------------------------------------------------------TC---T---------GA
droBip1	scf7180000394965:14885-15019 +	LASTZ	0	GTTAGATTTTTATTTTATTT------TATTTTTTTATATTTTTTTTTGTATATTTTTT-------------------------------------------------------ATAT--------AAA--TATA-------------------------------------------------TATAATTT-----------TAT---------ATATATATAT-------ATATATGTATT------------------------------TTTTTTATTGTGTACATGTATGTATCTATATTTAT--TC---T---------TT
dp4	Unknown_singleton_1998:3876-4037 -	LASTZ	0	ACTTGTGTTTTGTTGTC-GC------ATTAATGGGTTACAGATCTCTGTTTACA---CCCGTGTAGTCATAAATTGTCTACTTTATGTGATTTCTTTAGAGAATATATAGATCAAATATG----------------------------------------------------------------------T-----------AAC---------AAATATGTAACAC-----------------------------ATGTAA----CACATCCATACATATAT------AGACGT--------------------------AAATA
droPer1	super_28:207610-207724 -	LASTZ	0	TATTTTC------AGTT-TT------CGGATTAAAGCTAATGAAAGTGTATGAAAATT-------------------------------------------------------AAATTATT----------AAA---------------------------------------------------------TTGATT---AAAAT---------AAATATACATAAT-----------------------------ATGTAA----TATATTTA------ATT------AAATAAAT--AAAT-----------------ATTAAT
droWil1	scaffold_181089:9808790-9808940 +	LASTZ	0	TTTTGTTTTTATTTTTA-TA------TATATTTATATATATATATATATATATTGTAT-------------------------------------------------------ATAT--------AAT--TTGT----------------------TCT-------GTTTTTTTTTTTT---T-------------ATTTACTTTT-GT-----TTAAATT-----------------------CATTTCCCTATTAAGTTA----CACACACATATGTATAT------GTATATAT--ATAC-----------------ATATAC
droVir3	scaffold_12723:5508367-5508489 +	LASTZ	0	TGTGCTTGTATTTAAAG-AT------TTAAAATTTTTA-------------TTATAAT-------------------------------------------------------ATAT--------ATT--GTTATTAAGAGCTAAATAT-----------------------------------------------------------------AAAAATATATAAGATAA-----------A-GATACCGTTATA----AATATAGAAACA-----------------------------------CTA-ACGAAGAT-ATATAT
droMoj3	scaffold_6541:2286599-2286731 -	LASTZ	0	ATTTTTGTATAGTAGTT-TTAG---TCTAGATTTGGT---GACAATTGAAGACGGTTT---------------------A-------------------------------TTAAATATAA--------------------------------------------------------------AATCAAGCTTTATG--------------------AATATAAAACCAAA-----------C-AACACTGTTATT----ATTTCACTATAA-----------------------------------TTA-ATCAACCTTGGAGGG
droGri2	scaffold_6998:1526-1648 -	LASTZ	0	ATTTGTGTGTGTGTGTG-TG------TATATATACATACATACACACAGATATATGTT-------------------------------------------------------ATGT--------ATA--TGTA-------------------------------------------------TATATTTT-----------TAT---------AAATATGTAT-------ATATATATATG------------------------------TATATATATAT------ATATACAT--ATAT-----------------ATATAT

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	ATTTGTTTTCGGTTGTTTTCTTATTTTCGTATATAAAATTATAAATGGGTTACATAATGTTATATAATGCTACATAAATGTATAATATGTAACCCATTTATAATTTTATATACGAAAATACTTATCCTCTGAGGGAGTGA

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

ATTTGTTTTCGGTTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTGC-------------GATGATA---------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..TTGTTTTCAGTTATT-TT------C...........................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00

droSec1

ATTTGTTTTCGATTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTAC-------------TATAATATAAAAT-----ATGG------------------------TATTATTT----------------------------------------------------------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................TAAATGGATT-------------------------------------------------------TTGGGTTA-CAT.........................................................................................................................................................................................................	21	35	0.03	0.03	0.00	0.00
............................................ATTATAAATGGATT-------------------------------------------------------TTGGGTT..............................................................................................................................................................................................................	21	35	0.03	0.03	0.00	0.00
......................................................................................................................................................ATAAGAACA-------ATAATAATAAGT....................................................................................................................................................	21	33	0.03	0.00	0.03	0.00
..............................................TATAAATGGATT-------------------------------------------------------TTGGGTTA-C...........................................................................................................................................................................................................	21	35	0.03	0.03	0.00	0.00

droYak2

ATTATTTTTTGCTTGTT-TT------CTGAATTTTTTATATAAAACAGTTAGTGGATT-------------------------------------------------------TAGTGTAA-AAATTT--TTGATAGGACAAGAAAAATTATAAGAACA-------ATAACTAAAATTATTAT-------------AGTTGCATAAAAT-----GTGG------------------------TATTATTT-----------------------------------------------------------TC---T---------GA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................................................CATTATAAGAACA-------ATAGCT..........................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33	0.00
.............................AATTCTTTAxATAAAACAGT.....................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

ATTTGTTTTCGGTTGTT-TT------CTTTTTTTCGTATATAAAATTATAAATGGGTT-------------------------------------------------------ACAT--------ATT--TTGATAATCCGTATAGTATAATAAG----------------------TTTTAT-------------GATAATATAAAAT-----ATGA------------------------TATTATTT-----------------------------------------------------------T-----------TTTGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......TTTTGTTGTT-TT------CTTTTT......................................................................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
.....................................................................................................................................................................................................................................................TATTT-----------------------------------------------------------A-----------TTTGA	18	4	0.25	0.00	0.00	0.00	0.25

droEug1

ATTATTTTTTGATTGTT-TT------CTAAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTATAA-ACAATT--TT-A--------------TAATATGATCATTTTATGATAACTACTAATATTAT-------TAT---TATATTTTAAAAT-----GTC--------------------------ATTATGT-----------------------------------------------------------TC---T-----------

Size

Hit Count

Total Norm

droBia1

ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGATAAGTGGATT-------------------------------------------------------AAGTGAGAAACAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTA---T-------------AATCACTTAA-GT-----GTAGA-----------------------TTTTATTT-----------------------------------------------------------TC---T---------GA

Size

Hit Count

Total Norm

droTak1

TTCTGTACTCTTTTGTG-TATCTTCCTTTGGTTTTACATATTTTACAATAAGTTTTCT-------------------------------------------------------TGGTATGC-TCTT-AAATTTAT---------------------ACA-------ATAACAAAGGTTGTTAA-------AGT---GATTATTTGGAATACATTATAA------------------------TATTTTGT----------------------------------------------------------------------GTGTGA

Size

Hit Count

Total Norm

droEle1

ATTATTTTTTGCTTGTC-TT------CTTAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTGATA-AAATTG--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTATAATTATTAT-------------AATTACGTAAAGA-----GTGG------------------------TATTATCA-----------------------------------------------------------G-----------ATGAA

Size

Hit Count

Total Norm

droRho1

ATTATTTTTTGCTTGTT-TT------TTAAATTTTGTATATGAAAAGGTAAGTGGGTT-------------------------------------------------------TAGTGTAC-ACATTT--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTACAATTATTAT-------------AATTACAAAA-----------------------------------------------------------------------------------------------------------------------A

Size

Hit Count

Total Norm

droFic1

ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGGTGAGTGGATT-------------------------------------------------------TAGTGTAA-AAAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTATTAT-------------AATTACGTAAAGT-----GTAG------------------------TGTTATTT-----------------------------------------------------------TC---T---------GA

Size

Hit Count

Total Norm

droKik1

ATAATGTTTTGATTGTT-TT------CTGAATTTTGTATATAAAAGAGTAAGTGGCTT-------------------------------------------------------TTTTTTTA-TTTATTTATTTAT------------TTATTAAGAA---------------------------------T-----------AGC---------AAATATCTGCCAT-----------------------------TTTAAATCCATATCCT-----------------------------------TTC-CTCAGACC-GGATAA

Size

Hit Count

Total Norm

droAna3

ATTGTCTTTTACTTGTT-TT------CTTAGTTTTTTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAAAGTAA-AGAATT--TTGAAAGGACAAATAAAATAATAATAACA-------ATAACTAAAATTATTAT-------------AATTATATAATTT-----GTGG------------------------AATTATTT-----------------------------------------------------------TC---T---------GA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................AAAGGGAAGTGCATT-------------------------------------------------------T....................................................................................................................................................................................................................	16	5	0.20	0.00	0.00	0.20	0.00
...................................................GTGGATT-------------------------------------------------------TGAAGxAA-AGAA........................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.......................................................................................................................AA-AGAATT--TTGAAAAGAGA.........................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00

droBip1

GTTAGATTTTTATTTTATTT------TATTTTTTTATATTTTTTTTTGTATATTTTTT-------------------------------------------------------ATAT--------AAA--TATA-------------------------------------------------TATAATTT-----------TAT---------ATATATATAT-------ATATATGTATT------------------------------TTTTTTATTGTGTACATGTATGTATCTATATTTAT--TC---T---------TT

Size

Hit Count

Total Norm

dp4

ACTTGTGTTTTGTTGTC-GC------ATTAATGGGTTACAGATCTCTGTTTACA---CCCGTGTAGTCATAAATTGTCTACTTTATGTGATTTCTTTAGAGAATATATAGATCAAATATG----------------------------------------------------------------------T-----------AAC---------AAATATGTAACAC-----------------------------ATGTAA----CACATCCATACATATAT------AGACGT--------------------------AAATA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........TGTTGTC-GT------ATTAATGGGTTACA..............................................................................................................................................................................................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
............TTGTC-GT------ATTAATGGGTTACAGATC..........................................................................................................................................................................................................................................................................................	25	1	4.00	4.00	0.00	0.00	0.00
..........TGTTGTC-GT------AATAATGGGTTACAGA............................................................................................................................................................................................................................................................................................	25	1	3.00	3.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAATGGGTTACAGA............................................................................................................................................................................................................................................................................................	25	1	3.00	3.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAATGGGTTAC...............................................................................................................................................................................................................................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
........TTTGTTGTC-GT------ATTAATGGG...................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..................................................TACA---CCAGTGCAGTCATAAA.............................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............TC-GT------ATTGATGGGTTACAG.............................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAATGGGTTA................................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...TGTGTTTTGTTGTC-GT------ATTAATGGGT..................................................................................................................................................................................................................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTA-GT------ATTAATGGGTTACAGATC..........................................................................................................................................................................................................................................................................................	27	1	1.00	1.00	0.00	0.00	0.00
..TTGTGTTTTGTTGTC-GT------ATTA........................................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...........GTTGTC-GT------ATTAATGGGTTACA..............................................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTGATGGGTTAC...............................................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......TTTTGTTGTC-GT------ATTAATGGG...................................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...........GTTGTC-GT------ATTAATGGGTTAC...............................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
......GTTTTGTTGTC-GT------ATTAATGG....................................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..................................................TACA---CCAGTGTAGTCATAACTTGTCT.......................................................................................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.............TGTC-GT------ATTAATGGGTTTCAGATC..........................................................................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
............TTGTC-GT------ATTAATGGGTTACAGA............................................................................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............GTC-GT------ATTAATGGGTTACAGATCTCTGT.....................................................................................................................................................................................................................................................................................	28	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAATGGGTTACAGATC..........................................................................................................................................................................................................................................................................................	27	1	1.00	1.00	0.00	0.00	0.00
..........TGATGTC-GT------ATTAATGGGTTACAGATC..........................................................................................................................................................................................................................................................................................	27	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAACGGGTTACAGA............................................................................................................................................................................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
..........TGTTGTC-GT------ATTAATGGGTT.................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

TATTTTC------AGTT-TT------CGGATTAAAGCTAATGAAAGTGTATGAAAATT-------------------------------------------------------AAATTATT----------AAA---------------------------------------------------------TTGATT---AAAAT---------AAATATACATAAT-----------------------------ATGTAA----TATATTTA------ATT------AAATAAAT--AAAT-----------------ATTAAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................................................................................................................................................................................................................................................................................AT	18	22	0.05	0.00	0.05	0.00	0.00	0.00
..........................................AAAGTGTxTGAAAATT-------------------------------------------------------AAAA.................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................................................................................................................TT----------AAA---------------------------------------------------------TTGATT---CTAAT---------AAA.............................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..GTTTC------AGTT-TT------CGGATTGA....................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
TATCATC------AGTT-TT------CGGAT.......................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................................................GT	19	11	0.09	0.09	0.00	0.00	0.00	0.00

droWil1

TTTTGTTTTTATTTTTA-TA------TATATTTATATATATATATATATATATTGTAT-------------------------------------------------------ATAT--------AAT--TTGT----------------------TCT-------GTTTTTTTTTTTT---T-------------ATTTACTTTT-GT-----TTAAATT-----------------------CATTTCCCTATTAAGTTA----CACACACATATGTATAT------GTATATAT--ATAC-----------------ATATAC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................................T-------------------------------------------------------ATAT--------TGT--TTGT----------------------TCT-------GTTT............................................................................................................................................................	19	2	1.50	0.00	1.50	0.00	0.00
.............................................................................................................................................................................................................................................................ATTxAGTTA----CACACACATAG.................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................T----------------------TCT-------GTGTTTCTTTTTT---T-------------..................................................................................................................................	18	11	0.09	0.00	0.09	0.00	0.00
...........................................................................................................................................................................................................................................................................ACATACATATGTATAT------ATATATAT--ATA........................	27	28	0.04	0.00	0.00	0.04	0.00
.................................................................................................................................................................................................................................................................................ATATGTATAT------GTATATAT--GGAC-----------------......	22	2	0.50	0.00	0.00	0.00	0.50
............................TATTTATATATGTATATAT.......................................................................................................................................................................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................TAT	18	18	0.06	0.00	0.06	0.00	0.00
.....................................ATATATATATATAAAGTGT..............................................................................................................................................................................................................................................................................	19	26	0.04	0.00	0.04	0.00	0.00
........................................................AT-------------------------------------------------------ATAx--------CAT--TTGT----------------------TCG-------GTT.............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................ATTAATATATATATATATATATA..................................................................................................................................................................................................................................................................................	23	15	0.07	0.00	0.07	0.00	0.00
.............................................................................................................................................................................TTTTTG---T-------------ATTTCCTTTT-GT-----................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
.................................................................................................................................................................................................................................................................................ATACGTATGT------GTATATAT--ATA........................	21	19	0.05	0.05	0.00	0.00	0.00
.............................ATTTCTATATATATATATATATA..................................................................................................................................................................................................................................................................................	23	13	0.08	0.00	0.08	0.00	0.00
...................A------TCTATTTATATATATATAT.........................................................................................................................................................................................................................................................................................	20	422	0.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................T------GAACATAT--ATAC-----------------ATATA.	18	31	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................................................................................................................................ACACACATATATCTAT------GT...................................	18	11	0.09	0.00	0.09	0.00	0.00
.....................................ATATATATATAGAGATTGTAT-------------------------------------------------------.....................................................................................................................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
...................................................ATTGTAT-------------------------------------------------------ATAT--------AAG--GTGT----------------------..........................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................TATTGTAT-------------------------------------------------------xTAT--------AAT--TGGT----------------------..........................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................................................................................................................................CA----CACACACATATATATAT------GTATAT...............................	25	6	0.17	0.00	0.17	0.00	0.00

droVir3

TGTGCTTGTATTTAAAG-AT------TTAAAATTTTTA-------------TTATAAT-------------------------------------------------------ATAT--------ATT--GTTATTAAGAGCTAAATAT-----------------------------------------------------------------AAAAATATATAAGATAA-----------A-GATACCGTTATA----AATATAGAAACA-----------------------------------CTA-ACGAAGAT-ATATAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................................................................................................................................................................................................AAAAGATAA-----------A-CATACC............................................................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

ATTTTTGTATAGTAGTT-TTAG---TCTAGATTTGGT---GACAATTGAAGACGGTTT---------------------A-------------------------------TTAAATATAA--------------------------------------------------------------AATCAAGCTTTATG--------------------AATATAAAACCAAA-----------C-AACACTGTTATT----ATTTCACTATAA-----------------------------------TTA-ATCAACCTTGGAGGG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ATTTGTGTGTGTGTGTG-TG------TATATATACATACATACACACAGATATATGTT-------------------------------------------------------ATGT--------ATA--TGTA-------------------------------------------------TATATTTT-----------TAT---------AAATATGTAT-------ATATATATATG------------------------------TATATATATAT------ATATACAT--ATAT-----------------ATATAT	Size	Hit Count	Total Norm	V109 Male body
...AGTGTGTGTGTGTG-TG------TA..........................................................................................................................................................................................................................................................................................................	18	49	0.02	0.02
AGTTGTGTGTGTGTGCG-TG------............................................................................................................................................................................................................................................................................................................	19	10	0.10	0.10
.CTCGTGTGTGTGTGTG-TG------T...........................................................................................................................................................................................................................................................................................................	19	51	0.02	0.02
TTTTGTGTGCGTGTGTG-TG------............................................................................................................................................................................................................................................................................................................	19	41	0.02	0.02
.TTTGTGTGTGTGTGTG-TG------CATG........................................................................................................................................................................................................................................................................................................	22	30	0.03	0.03
..TTGTGCGTGTGTGAG-TG------T...........................................................................................................................................................................................................................................................................................................	18	29	0.03	0.03

Generated: 04/20/2012 at 05:22:57 EDT

sblock222077

chr3RHet:576709-576818 +

Candidate

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