sblock1267- Best orthologs

sblock1267	chr2L:1163545-1163636 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1163600-1163621
   star strand at position 1163556-1163579
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:1163530-1163651 -		1	CGAATATG-----T-CCAACCT----------ACAGC--AGAAA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCA---------------ACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCCGAATGC
droSim1	chr2L:1135602-1135722 -	LASTZ	5	CGAATATG-----T-TCAACCT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCAT-T-CTGACCCAATTT----CCCGAATGC
droSec1	super_12247:184-305 -	LASTZ	5	CGAATATG-----T-TTAACGT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCATTT-CTGACCCAATTT----CCCGAATGC
droYak2	chr2L:1142840-1142972 -	LASTZ	5	CGAATATA-----T-TCAACCT----------ACAACCCAGTAA-----------TC-TCCAGGAA---------------AATTCC-------A-ACTTCTGCTCATTCACGTTGGCCT---------A-------------ATTGTAATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTTTTTGCTGACCCAATTC----CCTGAATGC
droEre2	scaffold_4929:1208206-1208337 -	LASTZ	5	CGAACATA-----T-TCAACCT----------ACAACCTATTAA-----------TC-TCGAGGGA---------------AATTGC-------A-ATTCCTACCCATTCACGGTGGTCT---------T-------------ATTGTTATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTATAG-CTGACCCCATTC----CCTGAATGC
droEug1	scf7180000409005:43469-43592 +	LASTZ	5	TAAAAACA----AT-TCGG--------------------------------CCTATC-TTGAGACG---------------TTTTTA----TTAA---TTTTCTTTAATAAAAGCGGCTT---------TT--TA--------------ATTTTATTT-----TTTGCTCTCG------TA------AATTT--AA-ATCGCTTATTT-CTGACCCAATTT----CCTCAATGC
droBia1	scf7180000302188:691215-691325 +	LASTZ	5	AGATTT------------G--------------------------------CCTATC-TGGAGGCT---------------TTTTCG-------A-TTTCTTACTCATTAACGGTGGCGT---------TT--TT--------------AT------T-----TTCGCACTCG------TA------CATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCGCAATGC
droTak1	scf7180000415264:198414-198531 +	LASTZ	5	CAAATACA-----T-TCGC--------------------------------CCTATC-TTGGGAGA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCTT---------TT--T-----------------TTTAT-T-----TTTGCGCTCG------TA------AATTT--CA-CTTGCTTATTT-CTGACCCAATTT----CCTCAATGC
droEle1	scf7180000491273:2316499-2316606 +	LASTZ	5	TGTACAAG-----T-TCTG--------------------------------TCTATC-TTGAGACA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCAT---------TT--TT--------------TTTTTAA---------------------------------TTCCACG-CTCATTAATTT-CTGACCCAATTT----CCCCAATGC
droRho1	scf7180000766778:451-555 +	LASTZ	5	TGAATACA-----T-GATAGAC----------AGAA---------------CCTATC-TTGAGACA---------------TTTTCA-------A-TTTTGTACTCATTAACGGTGGCTT---------TT--T------------------------------CAA---------------------------CG-CTCGTTAATTT-CTGACCCAATTT----CCCCAATGC
droFic1	scf7180000454155:379877-379982 -	LASTZ	5	CGAATATA-----T-TCAG--------------------------------TCTATC-TTGAGGCG---------------T---------------TTATTACTCATTGATGGTGCCGT---------T-------------AT------------T-----TTTGCGCTCG------TA------AATTT--AA-CTCGCTTGTTT-CTGACCCAATTT----CCTCAATGC
droKik1	scf7180000302405:402582-402723 -	LASTZ	5	AAAATAGG-----T-TCAGGTTTTCATTC---TCTATGTATATA-----------TG-TATATGGG-------------G-TTTTCA-------A-TTCTTCGCTTATTAACTAGGGCAG---------TT--GA--------------TGTGCGATT-----TTTGAGCTCG------TA------AATTT--CATTTCGCATATTT-CTGACCCAATTT----CCCAAATGC
droAna3	scaffold_12916:4636831-4636951 -	LASTZ	5	TCAAAC---------------A----------ATAACATATATA-----------TA-CCTAGACT---------------TTTTTTATTGTTGATATTTTTATTCATTAAA-GTGTTGT---------TT--T------------------------------TAATGGCCG------TT------AAATT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATAC
droBip1	scf7180000396737:128183-128307 +	LASTZ	5	AACAATAA-----A-ATTTTAT----------ACAA---------------ACAAGC-CTAGAACT---------------TTTTTTTTTATTGATATTTTTGCTCATTAAAAGTGTCGT---------TG--T------------------------------TTATGCCCG------T-------AATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATGC
dp4	chr4_group3:9617618-9617737 -	LASTZ	5	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG-G-TG---------------TTTTTA-------ATTTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droPer1	super_8:811321-811439 -	LASTZ	5	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG--GTG---------------TTTTTA-------A-TTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droWil1	scaffold_181132:349232-349350 -	LASTZ	5	CAGATAAGGACATT-GTGT--------------------------------TTTGTT-TTGGGACCACAGCAAAAAAAAAAAAAAG-------------------------CA-----GAAATTCGCGT--GCTA-------------------------------------ATGAACGTAATTAAATTTTC--CC-TTTACATATTT-ATGACCCAATTT----TG----TTT
droVir3	scaffold_12963:5860254-5860409 +	LASTZ	5	AGGACATG-----T-TATTAAT-TCACATGTTATGTT-----AA-----------TT-AATGA------------------AATATA-------A-TTTAAATAA------TAATAATA------------GTAATTGAACACATTTTATTTACAATGTTCAGCTTGTGCTCA------TTAAAAAGCATTT--CC-CTTGCTTATTT-CTGACCCAATTATCGCCCTGTATTT
droMoj3	scaffold_6500:24978110-24978147 +	LASTZ	5	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT--CA-CTTACATATAT-CTGACCCAATTT----CCTGCTTGC
droGri2	scaffold_15252:5770092-5770236 +	LASTZ	5	AGGACATA-----C-ATAGTAT----------TTATT--------ATTCCATTTATT-TGT--GTA---------------TATTTG-------T-TTTCTTTTTTAATAAAAATAAT------------------TGAAC-CGTTTTTTTTA-AA---TCAGACTGTGCTCATTAA--AG------CATTT--CA-CTTGCATATTT-TTGACCCATTTT----CCTTCTTTT

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	CGAATATG-----T-CCAACCT----------ACAGC--AGAAA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCA---------------ACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCCGAATGC
droSim1	CGAATATG-----T-TCAACCT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCAT-T-CTGACCCAATTT----CCCGAATGC
droSec1	CGAATATG-----T-TTAACGT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCATTT-CTGACCCAATTT----CCCGAATGC
droYak2	CGAATATA-----T-TCAACCT----------ACAACCCAGTAA-----------TC-TCCAGGAA---------------AATTCC-------A-ACTTCTGCTCATTCACGTTGGCCT---------A-------------ATTGTAATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTTTTTGCTGACCCAATTC----CCTGAATGC
droEre2	CGAACATA-----T-TCAACCT----------ACAACCTATTAA-----------TC-TCGAGGGA---------------AATTGC-------A-ATTCCTACCCATTCACGGTGGTCT---------T-------------ATTGTTATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTATAG-CTGACCCCATTC----CCTGAATGC
droEug1	TAAAAACA----AT-TCGG--------------------------------CCTATC-TTGAGACG---------------TTTTTA----TTAA---TTTTCTTTAATAAAAGCGGCTT---------TT--TA--------------ATTTTATTT-----TTTGCTCTCG------TA------AATTT--AA-ATCGCTTATTT-CTGACCCAATTT----CCTCAATGC
droBia1	AGATTT------------G--------------------------------CCTATC-TGGAGGCT---------------TTTTCG-------A-TTTCTTACTCATTAACGGTGGCGT---------TT--TT--------------AT------T-----TTCGCACTCG------TA------CATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCGCAATGC
droTak1	CAAATACA-----T-TCGC--------------------------------CCTATC-TTGGGAGA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCTT---------TT--T-----------------TTTAT-T-----TTTGCGCTCG------TA------AATTT--CA-CTTGCTTATTT-CTGACCCAATTT----CCTCAATGC
droEle1	TGTACAAG-----T-TCTG--------------------------------TCTATC-TTGAGACA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCAT---------TT--TT--------------TTTTTAA---------------------------------TTCCACG-CTCATTAATTT-CTGACCCAATTT----CCCCAATGC
droRho1	TGAATACA-----T-GATAGAC----------AGAA---------------CCTATC-TTGAGACA---------------TTTTCA-------A-TTTTGTACTCATTAACGGTGGCTT---------TT--T------------------------------CAA---------------------------CG-CTCGTTAATTT-CTGACCCAATTT----CCCCAATGC
droFic1	CGAATATA-----T-TCAG--------------------------------TCTATC-TTGAGGCG---------------T---------------TTATTACTCATTGATGGTGCCGT---------T-------------AT------------T-----TTTGCGCTCG------TA------AATTT--AA-CTCGCTTGTTT-CTGACCCAATTT----CCTCAATGC
droKik1	AAAATAGG-----T-TCAGGTTTTCATTC---TCTATGTATATA-----------TG-TATATGGG-------------G-TTTTCA-------A-TTCTTCGCTTATTAACTAGGGCAG---------TT--GA--------------TGTGCGATT-----TTTGAGCTCG------TA------AATTT--CATTTCGCATATTT-CTGACCCAATTT----CCCAAATGC
droAna3	TCAAAC---------------A----------ATAACATATATA-----------TA-CCTAGACT---------------TTTTTTATTGTTGATATTTTTATTCATTAAA-GTGTTGT---------TT--T------------------------------TAATGGCCG------TT------AAATT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATAC
droBip1	AACAATAA-----A-ATTTTAT----------ACAA---------------ACAAGC-CTAGAACT---------------TTTTTTTTTATTGATATTTTTGCTCATTAAAAGTGTCGT---------TG--T------------------------------TTATGCCCG------T-------AATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATGC
dp4	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG-G-TG---------------TTTTTA-------ATTTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droPer1	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG--GTG---------------TTTTTA-------A-TTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droWil1	CAGATAAGGACATT-GTGT--------------------------------TTTGTT-TTGGGACCACAGCAAAAAAAAAAAAAAG-------------------------CA-----GAAATTCGCGT--GCTA-------------------------------------ATGAACGTAATTAAATTTTC--CC-TTTACATATTT-ATGACCCAATTT----TG----TTT
droVir3	AGGACATG-----T-TATTAAT-TCACATGTTATGTT-----AA-----------TT-AATGA------------------AATATA-------A-TTTAAATAA------TAATAATA------------GTAATTGAACACATTTTATTTACAATGTTCAGCTTGTGCTCA------TTAAAAAGCATTT--CC-CTTGCTTATTT-CTGACCCAATTATCGCCCTGTATTT
droMoj3	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT--CA-CTTACATATAT-CTGACCCAATTT----CCTGCTTGC
droGri2	AGGACATA-----C-ATAGTAT----------TTATT--------ATTCCATTTATT-TGT--GTA---------------TATTTG-------T-TTTCTTTTTTAATAAAAATAAT------------------TGAAC-CGTTTTTTTTA-AA---TCAGACTGTGCTCATTAA--AG------CATTT--CA-CTTGCATATTT-TTGACCCATTTT----CCTTCTTTT

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

CGAATATG-----T-TCAACCT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCAT-T-CTGACCCAATTT----CCCGAATGC

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

CGAATATG-----T-TTAACGT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCATTT-CTGACCCAATTT----CCCGAATGC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CGAATATA-----T-TCAACCT----------ACAACCCAGTAA-----------TC-TCCAGGAA---------------AATTCC-------A-ACTTCTGCTCATTCACGTTGGCCT---------A-------------ATTGTAATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTTTTTGCTGACCCAATTC----CCTGAATGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................................................AA-------TTCG-CTTCG------GA------AA-TT--C.......................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
..................................................................................ATTCC-------A-ACTTCGGCTCCT..............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CGAACATA-----T-TCAACCT----------ACAACCTATTAA-----------TC-TCGAGGGA---------------AATTGC-------A-ATTCCTACCCATTCACGGTGGTCT---------T-------------ATTGTTATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTATAG-CTGACCCCATTC----CCTGAATGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................................................................................................AA-------TTCG-CCTCG------TT------AA-TT--CC-.....................................	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

TAAAAACA----AT-TCGG--------------------------------CCTATC-TTGAGACG---------------TTTTTA----TTAA---TTTTCTTTAATAAAAGCGGCTT---------TT--TA--------------ATTTTATTT-----TTTGCTCTCG------TA------AATTT--AA-ATCGCTTATTT-CTGACCCAATTT----CCTCAATGC

Size

Hit Count

Total Norm

droBia1

AGATTT------------G--------------------------------CCTATC-TGGAGGCT---------------TTTTCG-------A-TTTCTTACTCATTAACGGTGGCGT---------TT--TT--------------AT------T-----TTCGCACTCG------TA------CATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCGCAATGC

Size

Hit Count

Total Norm

droTak1

CAAATACA-----T-TCGC--------------------------------CCTATC-TTGGGAGA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCTT---------TT--T-----------------TTTAT-T-----TTTGCGCTCG------TA------AATTT--CA-CTTGCTTATTT-CTGACCCAATTT----CCTCAATGC

Size

Hit Count

Total Norm

droEle1

TGTACAAG-----T-TCTG--------------------------------TCTATC-TTGAGACA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCAT---------TT--TT--------------TTTTTAA---------------------------------TTCCACG-CTCATTAATTT-CTGACCCAATTT----CCCCAATGC

Size

Hit Count

Total Norm

droRho1

TGAATACA-----T-GATAGAC----------AGAA---------------CCTATC-TTGAGACA---------------TTTTCA-------A-TTTTGTACTCATTAACGGTGGCTT---------TT--T------------------------------CAA---------------------------CG-CTCGTTAATTT-CTGACCCAATTT----CCCCAATGC

Size

Hit Count

Total Norm

droFic1

CGAATATA-----T-TCAG--------------------------------TCTATC-TTGAGGCG---------------T---------------TTATTACTCATTGATGGTGCCGT---------T-------------AT------------T-----TTTGCGCTCG------TA------AATTT--AA-CTCGCTTGTTT-CTGACCCAATTT----CCTCAATGC

Size

Hit Count

Total Norm

droKik1

AAAATAGG-----T-TCAGGTTTTCATTC---TCTATGTATATA-----------TG-TATATGGG-------------G-TTTTCA-------A-TTCTTCGCTTATTAACTAGGGCAG---------TT--GA--------------TGTGCGATT-----TTTGAGCTCG------TA------AATTT--CATTTCGCATATTT-CTGACCCAATTT----CCCAAATGC

Size

Hit Count

Total Norm

droAna3

TCAAAC---------------A----------ATAACATATATA-----------TA-CCTAGACT---------------TTTTTTATTGTTGATATTTTTATTCATTAAA-GTGTTGT---------TT--T------------------------------TAATGGCCG------TT------AAATT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................................................................................ATATTGTTGATGTTTTTA...................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
TCACAx---------------A----------ATAACATATATA-----------...................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droBip1

AACAATAA-----A-ATTTTAT----------ACAA---------------ACAAGC-CTAGAACT---------------TTTTTTTTTATTGATATTTTTGCTCATTAAAAGTGTCGT---------TG--T------------------------------TTATGCCCG------T-------AATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATGC

Size

Hit Count

Total Norm

dp4

AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG-G-TG---------------TTTTTA-------ATTTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG--GTG---------------TTTTTA-------A-TTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................A-------ATTCTCTCTTCG-GCCTC..............................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................AATGT--CA-CTTGCATATTT-CT.......................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

CAGATAAGGACATT-GTGT--------------------------------TTTGTT-TTGGGACCACAGCAAAAAAAAAAAAAAG-------------------------CA-----GAAATTCGCGT--GCTA-------------------------------------ATGAACGTAATTAAATTTTC--CC-TTTACATATTT-ATGACCCAATTT----TG----TTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................AAAAAAAAAGAA-------------------------CA-----GAAA................................................................................................................	18	51	0.06	0.00	0.06	0.00	0.00
.......................................................................AAAAAAAAAAAAAAG-------------------------AA-----GA..................................................................................................................	19	15	0.20	0.00	0.20	0.00	0.00
..GATAAxGACATT-GTTT--------------------------------TTT....................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
........................................................................AAAAAAAAAAAAAG-------------------------AA-----GA..................................................................................................................	18	20	0.10	0.00	0.10	0.00	0.00
.........................................................................AAAAAAAAAAGAA-------------------------CA-----GAA.................................................................................................................	18	49	0.04	0.00	0.04	0.00	0.00
.......................................................................AAAAAAAAAAAAAGG-------------------------AA-----GA..................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
........................................................................AATAAAAAAAAAAG-------------------------AA-----GAAA................................................................................................................	20	26	0.04	0.00	0.04	0.00	0.00
...........................................................................AAAAAAAACAG-------------------------AA-----GAAAT...............................................................................................................	18	13	0.08	0.08	0.00	0.00	0.00
........................................................................AAAAAAAAAAAAAG-------------------------GA-----GC..................................................................................................................	18	16	0.06	0.00	0.06	0.00	0.00
....................................................................AGCAAATAAAAGAAAAAG-------------------------...........................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.......................................................................AAAACAAAAAAAAAG-------------------------CA-----G...................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
........................................................................AAAAAGAAAAAAAG-------------------------CA-----AAA.................................................................................................................	19	25	0.04	0.00	0.04	0.00	0.00
............................................................................................................................................................................................................ATTT-ATGAACCAATTG----TG----TT.	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................AAAAACAAAAAAAG-------------------------CA-----GGA.................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.................................................................AACAGCCAAAAAAAAAAA.......................................................................................................................................................	18	16	0.06	0.00	0.06	0.00	0.00
.................................................................AACAGCGAAAAAAAAAAA.......................................................................................................................................................	18	18	0.06	0.00	0.00	0.06	0.00
.........................................................................AAAAAAAAAAGAG-------------------------AA-----GAAA................................................................................................................	19	31	0.03	0.03	0.00	0.00	0.00
..................................................................ATTGCAAAAAAAAAAAAA......................................................................................................................................................	18	50	0.02	0.00	0.02	0.00	0.00
..........................................................................AAAAAAAAAAAG-------------------------GA-----GAAAAT..............................................................................................................	20	6	0.17	0.00	0.17	0.00	0.00
..........................................................................AAAGAAAAAGAG-------------------------CA-----GAAATT..............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................AACAGCAAAAAAAGAAAA.......................................................................................................................................................	18	10	0.10	0.00	0.10	0.00	0.00
...................................................................CAGCGAAAAAAAAAGAAA.....................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
.............................................................................AAAAAAAAG-------------------------CA-----GAAAAAC.............................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
.......................................................................AAAAAAAAAAACAAG-------------------------AA-----GA..................................................................................................................	19	34	0.03	0.00	0.03	0.00	0.00
........................................................................AAAAACAAAAAAAG-------------------------AA-----GAA.................................................................................................................	19	27	0.04	0.00	0.04	0.00	0.00
.......................................................................AAAAAAAAAACAAAG-------------------------AA-----GAA.................................................................................................................	20	14	0.07	0.00	0.07	0.00	0.00
...................................................................CCCCAAAAAAAAAAAAAA.....................................................................................................................................................	18	50	0.02	0.00	0.00	0.00	0.02
.......................................................................AAAAAAAAACAAAAG-------------------------AA-----GA..................................................................................................................	19	32	0.03	0.00	0.03	0.00	0.00
.........................................................................AAAAAAAAAAGAG-------------------------CA-----CAA.................................................................................................................	18	7	0.14	0.00	0.14	0.00	0.00
........................................................................AAAAAAAAAAAACC-------------------------CA-----GAA.................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...................................................................CAGAAAAAAAAAACAAAAG-------------------------...........................................................................................................................	19	10	0.10	0.00	0.00	0.10	0.00
.................................................................CACAGCACAAAAAAACAAAA.....................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................................AAAAAAAAAAGG-------------------------AA-----GAAA................................................................................................................	18	46	0.02	0.00	0.02	0.00	0.00
........................................................................AAAAACAAAAAAGG-------------------------CA-----GA..................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
........................................................................AAAAAAAAAAAAAG-------------------------AA-----GACA................................................................................................................	20	25	0.04	0.00	0.04	0.00	0.00
.......................................................................AAAAAAAAAGAAAAG-------------------------CA-----GA..................................................................................................................	19	10	0.10	0.00	0.10	0.00	0.00
.................................................................TACAGCAAAAAAAAAAAA.......................................................................................................................................................	18	22	0.05	0.00	0.05	0.00	0.00
................................................................CCACAGGAAGAAAAAAAA........................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..................................................................ACAGCCAAACAAAAAAAAA.....................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00

droVir3

AGGACATG-----T-TATTAAT-TCACATGTTATGTT-----AA-----------TT-AATGA------------------AATATA-------A-TTTAAATAA------TAATAATA------------GTAATTGAACACATTTTATTTACAATGTTCAGCTTGTGCTCA------TTAAAAAGCATTT--CC-CTTGCTTATTT-CTGACCCAATTATCGCCCTGTATTT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT--CA-CTTACATATAT-CTGACCCAATTT----CCTGCTTGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AGGACATA-----C-ATAGTAT----------TTATT--------ATTCCATTTATT-TGT--GTA---------------TATTTG-------T-TTTCTTTTTTAATAAAAATAAT------------------TGAAC-CGTTTTTTTTA-AA---TCAGACTGTGCTCATTAA--AG------CATTT--CA-CTTGCATATTT-TTGACCCATTTT----CCTTCTTTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:43 EDT

sblock1267

chr2L:1163545-1163636 -

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