dme-mir-13b-2-as- Best orthologs

dme-mir-13b-2-as	chrX:8985263-8985332 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 8985267-8985285
   star strand at position 8985312-8985331
   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	chrX:8985248-8985347 -		1	AGGCT-GGCTGTC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-A--GG-----------TAGA
droSim1	chrX_random:2632466-2632565 -	LASTZ	1	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGA
droSec1	super_34:345603-345702 -	LASTZ	1	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGG
droYak2	chrX:12330556-12330651 +	LASTZ	1	A-----GACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-ACTAGACAGCAG-G--GG-----------TAAG
droEre2	scaffold_4690:6132295-6132393 +	LASTZ	4	G-----GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCACTTTGACGCGCT-AATAGACAGCAG-G--GG------GT--TTAAA
droEug1	scf7180000409631:397666-397764 -	LASTZ	4	ATG-T-GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCAACATAGCTCACAGTCATTTTAACGCGTT-AATAGACAGCAA-A--GG-----------TAAG
droBia1	scf7180000301760:4584589-4584685 -	LASTZ	4	ATGC--GCATGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAG-G-TTAA----ATGCACATAGCTCACAGTCATTTTGACGCGCT-GATAGACAGCAG-A--AG-----------TA--
droTak1	scf7180000415169:933669-933769 +	LASTZ	4	AATGC-GACTGGC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-G--GT----------ATAAA
droEle1	scf7180000491006:2500509-2500618 -	LASTZ	4	ATG-T-GCCTGCC-CACCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-T--AGCAGAGGCATAAGAGA
droRho1	scf7180000779841:510723-510819 -	LASTZ	4	T-----GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAA-A--GC-----------TGAA
droFic1	scf7180000453829:954200-954296 -	LASTZ	4	A-----GGCTGTC-CGCCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATCTTGACGCTTT-GAAAGACAGCAG-A--TG----------ATGGA
droKik1	scf7180000301542:45346-45455 -	LASTZ	4	ATG-A-GTCTGTC-CATCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAAAT---TCAACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAA-A--GC-ACAGGTGGAGGAGA
droAna3	scaffold_13047:797460-797571 -	LASTZ	3	ACTTT-CACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGAC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGCT-GGGAAACAGGTAATGAAGCAGAAGCG--GGACA
droBip1	scf7180000396431:582372-582471 -	LASTZ	4	GTTAT-GACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGGC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGTT-GGGAAACAGCAA-G--AT-----------TAGC
dp4	chrXL_group1e:7000785-7000885 +	LASTZ	1	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droPer1	super_13:1553253-1553353 -	LASTZ	1	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droWil1	scaffold_181089:4662175-4662263 +	LASTZ	1	CTGCC-TTCAGCT----CCAATTC-----AA-----TGTTGAGCAA-G-GCAA----TCTTGCACTTCTCATAGGCTTTGGGGGCCATCTCAAAGCCAGCAT-A--GG-----------AAAA
droVir3	scaffold_12970:9304312-9304422 -	LASTZ	1	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATG-GCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCC-AATATGGAGCAT-T--GGCAGCAGCG--AGAGA
droMoj3	scaffold_6473:13342549-13342650 +	LASTZ	1	TTGGT-GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAT-AATCTC----ATAAACATAGCTCACAGTCAATTTGACGCGCA-AATATGGAGCAT-T--AG-----------AGGA
droGri2	scaffold_15203:306998-307104 -	LASTZ	4	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATT-ACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCC-AATATGGAGCAC-T--GATAGC------AACGA

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	AGGCT-GGCTGTC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-A--GG-----------TAGA
droSim1	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGA
droSec1	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGG
droYak2	A-----GACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-ACTAGACAGCAG-G--GG-----------TAAG
droEre2	G-----GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCACTTTGACGCGCT-AATAGACAGCAG-G--GG------GT--TTAAA
droEug1	ATG-T-GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCAACATAGCTCACAGTCATTTTAACGCGTT-AATAGACAGCAA-A--GG-----------TAAG
droBia1	ATGC--GCATGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAG-G-TTAA----ATGCACATAGCTCACAGTCATTTTGACGCGCT-GATAGACAGCAG-A--AG-----------TA--
droTak1	AATGC-GACTGGC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-G--GT----------ATAAA
droEle1	ATG-T-GCCTGCC-CACCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-T--AGCAGAGGCATAAGAGA
droRho1	T-----GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAA-A--GC-----------TGAA
droFic1	A-----GGCTGTC-CGCCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATCTTGACGCTTT-GAAAGACAGCAG-A--TG----------ATGGA
droKik1	ATG-A-GTCTGTC-CATCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAAAT---TCAACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAA-A--GC-ACAGGTGGAGGAGA
droAna3	ACTTT-CACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGAC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGCT-GGGAAACAGGTAATGAAGCAGAAGCG--GGACA
droBip1	GTTAT-GACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGGC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGTT-GGGAAACAGCAA-G--AT-----------TAGC
dp4	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droPer1	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droWil1	CTGCC-TTCAGCT----CCAATTC-----AA-----TGTTGAGCAA-G-GCAA----TCTTGCACTTCTCATAGGCTTTGGGGGCCATCTCAAAGCCAGCAT-A--GG-----------AAAA
droVir3	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATG-GCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCC-AATATGGAGCAT-T--GGCAGCAGCG--AGAGA
droMoj3	TTGGT-GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAT-AATCTC----ATAAACATAGCTCACAGTCAATTTGACGCGCA-AATATGGAGCAT-T--AG-----------AGGA
droGri2	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATT-ACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCC-AATATGGAGCAC-T--GATAGC------AACGA

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

AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................CAAACTCGTCAAATCGGC........................................................................................	18	3	4.67	0.00	0.00	1.00	3.67
......................................................................ACAGACATTTTGACGAGT...................................	18	7	1.14	1.14	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGCGT...................................	18	7	0.86	0.86	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACG......................................	19	7	0.57	0.00	0.57	0.00	0.00
..................................................................GATCACAGCCATTTTGACGCGT...................................	22	5	0.60	0.60	0.00	0.00	0.00
..................................................................TCTCACAGCCATTTTGACGCGT...................................	22	5	0.60	0.60	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACGCGTT-.................................	23	5	0.40	0.40	0.00	0.00	0.00
...............AACAAACTCGTCAAAAAG..........................................................................................	18	2	1.00	0.00	0.00	0.00	1.00
...............AACAAACTCGTCAAAATGGCTGG.....................................................................................	23	2	0.50	0.00	0.00	0.50	0.00
..................................................................GATCACAGCCATTTTGACGCG....................................	21	5	0.20	0.20	0.00	0.00	0.00
................AAAAACTCGTCCAAATGG.........................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
......................................................................ACAGCCATTTTGACGCGTT-.................................	19	7	0.14	0.14	0.00	0.00	0.00
...................................................................ATCACAGTCATTTTGACGAGT...................................	21	7	0.14	0.14	0.00	0.00	0.00
......................................................................ACAGACATTTTGACGAGTT-.................................	19	7	0.14	0.14	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGTGT...................................	18	7	0.14	0.14	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACGCGT...................................	22	5	0.20	0.20	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGGGT...................................	18	7	0.14	0.14	0.00	0.00	0.00
.........................................................................GTCATTTTGxCGCGTG-GATA.............................	19	2	0.50	0.00	0.00	0.50	0.00
..................................................................TCTCACAGCCATTTTGACGCGTT-.................................	23	5	0.20	0.20	0.00	0.00	0.00
..................................................................GATCACAGTCATTTTGACGAGTT-.................................	23	5	0.20	0.20	0.00	0.00	0.00
..................................................................TCTCACAGACATTTTGACGCGT...................................	22	2	0.50	0.50	0.00	0.00	0.00
..................................................................GGTCACAGTCATTTTGACGAGT...................................	22	2	0.50	0.50	0.00	0.00	0.00
...........CG-CAACAAACTCGTCAAAAAG..........................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
..................................................................GATCACAGTCATTTTGACGAGT...................................	22	5	0.20	0.20	0.00	0.00	0.00
......................................................................ACAGCCATTTTGATGCGTT-.................................	19	7	0.14	0.14	0.00	0.00	0.00

droSec1

AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................CAAACTCGTCAAATCGGC........................................................................................	18	3	1.00	0.00	1.00	0.00
......................................................................ACAGCCATTTTGACGGGT...................................	18	7	0.43	0.00	0.00	0.43
......................................................................ACAGTCATTTTGACGAGT...................................	18	7	0.29	0.00	0.14	0.14
...................................................................CTCACAGCCATTTTGACGAGT...................................	21	7	0.29	0.00	0.29	0.00
..................................................................TCTCACAGCCATTTTGACGCGT...................................	22	5	0.20	0.00	0.00	0.20
......................................................................ACAGCCATTTTGACGGGTT-.................................	19	7	0.14	0.00	0.14	0.00
......................................................................ACAGCCATTTTGACGTGTT-.................................	19	7	0.14	0.00	0.00	0.14
......................................................................ACAGTCATTTTGACGAGTT-.................................	19	7	0.14	0.00	0.14	0.00
....................................................................TCACAGCCATTTTGACGTGT...................................	20	7	0.14	0.00	0.00	0.14
......................................................................ACAGCCATTTTGACGCGTT-.................................	19	7	0.14	0.00	0.14	0.00
..................................................................GCTCACAGCCATTTTGACGAGTT-.................................	23	5	0.20	0.00	0.00	0.20
......................................................................ACAGCCATTTTGACGAGTT-G................................	20	7	0.14	0.00	0.14	0.00
......................................................................ACAGACATTTTGACGAGT...................................	18	7	0.14	0.00	0.00	0.14
......................................................................ACAGCCATTTTGACGCGT...................................	18	7	0.14	0.00	0.00	0.14

droYak2

A-----GACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-ACTAGACAGCAG-G--GG-----------TAAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................ACAGCCATTTTGACGCGTT-.................................	19	9	1.11	0.22	0.00	0.00	0.89	0.00
......................................................................ACAGCCATTTTGACGCGT...................................	18	9	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................ACAGCCATTTTGACGAGTT-A................................	20	9	0.78	0.56	0.11	0.00	0.11	0.00
..................................................................TCTCACAGCCATTTTGACGCGT...................................	22	7	0.86	0.43	0.14	0.00	0.29	0.00
..................................................................TATCACAGTCATTTTGACGCGT...................................	22	7	0.86	0.29	0.00	0.00	0.57	0.00
..................................................................TCTCACAGCCATTTTGACGCGTT-.................................	23	7	0.86	0.14	0.00	0.00	0.71	0.00
..................................................................TATCACAGTCATTTTGACGCGTT-.................................	23	7	0.57	0.29	0.00	0.00	0.29	0.00
......................................................................ACAGACATTTTGACGAGTT-.................................	19	9	0.33	0.11	0.00	0.00	0.22	0.00
..................................................................TCTCACAGTCATTTTGACGAGT...................................	22	7	0.29	0.00	0.00	0.00	0.29	0.00
.......................................................................CAGCCATTTTGACGAGTT-A................................	19	9	0.22	0.22	0.00	0.00	0.00	0.00
..................................................................GCTCACAGCCATTTTGACGAGT...................................	22	7	0.29	0.29	0.00	0.00	0.00	0.00
......................................................................ACAGACATTTTGACGAGT...................................	18	9	0.22	0.22	0.00	0.00	0.00	0.00
....................................................................TCACAGCCATTTTGACGAGTT-A................................	22	9	0.22	0.22	0.00	0.00	0.00	0.00
......................................................................ACAGCCATTTTGATGCGTT-.................................	19	9	0.11	0.00	0.00	0.00	0.11	0.00
......................................................................ACAGGCATTTTGACGAGT...................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
..................................................................GCTCACAGCCATTTTGACGAGTT-.................................	23	7	0.14	0.00	0.14	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGTGT...................................	18	9	0.11	0.00	0.00	0.00	0.11	0.00
..................................................................AATCACAGTCATTTTGACGCGT...................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
......................................................................ACAGACATTTTGACGCGT...................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
..................................................................GATCACAGCCATTTTGACGCGT...................................	22	7	0.14	0.14	0.00	0.00	0.00	0.00
..................................................................GATCACAGCCATTTTGACGCGTT-.................................	23	7	0.14	0.00	0.00	0.00	0.14	0.00
..................................................................GATCACAGTCATTTTGACGTGT...................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00
....................................................................TCACAGCCCTTTTGACGCGT...................................	20	7	0.14	0.00	0.00	0.00	0.14	0.00
.....................................................................CACAGCCATTTTGACGCGT...................................	19	9	0.11	0.00	0.00	0.00	0.11	0.00
......................................................................ACAGCCATTTTGACGCAT...................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
......................................................................ACAGCCATTTTGCCGCGT...................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
......................................................................ACAGTCATTTTGATGAGTT-.................................	19	9	0.11	0.11	0.00	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGGGTT-.................................	19	9	0.11	0.11	0.00	0.00	0.00	0.00
......................................................................ACAGTCATTTTGACGCGC...................................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGCCT...................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
......................................................................ACAGCCATTTTGACGGG....................................	17	9	0.11	0.00	0.00	0.00	0.11	0.00
...................................................................ATCACAGCCATTTTGACGCGTT-.................................	22	9	0.11	0.00	0.00	0.00	0.11	0.00
..................................................................TCTCACAGTAATTTTGACGCGT...................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00
......................................................................ACAGTCATTTTGACGAGTT-.................................	19	9	0.11	0.11	0.00	0.00	0.00	0.00
........................................................................AGCCATTTTGACGAGTT-A................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACG......................................	19	9	0.11	0.00	0.11	0.00	0.00	0.00
...........................................................................................CTAGACAGCGG-G--GG-----------AA..	16	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

G-----GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCACTTTGACGCGCT-AATAGACAGCAG-G--GG------GT--TTAAA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

ATG-T-GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCAACATAGCTCACAGTCATTTTAACGCGTT-AATAGACAGCAA-A--GG-----------TAAG

Size

Hit Count

Total Norm

droBia1

ATGC--GCATGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAG-G-TTAA----ATGCACATAGCTCACAGTCATTTTGACGCGCT-GATAGACAGCAG-A--AG-----------TA--

Size

Hit Count

Total Norm

droTak1

AATGC-GACTGGC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-G--GT----------ATAAA

Size

Hit Count

Total Norm

droEle1

ATG-T-GCCTGCC-CACCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-T--AGCAGAGGCATAAGAGA

Size

Hit Count

Total Norm

droRho1

T-----GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAA-A--GC-----------TGAA

Size

Hit Count

Total Norm

droFic1

A-----GGCTGTC-CGCCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATCTTGACGCTTT-GAAAGACAGCAG-A--TG----------ATGGA

Size

Hit Count

Total Norm

droKik1

ATG-A-GTCTGTC-CATCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAAAT---TCAACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAA-A--GC-ACAGGTGGAGGAGA

Size

Hit Count

Total Norm

droAna3

ACTTT-CACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGAC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGCT-GGGAAACAGGTAATGAAGCAGAAGCG--GGACA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................ACAGCCATTTCGACGAGC...................................	18	5	0.40	0.00	0.00	0.00	0.40
..............................ATGGxTGTGACATGAC-A-T.........................................................................	17	2	0.50	0.00	0.00	0.50	0.00

droBip1

GTTAT-GACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGGC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGTT-GGGAAACAGCAA-G--AT-----------TAGC

Size

Hit Count

Total Norm

dp4

GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................ACAGACATTTTGACGAGT...................................	18	8	1.13	0.00	0.88	0.25	0.00
..................................................................TCTCACAGCCATTTTGACGCGT...................................	22	5	1.00	0.00	0.80	0.20	0.00
......................................................................ACAGCCATTTTGACGCGT...................................	18	8	0.50	0.00	0.38	0.13	0.00
......................................................................ACAGCCATTTTGACGCGTT-.................................	19	8	0.50	0.13	0.25	0.13	0.00
..................................................................TATCACAGTCATTTTGACGCGT...................................	22	5	0.80	0.00	0.40	0.40	0.00
..................................................................GATCACAGCCATTTTGACGCGT...................................	22	5	0.60	0.00	0.00	0.60	0.00
......................................................................ACAGTCATTTTGACGAGT...................................	18	8	0.25	0.00	0.25	0.00	0.00
......................................................................ACAGCCATTTTGACGTGT...................................	18	8	0.25	0.00	0.13	0.13	0.00
..................................................................GGTCACAGTCATTTTGACGGGT...................................	22	2	0.50	0.00	0.50	0.00	0.00
......................................................................ACAGGCATTTTGACGTGT...................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................................ACAGCCATTTTGCCGCGT...................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................................ACAGCCATTTTGACGGGT...................................	18	8	0.13	0.00	0.00	0.13	0.00
....................................................................TCACAGCCATTTTGACGCGTT-.................................	21	8	0.13	0.00	0.13	0.00	0.00
......................................................................ACAGTCATTTTGATGGGT...................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................................ACAGCCATTTTGACCCGT...................................	18	5	0.20	0.00	0.00	0.20	0.00
......................................................................ACAGCCATTTTGACGAGTA-A................................	20	5	0.20	0.00	0.20	0.00	0.00
.....................................................................CACAGCCATTTTGACGCGTT-.................................	20	8	0.13	0.00	0.13	0.00	0.00
......................................................................ACAGGCATTTTGACGAGT...................................	18	8	0.13	0.00	0.13	0.00	0.00
......................................................................ACAGCCATTTTGTCGCGT...................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................................ACAGTTATTTTGACGAGT...................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................................ACAGACATTTTGAAGCGT...................................	18	2	0.50	0.00	0.00	0.50	0.00
......................................................................ACAGTCATTTTGACGAGG...................................	18	5	0.20	0.00	0.20	0.00	0.00

droPer1

GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................................................TATCACAGTCATTTTGACGCGT...................................	22	5	1.40	0.00	0.20	0.00	1.20	0.00
......................................................................ACAGCCATTTTGACGCGT...................................	18	8	0.75	0.00	0.13	0.13	0.50	0.00
..................................................................TCTCACAGCCATTTTGACGCGT...................................	22	5	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................ACAGACATTTTGACGAGT...................................	18	8	0.38	0.00	0.13	0.25	0.00	0.00
......................................................................ACAGCCATTTTGACGTGT...................................	18	8	0.38	0.00	0.00	0.00	0.38	0.00
......................................................................ACAGCCATTTTGACGCGTT-.................................	19	8	0.38	0.00	0.00	0.00	0.38	0.00
......................................................................ACAGCCATTTTGACGGGT...................................	18	8	0.13	0.00	0.13	0.00	0.00	0.00
................................................................TAGCTCACAGTCATTTTGACGCG....................................	23	2	0.50	0.00	0.00	0.00	0.50	0.00
.........................................................AAACACAGAGCTCACAGTA...............................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00
......................................................................ACAGGCATTTTGACGCGTT-.................................	19	5	0.20	0.00	0.00	0.00	0.20	0.00
...................................................................ATCACAGCCATTTTGACGCGT...................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
.....................................................................CACAGCCATTTTGACGCGTT-.................................	20	8	0.13	0.00	0.00	0.00	0.13	0.00
..................................................................GCTCACCGTCATTTTGACGAGT...................................	22	2	0.50	0.00	0.50	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACGCG....................................	21	5	0.20	0.00	0.00	0.00	0.20	0.00
......................................................................CCAGTCATTTTGACGCCT...................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
..................................................................GATCACAGCCATTTTGACGCGT...................................	22	5	0.20	0.00	0.00	0.00	0.20	0.00
......................................................................ACAGCCATTTTGACGAGTA-.................................	19	8	0.13	0.00	0.00	0.00	0.13	0.00

droWil1

CTGCC-TTCAGCT----CCAATTC-----AA-----TGTTGAGCAA-G-GCAA----TCTTGCACTTCTCATAGGCTTTGGGGGCCATCTCAAAGCCAGCAT-A--GG-----------AAAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........AGCT----CCAATGA-----AA-----TGTTG..................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATG-GCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCC-AATATGGAGCAT-T--GGCAGCAGCG--AGAGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................ACAGCCATTTTGACGAGC...................................	18	10	1.10	0.10	0.90	0.10	0.00	0.00
......................................................................ACAGCCATTTTGACGCGT...................................	18	10	0.30	0.00	0.30	0.00	0.00	0.00
..................................................................GCTCACAGCCATTTTGACGAGCC-.................................	23	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................................................ACAGTCATTTTGACGAGT...................................	18	10	0.10	0.00	0.10	0.00	0.00	0.00
..................................................................TATCACAGTCATTTTGACG......................................	19	10	0.10	0.00	0.10	0.00	0.00	0.00
......................................................................ACAGACATTTTGACGAGC...................................	18	7	0.14	0.00	0.14	0.00	0.00	0.00
.............................................................................................ATGGAGCAT-T--GGCAGCAGC........	19	2	0.50	0.50	0.00	0.00	0.00	0.00

droMoj3

TTGGT-GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAT-AATCTC----ATAAACATAGCTCACAGTCAATTTGACGCGCA-AATATGGAGCAT-T--AG-----------AGGA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................AAGATGTCTGTGATATGAT-............................................................................	19	3	26.00	24.67	0.67	0.67	0.00
...........................AAGATGTCTGTGATATGAT-A...........................................................................	20	3	8.33	7.67	0.33	0.33	0.00
............................AGATGTCTGTGATATGAT-A...........................................................................	19	3	0.67	0.67	0.00	0.00	0.00
......................................................................ACAGCCATTTTGACGCGC...................................	18	5	0.20	0.00	0.00	0.20	0.00
..........................CAAGATGTCTGTGATATGAT-A...........................................................................	21	3	0.33	0.33	0.00	0.00	0.00
.............................GATGTCTGTGATATGAT-A...........................................................................	18	3	0.33	0.33	0.00	0.00	0.00

droGri2

T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATT-ACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCC-AATATGGAGCAC-T--GATAGC------AACGA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:32:37 EDT

dme-mir-13b-2-as

chrX:8985263-8985332 -

Candidate

antisense_to_intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup