block2035391- Best orthologs

block2035391	chr3R:4777401-4777494 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 4777417-4777438
   star strand at position 4777452-4777478
   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	chr3R:4777386-4777509 -		1	AAGCC--ACA----------------------------------AAA----TTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGGAATG-----------------------------CTATATATACATACTT---------TGCAGCTTT------------------------TCAAGTGATTTGAAATCACTAAAAG-CC----------------TTAAATATTGTT
droSim1	chr3R_random:312343-312466 -	LASTZ	4	GTACC--ACC----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTATATATACATACTT---------TGCAGCGTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT
droSec1	super_0:17102132-17102255 +	LASTZ	1	GAGCC--ACC----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTATATATACATACTT---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT
droYak2	chr3R:8821825-8821935 -	LASTZ	4	AAGCC--ACA----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------T------------------------------------------TACATACTA---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT
droEre2	scaffold_4770:16826046-16826169 +	LASTZ	1	AAGCC--ACA----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTACATATACATACTG---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT
droEug1	scf7180000409467:702681-702800 +	LASTZ	0	AACCC--TCG----------------------------------TAA----GGGT--TTAGTGATTAAAAAGTTCT-------TGAAACTGCGCCTAAGGATG-----------------TGCAATG--------------------------------TATGT-----TTG---------AGCAGCTTT------------------------TCAAGGCATTTAAAATCATTAAAAT-TA-------------ATAGCAAATGAGGTT
droBia1	scf7180000302402:7483054-7483157 -	LASTZ	0	AAGTC--ACT----------------------------------CAA----ATCT--CTAGGGATTTCAAATCTCC-------TGAAATTGTGCCTTAATGTA------------------GCAATG----------------------------------------TTTTT---------TGCAGCTAT------------------------TCTAGT---------TCACCAAAAA-CC----------------CTAGAAATTGTT
droTak1	scf7180000415653:147145-147268 +	LASTZ	0	AAGCC--ACG----------------------------------AATAATAAGAT--ACAGG-GTGTTTAAACTCTAAACTACGTAGGATGGGTC----------------------------GATTTGAGTCGG----------------------TGCATTAAAGTTATC---------TAAGCCATT-----------------------------TAGTCTG-AATCA-TATATA-TA----------------TTTTATATTATC
droEle1	scf7180000491011:146343-146464 +	LASTZ	0	AAATG--GCA----------------------------------AATGCTAATTT--ATGAG-G-TTGTAAACTTT-------TATAAATGTCGT-AAATCTT-----------------TCATA-A---------------------------CAAGC----TCTATGATA---------TATGGCTGT------------------------TTAAATA---TCAAACAACTAT---------------TTAGATATAAAACAGGGCT
droRho1	scf7180000779309:21519-21643 +	LASTZ	0	GTGCC--ACA----------------------------------GAA----ATCA--CTTGGTTTTTGAAATCTCT-------TTTAAAAGTGTGCAAAAGTA-----------------TGCAACA-----------------------------ATATATGTTAAGTTCA---------GGAGTCCGT------------------------TAGATTCATTTAGTAACACGACTTT-AC----------------TTAAGATACATA
droFic1	scf7180000453493:153900-154030 -	LASTZ	0	CTGCC--GTA----------------------------------AAAA---TTCC--CTTAA-ATTCAAAAAACA---------GA-AGATTAAGTGATTGTA-----------------TTAGAAT-----------------------------TTATCCAATATACACT-TAATGCTATCCG-ATTTTGAATTTACTGGAGATTTCTGT-------------GG---CA-----CG-CC----------------TTAACTTTCG-C
droKik1	scf7180000302471:78852-78973 -	LASTZ	0	AATTACCTTC----------------------------------GTA----GTCT--CGAGTGTTTTGTAATCTCT-------CGAAAAGTTGTATAAGTGTT-----------------TGGAATT-----------------------------CTATATTTTTATAATT---------TAATATAGT-----------------------------TAATTTGTAATTTTAAAAAA-TT----------------ATTCTTAGCATT
droAna3	scaffold_13248:2394513-2394634 +	LASTZ	0	TAGTG--GCA----------------------------------GGA----TACT--AGAGG-ATTAAAAAACTTC-------ACAGAATACATTTTCTTTTA-----------------AGAAAAG----TTGGAATTTTTAGA---------TTAG---------CTTTT---------TGTTTTAAA---------------------------------CAAATTATATTTGAAA-CT----------------ATGGGTTCTATC
droBip1	scf7180000396429:87234-87334 +	LASTZ	0	TAAAA--ATT----------------------------------GAA----GA------------------AATAA-------TAATAATGTGAAAA-------------------------AAATA-----------------------------ATAAATAAAAATAATT---------TAAATATTT------------------------TAAAACATTTTGAAATAATAAAGTT-AA----------------AAAAATTAAATA
dp4	chr3:17930285-17930408 -	LASTZ	0	ACC----AACACAATTTTTGAATATTTTGGGAAAATACTAGAAA-------TGGT--ATAAATACT----------A-----------------------------------AAAAGAAA------G---AT-AGAAA-------TACCATTCT------------------------------------AGAAATTGTCTCTGAATTCTTT-------------GG---TATC----CCAG----------------TTAATTTTGGTT
droPer1	super_73:125535-125658 +	LASTZ	0	ACC----AACACAATTTTTGAACATTTTGGGAAAATACTAGAAA-------TGGT--ATAAATACT----------A-----------------------------------AAAAGAAA------G---AT-AGAAA-------TACCATTCT------------------------------------AGAAATTGTCTCTGAATTCTTT-------------GG---TATC----CCAG----------------TTAATTTTGGTT
droWil1	scaffold_181130:13457303-13457435 -	LASTZ	0	AAGGC--GCA----------------------------------CAG----TTCT--TCAGCAATTT---------------------------TCAGGCGAATGAAATGTTTTG-----TAAAG----AATTGG------------------------TATATAAATACCTACAA----ATGGAATTTT------------------------TCAA------TTAAACGGCCAAGAG-CCCAAAAATAAATAAATATAGACTAATATT
droVir3	scaffold_12875:4361310-4361428 +	LASTZ	0	AAACC--AGA---ACGTA---------------------------AA----AGCT--T--TA-TTGTAAAATGCAC-------TGAAAATGCGGCAAAGCAGA-----------------TAA-A--------------------------------TATATATTTATATAT---------AGGAACTAC------------------------TGA--TTATATAAAGGAAGGAATCA-CG----------------TTAAACA-TATT
droMoj3	scaffold_6496:24941044-24941173 -	LASTZ	0	AATGA--TGG---TCACT--------------------------TGA----TTTTCAAGCTG-ATTT----ATGCA-------TCAAAATTATTCAAAGAGTA-----------------GGCA-CG-----------------------------CGATATATACATACATATAT----ATGCATATAT------------------------ATACGTGTGTATATAT-AGACATAA-CT----------------TTAGATTTTTAG
droGri2	scaffold_14822:484637-484751 -	LASTZ	0	GGACG--GAA----------------------------------GTG----CTT------CC-TTCTATATACTCT-------TT-AATAGCGCGTAGCTGTG-------------------AAA-A-----------------------------GTAAGCATG--TATTT---------TGTGGTGAT----------------TTTTGCAA-GGATATTTCTCAAATCAATGAA---------------------TTAA--TTTGCT

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	AAGCCACAAAATTCTCTAGGATTTAAAAACTCTTGAAAATGTGCCTAAGTGTATGGAATGCTATATATACATACTTTGCAGCTTTTCAAGTGATTTGAAATCACTAAAAGCCTTAAATATTGTT
droSim1	GTACCACCGAAGTCTCTAGGATTTAAAAACTCTTGAAAATGTGCCTAAGTGTATGCAATACTATATATACATACTTTGCAGCGTTTCAAGTGATTTCAAATCACTAAAAGCCTTAAATATTGTT
droSec1	GAGCCACCGAAGTCTCTAGGATTTAAAAACTCTTGAAAATGTGCCTAAGTGTATGCAATACTATATATACATACTTTGCAGCTTTTCAAGTGATTTCAAATCACTAAAAGCCTTAAATATTGTT
droYak2	AAGCCACAGAAGTCTCTAGGATTTAAAAACTCTTGAAAATGTGCCTAAGTGTAT-------------TACATACTATGCAGCTTTTCAAGTGATTTCAAATCACTAAAAGCCTTAAATATTGTT
droEre2	AAGCCACAGAAGTCTCTAGGATTTAAAAACTCTTGAAAATGTGCCTAAGTGTATGCAATACTACATATACATACTGTGCAGCTTTTCAAGTGATTTCAAATCACTAAAAGCCTTAAATATTGTT

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

GTACC--ACC----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTATATATACATACTT---------TGCAGCGTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................TTTAAAACCGCT-------TGAAAATG...................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droSec1

GAGCC--ACC----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTATATATACATACTT---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................TTAAAACCGCT-------TGAAAATG...................................................................................................................................................................................	19	1	4.00	0.00	4.00	0.00
................................................................TTTAAAACCGCT-------TGAAAATG...................................................................................................................................................................................	20	1	4.00	0.00	4.00	0.00
.......................................................................................................................................................................TACTT---------TGCAGCTTT------------------------TCAAGTGA................................................	22	1	4.00	0.00	4.00	0.00
.................................................................TTAAAACCGCT-------TGAAAAT....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................................CTTT------------------------TCAAGTGTTTTAAA..........................................	18	1	1.00	0.00	1.00	0.00
................................................................TTTAAAACCGCT-------TGAAAA.....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

AAGCC--ACA----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------T------------------------------------------TACATACTA---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................TGAAAAGTCT-------TGAAAATGT..................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AAGCC--ACA----------------------------------GAA----GTCT--CTAGG-ATTTAAAAACTCT-------TGAAAATGTGCCTAAGTGTA-----------------TGCAATA-----------------------------CTACATATACATACTG---------TGCAGCTTT------------------------TCAAGTGATTTCAAATCACTAAAAG-CC----------------TTAAATATTGTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................................................................................................................................CTTT------------------------TCAAGTGTTTTAAAA.........................................	19	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................AATGTACCTAAATGTA-----------------TG....................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................TAAAACCGCT-------TGAAAATG...................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................TACTG---------TGCAGCTTT------------------------TCAAGTGA................................................	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

AACCC--TCG----------------------------------TAA----GGGT--TTAGTGATTAAAAAGTTCT-------TGAAACTGCGCCTAAGGATG-----------------TGCAATG--------------------------------TATGT-----TTG---------AGCAGCTTT------------------------TCAAGGCATTTAAAATCATTAAAAT-TA-------------ATAGCAAATGAGGTT

Size

Hit Count

Total Norm

droBia1

AAGTC--ACT----------------------------------CAA----ATCT--CTAGGGATTTCAAATCTCC-------TGAAATTGTGCCTTAATGTA------------------GCAATG----------------------------------------TTTTT---------TGCAGCTAT------------------------TCTAGT---------TCACCAAAAA-CC----------------CTAGAAATTGTT

Size

Hit Count

Total Norm

droTak1

AAGCC--ACG----------------------------------AATAATAAGAT--ACAGG-GTGTTTAAACTCTAAACTACGTAGGATGGGTC----------------------------GATTTGAGTCGG----------------------TGCATTAAAGTTATC---------TAAGCCATT-----------------------------TAGTCTG-AATCA-TATATA-TA----------------TTTTATATTATC

Size

Hit Count

Total Norm

droEle1

AAATG--GCA----------------------------------AATGCTAATTT--ATGAG-G-TTGTAAACTTT-------TATAAATGTCGT-AAATCTT-----------------TCATA-A---------------------------CAAGC----TCTATGATA---------TATGGCTGT------------------------TTAAATA---TCAAACAACTAT---------------TTAGATATAAAACAGGGCT

Size

Hit Count

Total Norm

droRho1

GTGCC--ACA----------------------------------GAA----ATCA--CTTGGTTTTTGAAATCTCT-------TTTAAAAGTGTGCAAAAGTA-----------------TGCAACA-----------------------------ATATATGTTAAGTTCA---------GGAGTCCGT------------------------TAGATTCATTTAGTAACACGACTTT-AC----------------TTAAGATACATA

Size

Hit Count

Total Norm

droFic1

CTGCC--GTA----------------------------------AAAA---TTCC--CTTAA-ATTCAAAAAACA---------GA-AGATTAAGTGATTGTA-----------------TTAGAAT-----------------------------TTATCCAATATACACT-TAATGCTATCCG-ATTTTGAATTTACTGGAGATTTCTGT-------------GG---CA-----CG-CC----------------TTAACTTTCG-C

Size

Hit Count

Total Norm

droKik1

AATTACCTTC----------------------------------GTA----GTCT--CGAGTGTTTTGTAATCTCT-------CGAAAAGTTGTATAAGTGTT-----------------TGGAATT-----------------------------CTATATTTTTATAATT---------TAATATAGT-----------------------------TAATTTGTAATTTTAAAAAA-TT----------------ATTCTTAGCATT

Size

Hit Count

Total Norm

droAna3

TAGTG--GCA----------------------------------GGA----TACT--AGAGG-ATTAAAAAACTTC-------ACAGAATACATTTTCTTTTA-----------------AGAAAAG----TTGGAATTTTTAGA---------TTAG---------CTTTT---------TGTTTTAAA---------------------------------CAAATTATATTTGAAA-CT----------------ATGGGTTCTATC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................................................................................................................TTGGGATTTTTAGA---------TCAG---------C......................................................................................................	19	1	5.00	0.00	5.00	0.00	0.00
...................................................................................................................................TTGGATTTTTTAGA---------TCAG---------C......................................................................................................	19	2	2.00	0.00	2.00	0.00	0.00
..............................................................................................................................G----TTGGGATTTTTAGA---------TCAG---------C......................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..............................................................................................................................G----TTGGGATTTTTAGA---------TCA.................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
............................................................................................................................................TTTGA---------TTAG---------CTTTT---------TGGT.....................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................GTTTGA---------TTAG---------CTTTT---------TGTT.....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droBip1

TAAAA--ATT----------------------------------GAA----GA------------------AATAA-------TAATAATGTGAAAA-------------------------AAATA-----------------------------ATAAATAAAAATAATT---------TAAATATTT------------------------TAAAACATTTTGAAATAATAAAGTT-AA----------------AAAAATTAAATA

Size

Hit Count

Total Norm

dp4

ACC----AACACAATTTTTGAATATTTTGGGAAAATACTAGAAA-------TGGT--ATAAATACT----------A-----------------------------------AAAAGAAA------G---AT-AGAAA-------TACCATTCT------------------------------------AGAAATTGTCTCTGAATTCTTT-------------GG---TATC----CCAG----------------TTAATTTTGGTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......................................................................................................................................................TTT------------------------------------AGAAATTGTCTCCGA.................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

ACC----AACACAATTTTTGAACATTTTGGGAAAATACTAGAAA-------TGGT--ATAAATACT----------A-----------------------------------AAAAGAAA------G---AT-AGAAA-------TACCATTCT------------------------------------AGAAATTGTCTCTGAATTCTTT-------------GG---TATC----CCAG----------------TTAATTTTGGTT

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AAGGC--GCA----------------------------------CAG----TTCT--TCAGCAATTT---------------------------TCAGGCGAATGAAATGTTTTG-----TAAAG----AATTGG------------------------TATATAAATACCTACAA----ATGGAATTTT------------------------TCAA------TTAAACGGCCAAGAG-CCCAAAAATAAATAAATATAGACTAATATT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................................................................................................AAAG----AATTGG------------------------TAxATAAAAA.....................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................................................CAA----TTGGAATTTT------------------------TCAC------TT............................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

AAACC--AGA---ACGTA---------------------------AA----AGCT--T--TA-TTGTAAAATGCAC-------TGAAAATGCGGCAAAGCAGA-----------------TAA-A--------------------------------TATATATTTATATAT---------AGGAACTAC------------------------TGA--TTATATAAAGGAAGGAATCA-CG----------------TTAAACA-TATT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................................................................................................................................................TGA--TTATTTAGAGGAAGG....................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

AATGA--TGG---TCACT--------------------------TGA----TTTTCAAGCTG-ATTT----ATGCA-------TCAAAATTATTCAAAGAGTA-----------------GGCA-CG-----------------------------CGATATATACATACATATAT----ATGCATATAT------------------------ATACGTGTGTATATAT-AGACATAA-CT----------------TTAGATTTTTAG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GGACG--GAA----------------------------------GTG----CTT------CC-TTCTATATACTCT-------TT-AATAGCGCGTAGCTGTG-------------------AAA-A-----------------------------GTAAGCATG--TATTT---------TGTGGTGAT----------------TTTTGCAA-GGATATTTCTCAAATCAATGAA---------------------TTAA--TTTGCT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:52 EDT

block2035391

chr3R:4777401-4777494 -

Candidate

three_prime_UTR

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