sblock97631- 12- and 20-way alignments

sblock97631	chr3L:4091108-4091180 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 4091154-4091176
   star strand at position 4091122-4091142
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr3L:4091093-4091195 +	CAG--AATCACGC-AGGGCTTCCAGTGCGTCGCC-TCGGAGGATGAGGATGCCCTCCCAAAAGGCA--------------TCCGAAATCCCCGGGACGGACACAACCCGTA--TTTAGGTGAT
droSim1	chr3L:3630503-3630604 +	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTCCCAA-AGGGA--------------TTCGTAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT
droSec1	super_2:4083741-4083842 +	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTACCAA-AGGGA--------------TTCGTAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT
droYak2	chr3L:4661209-4661310 +	CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCAACCAA-AGGAA--------------TCCAAAGCCCTCCGGACGGACACAACCCGTA--TTTAGATGAT
droEre2	scaffold_4784:6799989-6800090 +	CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTCCCAA-GGGAG--------------TCCAAAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT
droAna3	scaffold_13337:7133496-7133604 +	CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCT-TCGGAGGACGAGGCTTCCT--CCAA-AGGAATTTGAAGG-A----TCCTCAACTTCTGTTGTGGGCACAACCCATA--ATTAAGTGAT
dp4	chrXR_group6:6380836-6380933 -	CAG--AATCACGC-AGGGCTTCCAGTGTCCCCAC-GCTGGATAGAAGGATCACTCATCCC-T------------TGGGCATCCG-------GCGTGGGGGCACAACCCACAGTATTAGGTGA-
droPer1	super_82:217037-217134 +	CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTC-GCTGGATAGAAGGATCACTCATCCC-T------------TGGGCATCCG-------GCGTGGGGGCACAACCCACAGTATTAGGTGA-
droWil1	Unknown	CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCTCTG-AGCCGAGTCAAT------------------------------------TCTC------GCCACAAACCCCC--CTAAAAAGAA
droVir3	Unknown	CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATA-TGGGATACTGTTAATTCGGTT-----------------------AGCCAG-ATGCTCAGCACAAATAAAACCTA-AGGATTAGTTGTA
droMoj3	Unknown	CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCC---------------------------------------------------------CTGCACAAATACAAACCTAAGGATTAGTTG-T
droGri2	Unknown	CAA--AATCACAAAAGGGCTTCCAGTGCGGCATA-TCTGAAGGACATGGTGATATATCAA-AT------------A----GCCATA-TCCTTGGCACAAATACAAACCTAAGGATTAGTTGTA

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:4091093-4091195 +	NA	CAG--AATCACGC-AGGGCTTCCAGTGCGTCGCCTC--------GGAGGATGAGGATGCCC----TCCCAAAAGG------------------CATCCGAAATCCCCGG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSim1	chr3L:3630503-3630604 +	3	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSec1	super_2:4083741-4083842 +	1	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TACCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droYak2	chr3L:4661209-4661310 +	1	CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AACCAAA-GG------------------AATCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGATGA-----T
droEre2	scaffold_4784:6799989-6800090 +	1	CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAG-GG------------------AGTCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droEug1	scf7180000409466:1855824-1855927 +	3	CAA--GATCACAA-AGGGCTTCCAGTGGGCCGTCTA--------GGAGGATTAGGGTCTTTA---TACCAAATGG------------------GATCCGAATTCACCAG-GGCG------GACACAACCCCTAATT--------------AGGTGA-----T
droBia1	scf7180000302428:785187-785288 +	3	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATTAGGATCTTT-----CCTAAT-GC-----------------AGATCCGAATTCC-CCG-GGCG------CGCACAACCCGTATTTA-------------AGGTGA-----T
droTak1	scf7180000415778:104468-104585 -	4	CAA--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCTTT----TCCCAAATGG------------------GATCCTATATCCACCG-GACG------GACACAACCCGTATTG----ATTAGTAGTTAAGTGAGCTTCT
droEle1	scf7180000491249:4938292-4938395 +	13	CAG--AATCACAC-AGGGCTTCCAGTGCGCCAACTC--------GGAGGACGAGGATCCCT----AGCCAAAGGG------------------GATCCAAAGTCCTCCGTGGAG------GACACAACCCAATTTT--------------AAGTGA-----T
droRho1	scf7180000779198:68875-68978 -	5	CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AGCCAAAGGG------------------GATCCGAACTCATCCGTGGGG------GTCACAACCCATATTT--------------AAGTGA-----T
droFic1	scf7180000454113:1306944-1307044 +	5	CAG--AATCACAA-AGGGCTTCCAGTGCGCCGTTCC--------GGAGGATGTGGATCCTG----TC-GAAAGGG------------------GATCCTGCTACCTCCG-GACG------GACACAACCCGTAATT--------------AGGTGA------
droKik1	scf7180000302388:258053-258145 -	12	CAG--AATCACCC-AGGGCTTCCAGTGCTCC-CTTG--------GGGGGACGAGGATCTTC-------------G------------------GATCCTTCAATTCCCA-AGAG------GACACAACCCGTAATT--------------AAGTGA-----T
droAna3	scaffold_13337:7133496-7133604 +	5	CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGGCTTCCT------CCAAA-GGAATTTGA--AG-------GATCCTCAACTTCT-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
droBip1	scf7180000396418:140234-140343 +	2	CAA-AGATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGA-TATCC----T-TTAAA-GAAATTTGA--CG-------GATCCTCAACTTCC-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
dp4	chrXR_group6:6380845-6380933 -	10	CAG--AATCACGC-AGGGCTTCCAGTGTCCCCACGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droPer1	super_82:217037-217125 +	1	CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTCGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droWil1	scaffold_180949:5996173-5996259 -	11	CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCT---C----TGA-GCCGAGTC------------------AA-TT-----CTCGGT---TCGCAAG-------AA-TTTTGCCACAAA--CC-CCCC----T--------------A----A-----A
droVir3	scaffold_13049:15328257-15328357 -	34	CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATTGGCATC--------CATG-GGATACTG----TT-------AA-TT-----CG--GT---TAGC--CAGATGCA-GATGTCAGCACAAATAAAACC------T--------------AAG-GA-----T
droMoj3	scaffold_6680:21529581-21529704 +	19	CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCG-GTATCTATATCTGTATCAGGGTCTATA---T--------AACTCCGATATA--G-C--TCTT--CAGATGCC-GATGCCTGCACAAATACAAACC-----TAAGGATT-------AG-TTG-----T
droGri2	scaffold_15110:19733397-19733505 -	34	CAA--AATCACAAAAGGGCTTCCAGTGCGGCATTGGTATC----TGA----AGGACATGGTGATATATCAAATAG---------------CCATATCCAGA--TCCA-GTTGTTGGCACAAATACAAACC-----T--------------AAG-GA-----T

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CAG--AATCACGC-AGGGCTTCCAGTGCGTCGCC-TCGGAGGATGAGGATGCCCTCCCAAAAGGCA--------------TCCGAAATCCCCGGGACGGACACAACCCGTA--TTTAGGTGAT

Size

Hit Count

Total Norm

droSim1

CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTCCCAA-AGGGA--------------TTCGTAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................GA--------------TTCGTAGCCCTCCGGACGGAC......................	23	1	2.00	0.00	0.00	0.00	2.00
..................CTTCCAGGACGCCGCC-TC......................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................CGGAGGATGAGGATTCCC.....................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................................CGTAGCCCTCCGGACGGACACAAC.................	24	1	1.00	0.00	0.00	0.00	1.00
..........................................................AA-AGGGA--------------TTCGTAGCCCTCCGGACGGAC......................	28	1	1.00	0.00	0.00	0.00	1.00

droSec1

CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTACCAA-AGGGA--------------TTCGTAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................CGCCGCC-TCGGAGGATGAGGAT.........................................................................	22	1	1.00	0.00	1.00	0.00

droYak2

CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCAACCAA-AGGAA--------------TCCAAAGCCCTCCGGACGGACACAACCCGTA--TTTAGATGAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................TCCAGTGCGCCGCC-TCGGAGGATGAGG...........................................................................	27	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................AGTGCGCCGxA-TCGGAGGAT...............................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................CCAGTGCGCCGCC-TCGGAGGATGAGG...........................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
......................CAGTGCGCCGCC-TCGGAGGATGAGG...........................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCC-TCGGAGGATGAGGATCCCCTCCCAA-GGGAG--------------TCCAAAGCCCTCCGGACGGACACAACCCGTA--TTTAGGTGAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................CGCC-TxGCAGGATGAGGAT.........................................................................	18	1	5.00	0.00	0.00	0.00	5.00
..........................GCGCCGCC-TCGGAGGATGCGG...........................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droAna3

CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCT-TCGGAGGACGAGGCTTCCT--CCAA-AGGAATTTGAAGG-A----TCCTCAACTTCTGTTGTGGGCACAACCCATA--ATTAAGTGAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................AGTCTTCCGCT-TCAGAGG.................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................GGCTTCCAGTGTTCCGCT-TCGGAGGACGA.............................................................................	29	1	1.00	1.00	0.00	0.00	0.00

dp4

CAG--AATCACGC-AGGGCTTCCAGTGTCCCCAC-GCTGGATAGAAGGATCACTCATCCC-T------------TGGGCATCCG-------GCGTGGGGGCACAACCCACAGTATTAGGTGA-	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................CATCCC-T------------TGGGCATCCG-------GCGT............................	21	1	1.00	1.00	0.00	0.00	0.00
.........................TGTCCCCAC-GCTGGATGGAAGGAT.........................................................................	24	1	1.00	1.00	0.00	0.00	0.00

droPer1

CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTC-GCTGGATAGAAGGATCACTCATCCC-T------------TGGGCATCCG-------GCGTGGGGGCACAACCCACAGTATTAGGTGA-	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
CAG--AATCACGC-AGGGCTTCCA...................................................................................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
...................................GCTGGATAGAAGGATCACTC....................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................ATCCT-------GCGTGAGGGCACAA..................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...................TTCCAGTGGCCCCTG-GCTG....................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCTCTG-AGCCGAGTCAAT------------------------------------TCTC------GCCACAAACCCCC--CTAAAAAGAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................AGTGCATTTTTCTCTG-AGC................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................TGAATTTTTCTATG-AGCC...............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................TCAAT------------------------------------TCGG------GCCACAAAC................	18	1	1.00	0.00	0.00	0.00	1.00
.........ACTTAAGCGTTTCCAGTGC...............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................ATTTTTCTATG-AGCCTAG............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................ACTGAATTTTTCTCTG-AGCC...............................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................CTG-AGCCGAGTCAAT------------------------------------TCTC------.........................	19	1	1.00	0.00	1.00	0.00	0.00
.......................ACTGCATTTTTCTATG-AGCC...............................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..............................TTTTCTCTG-AGCCGAGTCAAT------------------------------------TCTC------.........................	25	1	1.00	0.00	0.00	0.00	1.00
.......................ACTGCATTTTTCTATG-AGC................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATA-TGGGATACTGTTAATTCGGTT-----------------------AGCCAG-ATGCTCAGCACAAATAAAACCTA-AGGATTAGTTGTA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................................CAAATAAAACCTA-AGGATTAGTTGT.	25	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................AATAAAAACTx-AGGATTAG.....	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................AACCTA-AGGAATCGTT...	16	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCC---------------------------------------------------------CTGCACAAATACAAACCTAAGGATTAGTTG-T

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CAA--AATCACAAAAGGGCTTCCAGTGCGGCATA-TCTGAAGGACATGGTGATATATCAA-AT------------A----GCCATA-TCCTTGGCACAAATACAAACCTAAGGATTAGTTGTA

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

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