dme-mir-4963- 12- and 20-way alignments

dme-mir-4963	chrX:5684785-5684894 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 5684851-5684872
   star strand at position 5684813-5684833
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:5684770-5684909 +	CACCCACTGCGAATTGCTGTAGGAAAT-------TTTTTGG-GGTACTTCTGGTTTCATAACGCAGAGAATCATC-----------AGCGTGAAGGAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGATTTTAA----CCAGG
droSim1	chrX:4425250-4425396 +	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATACTGCAGAGAATCTTC-----------AGCGTGCAGTAATGATATCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA----CCAGG
droSec1	super_4:1079282-1079434 -	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATAACTCAGAGAATCTTCATGATTTCTTAATCA-----TAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA----CCAGG
droYak2	chrX:2788913-2789034 -	CACCCACTGCGAAATGCTATAGGACATGATGGAGCTTCTGGAGGTACTTCTGGTTTTATAATGCAGAGAATCGTA-----------ATCGTGAAGGAATGATTCTATGCGTACTGAAATCGGGAGTCCTGCAG------------------------------
droEre2	scaffold_4690:3033374-3033524 +	CACCCACTGCGAAATGCTATAGGAAACGATGGGGTTTCTGG-GGTACTTCTGGTTTTATAACGCACGGAATCTGA-----------ATCGTGAATGAATGATTCCTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGATTTGAAGTTTCGGAG
droAna3	scaffold_13117:1117754-1117783 +	CACCCACTGCGACGTACTTTAGAGAGTTGT-------------------------------------------------------------------------------------------------------------------------------------
dp4	chr3:13862643-13862665 +	CACCAGCTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_4:1457976-1457998 -	CACCAACTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7345062-7345085 -	AACCCACTGTGATGTCCTGTAAAA-------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13324:2924689-2924720 +	CACGGCCTGTGGTGTGCTATAAATTTT--------ATGTG---------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:13804424-13804517 -	CACCAGCTGCGGCTTGCTCTAAATTCATGT--------A--------------------AATGTACGAAATTACC-----------AGTGATCAAGTAATATGCGATTCGTGTTTAGTTTTTTAGAAATGTCA------------------------------
droGri2	scaffold_15112:3786307-3786359 +	CACCAGCTGCGGCGTGCTATAAATTCT--------TTTCGT-TGTATTTCTGGGTGTTCAACT--------------------------A-----TAATTGTTCCGCATGAAATTTTACCAAACGTCCAA---------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:5684770-5684909 +	NA	CACCCACTGCGAATTGCTGTAGGAAAT--------------------------TTTTTGGGGTACTTCTGG-TTTCATAACGCAGAGAATCAT----CAGCGTGAAG--GAATGATTC--TCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droSim1	chrX:4425250-4425396 +	4	CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATACTGCAGAGAATCTT----CAGCGTGCAG--TAATGATAT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droSec1	super_4:1079282-1079434 -	3	CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATAACTCAGAGAATCTTCATGATTTCTTAATCATAATGATTT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droYak2	chrX:2788911-2789034 -	3	CACCCACTGCGAAATGCTATAGGACATG--------------ATG----GAGCTTCTGGAGGTACTTCTGG-TTTTATAATGCAGAGAATCGT----AATCGTGAAG--GAATGATTC--TATGCGTACTGAAATCGGGAGTCCTGCAGAT------------------------------------------------------------------------------------
droEre2	scaffold_4690:3033374-3033523 +	1	CACCCACTGCGAAATGCTATAGGAAACG--------------ATG----GGG-TTTCTGGGGTACTTCTGG-TTTTATAACGCACGGAATCTG----AATCGTGAAT--GAATGATTC--CTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGAT------------------------------------------TTGAAGTTTCGG---------------A
droEug1	scf7180000409061:10542-10726 -	3	AACCCACTGTGATATGCTATAGGAAAGC--------------ATG----GAG-TTTTTAAAGTACTTCTGA-TTTTACTCAGTAGAGAATCTC----ATCTGTTAAT--GGTTGATTC--TCTGCTGGGTAAAACCAGAAGTCCTTCATATGCTCCTTGAATGATTGTGGCATGTGGTGGCCAAAGAATCAATATGGAATCAGAGG----AA---TTCG---------------T
droBia1	scf7180000298389:804043-804185 +	1	CACCCACTGCGATATGGTGTAGGATAAG-----------C--ATA----GGG-TTTTTGGGGAACTTCTTG-TTTAACCCACTAGAGAACTTT----ATCTTATAAT--AGATGATAA--TCTGTGGGGTAAAACCAGAAGTTCTCCAAAGGTTCTTTTAATGAT------------------------------------------AT--------AG---------------G
droTak1	scf7180000415769:818285-818415 -	3	CACCCACTGCGATTTGCTATAGGAAAGG-----------GATACA----GGT-TTTTTGGGGTACTTTTGG-TCTTAACCTGCAGAGTAT-TC----ATCTGATTTT--GGATGATTC--TCTGCGGGTTGAAACCAGAAGTTCCGCCAAAGCTCCT------------------------------------------------------------------------------
droEle1	scf7180000491356:73896-74031 -	5	AGT---------------------------------------------------TTTTGGTGTACTTTTGGGTCCCATCCAGCAGAGAAATTT----ATCTGATATT--GGAAGTGAT--TTAGCTGTATGAAATCAGAAGTTCCTCAGCTGCTCCTTGATTGTT------------------AAGTATTGATTTAAGACTAAAAA----GC---TCGG---------------A
droRho1	scf7180000779467:553932-554101 +	2	AACCCACTGCGATATGCTTTAGGAGATC--------------AAG----GGG-TTTTTGGGGTGCTTCTGG-ACTTATCCAGCTGAGATTTTC----ATCTGATATT--GGATGTTTT--TCTGCTGACTAAAATCAGAAGCCCTTCAAATGCTCCTTGAAGGTA------------------AAGTATTGATAAA-AACCTGAGATTTTGC---TTCC---------------G
droFic1	scf7180000453927:1329186-1329343 +	2	CACCCACTGCGACGTGGTCTACTAGTCCGTTGGCCTGTGCAGGCG----GGC-TCTGTGGAGCACTTCTGG-TGCTGCCACGCGGAGGACCCG----AGTCCTT------------AT--TCCGCGGGGTGGGACCACAAGTGCCACAAGTGCTGCTGTC--------------------------------------------------GC---CTTCGAATGGATTCTCCAAA
droKik1	scf7180000302481:398483-398533 -	3	CACCGAATGCGGGCTGCTCTAGGCGGTT--------------AGTCAGTGGG-TT-----------TTAAA-TTTT----------------------------------------------------------------------------------------------------------------------------------------------G---------------T
droAna3	scaffold_13117:1117754-1117783 +	1	CACCCACTGCGACGTACTTTAGAGAGTT--------------GT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396425:998854-998938 -	4	CACCCACTGCGACGTGCTCTAGGTGGTTGCAAGCCTG-----GTC----ACAC------------------------TATTGTAGGTAGATTT----AAGTG-------TCACGATTTCATCTGCGAGC----------------------------------------------------------------------------------------------------------
dp4	chr3:13862643-13862665 +	1	CACCAGCTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_4:1457976-1457998 -	1	CACCAACTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7345062-7345085 -	5	AACCCACTGTGATGTCCTGTAAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13324:2924689-2924720 +	3	CACGGCCTGTGGTGTGCTATAAATTT------------------------------------------------------------------T----ATGT-------------------------------------------------------------------------------------------------------------------------------------G
droMoj3	scaffold_6496:13805954-13805976 -	3	CACCGACTGCGGCGTCCTCTGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15112:3786307-3786359 +	2	CACCAGCTGCGGCGTGCTATAAATTC---------------------------TTTTCGTTGTATTTCTGG-GTGTTCAAC----------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CACCCACTGCGAATTGCTGTAGGAAAT-------TTTTTGG-GGTACTTCTGGTTTCATAACGCAGAGAATCATC-----------AGCGTGAAGGAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGATTTTAA----CCAGG

Size

Hit Count

Total Norm

droSim1

CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATACTGCAGAGAATCTTC-----------AGCGTGCAGTAATGATATCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA----CCAGG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................GATGATATTTTACGGATT.............	18	1	3.00	0.00	0.00	3.00	0.00
...................................................................................................GATATCCTGCGGCCTGCC..............................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................GATATCCTGCGGCCTGCT..............................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................TGCGGGCTGCAACCAGAAGTC....................................	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................TGCGGGCTGCAACCAGAAGTCC...................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATAACTCAGAGAATCTTCATGATTTCTTAATCA-----TAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA----CCAGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................TGTTTGG-GCTACTTCTGGT.............................................................................................................	19	1	1.00	1.00	0.00	0.00
.......................AAATGATGGxGTTGTTGG-G........................................................................................................................	18	1	1.00	0.00	0.00	1.00
.......................AAATGATGGGGTTTCTGG-.........................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CACCCACTGCGAAATGCTATAGGACATGATGGAGCTTCTGGAGGTACTTCTGGTTTTATAATGCAGAGAATCGTA-----------ATCGTGAAGGAATGATTCTATGCGTACTGAAATCGGGAGTCCTGCAG------------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................CATGGTGGAGCTTCTGTAG........................................................................................................................	19	1	178.00	6.00	0.00	170.00	2.00	0.00
........................CATGGTGGAGCTTCTGTA.........................................................................................................................	18	1	14.00	1.00	1.00	4.00	4.00	4.00
.........................ATGGTGGAGCTTCTGTAG........................................................................................................................	18	1	6.00	0.00	0.00	6.00	0.00	0.00
.............................................................................................................GTACTGAAATCGGGAGTCCTGCA...............................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................ATTCTATGCGTACTGAAATCG..........................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................................................................ATTCTATGCGTACTGAAATCGG.........................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
........................CATGGTGGAGCTTCTGAAG........................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
........................CATGTTGGAGCTTCTGTAG........................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
........................CATGGTGGAGCTTCTGTAGG.......................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
........................CATGGTGGAGCTTCTGT..........................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CACCCACTGCGAAATGCTATAGGAAACGATGGGGTTTCTGG-GGTACTTCTGGTTTTATAACGCACGGAATCTGA-----------ATCGTGAATGAATGATTCCTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGATTTGAAGTTTCGGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................................................................AATGGTTTGCAGTTTCGG..	18	1	1.00	1.00	0.00	0.00	0.00

droAna3

CACCCACTGCGACGTACTTTAGAGAGTTGT-------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CACCAGCTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CACCAACTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AACCCACTGTGATGTCCTGTAAAA-------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CACGGCCTGTGGTGTGCTATAAATTTT--------ATGTG---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CACCAGCTGCGGCTTGCTCTAAATTCATGT--------A--------------------AATGTACGAAATTACC-----------AGTGATCAAGTAATATGCGATTCGTGTTTAGTTTTTTAGAAATGTCA------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................................................................TTCAGTTTTTTAGAAAAGT................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................ATATTCGTTTCGTGTTTAG..............................................	19	1	1.00	0.00	0.00	1.00	0.00

droGri2

CACCAGCTGCGGCGTGCTATAAATTCT--------TTTCGT-TGTATTTCTGGGTGTTCAACT--------------------------A-----TAATTGTTCCGCATGAAATTTTACCAAACGTCCAA---------------------------------

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									None

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																	None