dme-mir-4959- 12- and 20-way alignments

dme-mir-4959	chrX:19063163-19063281 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 19063234-19063255
   star strand at position 19063186-19063207
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:19063148-19063296 -	TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1	chrX:14724057-14724205 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1	super_8:1352288-1352436 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2	chrX:17654811-17654959 -	TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2	scaffold_4690:9326382-9326530 -	TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC
droAna3	scaffold_12903:667658-667806 +	TCCTGATGGCCCTGATGTCCGGCCTGAATTTGGTCTGTCGCGTGGCGATGATTATCAGCAAGACCCTAAGAGAGCAGATGATCCGGAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTCCAGAGGGCGCTGAGGGATCTGACGATCGGG
dp4	chrXL_group1e:10756223-10756371 -	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGG
droPer1	super_14:190427-190575 -	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTTCGCGACCTCACCATCGGG
droWil1	scaffold_181096:8247011-8247159 -	TGCTGATGGCCATCATGTCGGGCCTCAATCTACTCTGTCGCCTGGCCATGATGCTGAGCAAGAGTGTGCGTGAGCAAATGATTCGCAGTCAATTGCGTTTTATGCCCAAACGGCATATCCAACGAGCTCTCAGGGATCTAACCATTGGC
droVir3	scaffold_12726:998444-998592 -	TGCTGATGGCCTTCATGTCCGGCCTGAACCTGCTCTGCCGTCTGGCCATGATGCTCAGCCGGACGCTGCGTGAGCTGATGATACGCAGCCAATTGCGCTTCATGACCAAGCAGCATGTACAGCGCGTTTTCCGGGATCTAACCATCGGT
droMoj3	scaffold_6473:9166585-9166733 +	TGCTGATGGCCTTCATGTCCGGCCTGAATCTGCTCTGTCGCCTGGCCATGATGCTCAGCCGGACGCTGCGCGAGCTGATGATACGCAGCCAATTGCGCTATATGACCAAACAGCATGTGCAGCACGTCTTCAGGGATCTGACCATCGGC
droGri2	scaffold_14853:5433396-5433544 -	TCCTCATGGCGATCATCGCTGGCCTAAATCTGCTCTGTCGCCTAACCATGATGGTCAGCCGGACGCTGCGCGAACTGATGATTCGCAGCCAGTTGCGATTCATGACCAAAGAGCATGTGCAGCGCATCTTTAGCCATTTAACCATCGGC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:19063148-19063296 -	NA	TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1	chrX:14724057-14724205 -	25	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1	super_8:1352288-1352436 -	22	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2	chrX:17654811-17654959 -	102	TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2	scaffold_4690:9326382-9326530 -	39	TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC
droEug1	scf7180000409089:53868-54016 +	4	TGCTGATGGCTTTTATGTCTGGACTGAATCTTCTCTGCCGACTGGCCATGATCCTTAGCAGGAATCTCCGCGAGCAGATGATTCGCAGTCAGTTGCGTTTCATGAGCAAAAGGCATGTGAAGCGAGCCCTGGGCGACCTAACCATTGGG
droBia1	scf7180000302187:38542-38690 +	11	TCCTGATGGCCCTGATGTCCGGCCTGAACCTCCTCTCCCGGCTGGCCATGATCTGCAGCAGATACCTCCGCGAGCAGATGATCCGCAGCCAGCTGCGCTTCATGACCAAGCGGCATGTGAAGCGCGCTCTGCGCGACCTCACCATCGGG
droTak1	scf7180000415281:63891-64039 -	10	TCCTGATGGCCCTGATGTCCGGCCTGAATCTGCTCTGTCGGCTGGCGATGATCTGCAGCAGGAATCTGAGGGAGCAGATGATCCGCAGCCAGTTGCGCTTCATGGCCAAGCGGCATGTGAAGCGCGCCCTGCGGGATCTGACCATCGGG
droEle1	scf7180000490751:647069-647217 -	32	TGCTGATGGCCCTGATGTCCGGCCTGAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGAAACTGCGGGAGCAGATGATCCGCAGTCAGCTGCGATTCATGACCAAGCGGCATGTGCAGCGCGCCCTGCGCGACCTCACCATTGGC
droRho1	scf7180000778091:273360-273508 -	22	TGCTGATGGCCCTCATGTCCGGCCTGAATCTCCTTTGCCGGCTGGCGATGATCTGCAGCAGGAATCTGCGGGAGCAGATGATCCGCAGCCAGCTGCGCTTCATGACCAAGCGGCATGTGCAGCGGGCACTGCGCGACCTCACCATCGGC
droFic1	scf7180000451789:82400-82548 -	25	TGCTGATGGCCCTAATGTCCGGACTGAATCTCCTCTGCCGGCTGGCGATGATCTGCAGCCGGAACTTGCGGGAGCAGATGATTCGCAGCCAGCTGCGCTTCATGACCAAGCGGCATGTGCAGCGCGCCCTGCGCGACTTAACCATCGGT
droKik1	scf7180000302234:53857-54005 +	4	TGCTGATGGCCCTGATGTCCGGCCTGAATCTGCTCTGTCGGCTGGCCATGATCCTGAGCAGTTACCTGCGCGAACAGATGATTCGCAGCCAGTTGCGGTTCATGAGCATGCGGCATGTGCAGCGCGCTTTGCGGGACCTGACCATCGGT
droAna3	scaffold_12903:667658-667806 +	2	TCCTGATGGCCCTGATGTCCGGCCTGAATTTGGTCTGTCGCGTGGCGATGATTATCAGCAAGACCCTAAGAGAGCAGATGATCCGGAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTCCAGAGGGCGCTGAGGGATCTGACGATCGGG
droBip1	scf7180000395916:40365-40513 -	10	TGCTCATGGCCCTGATGTCCGGTCTGAACTTGGTCTGTCGCCTGGTGATGATTATCAGTAAGACCTTACGGGAACAGATGATCCGAAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTGCAGAGGGCGCTGAGGGATCTGACGATTGGG
dp4	chrXL_group1e:10756223-10756371 -	32	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGG
droPer1	super_14:190427-190575 -	31	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTTCGCGACCTCACCATCGGG
droWil1	scaffold_181096:8247011-8247159 -	25	TGCTGATGGCCATCATGTCGGGCCTCAATCTACTCTGTCGCCTGGCCATGATGCTGAGCAAGAGTGTGCGTGAGCAAATGATTCGCAGTCAATTGCGTTTTATGCCCAAACGGCATATCCAACGAGCTCTCAGGGATCTAACCATTGGC
droVir3	scaffold_12726:998444-998592 -	68	TGCTGATGGCCTTCATGTCCGGCCTGAACCTGCTCTGCCGTCTGGCCATGATGCTCAGCCGGACGCTGCGTGAGCTGATGATACGCAGCCAATTGCGCTTCATGACCAAGCAGCATGTACAGCGCGTTTTCCGGGATCTAACCATCGGT
droMoj3	scaffold_6473:9166585-9166733 +	14	TGCTGATGGCCTTCATGTCCGGCCTGAATCTGCTCTGTCGCCTGGCCATGATGCTCAGCCGGACGCTGCGCGAGCTGATGATACGCAGCCAATTGCGCTATATGACCAAACAGCATGTGCAGCACGTCTTCAGGGATCTGACCATCGGC
droGri2	scaffold_14853:5433396-5433544 -	134	TCCTCATGGCGATCATCGCTGGCCTAAATCTGCTCTGTCGCCTAACCATGATGGTCAGCCGGACGCTGCGCGAACTGATGATTCGCAGCCAGTTGCGATTCATGACCAAAGAGCATGTGCAGCGCATCTTTAGCCATTTAACCATCGGC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC

Size

Hit Count

Total Norm

droSim1

TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...................................................................................................TCATGACCAAGCTGGATG................................	18	1	2.00	0.00	2.00	0.00	0.00
......................................................................................AGCCAGCxGCGTTTCAAGAC...........................................	19	1	1.00	0.00	0.00	1.00	0.00
......................CTTGAACCTTCTGTGCCGGCTGGCCAT....................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00

droSec1

TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..CTCATGGCCCTTATGTCCT................................................................................................................................	19	1	3.00	0.00	0.00	3.00
.........................................CTGGCCATGATCTGCAGCAGGT......................................................................................	22	1	1.00	0.00	1.00	0.00
.........................................................................................CAGCTGCGTTTCATGACCAAGC......................................	22	1	1.00	0.00	1.00	0.00
....................................................................................GCCGCCAGCAGCGTTTCA...............................................	18	1	1.00	0.00	1.00	0.00
......................................................................................AGCCAGCxGCGTTTCAAGAC...........................................	19	1	1.00	1.00	0.00	0.00
..........................................................................................................................CGTGCCCAGCGTTACCTGA........	19	1	1.00	0.00	1.00	0.00
..CTCATGGCCCTTATGTCCC................................................................................................................................	19	1	1.00	0.00	0.00	1.00
....CATGGCCCTTATGTCCTG...............................................................................................................................	18	1	1.00	0.00	0.00	1.00
.CCTCATGGCCCTTATGTC..................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.............................................................................................................................GTCCTGxGCGACCTCACC......	17	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................CCTGGGCGACCTTACCA.....	17	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................TGACCAAGCGGCATGTGGA............................	19	1	1.00	0.00	0.00	1.00	0.00
.........................................CTGGCCATGATCTGCAGCAGGT......................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................................GCAAGTATCTACAGGAGC..........................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................ATGTCCAAGCTGCATGTGC.............................	19	1	1.00	0.00	0.00	1.00	0.00

droAna3

TCCTGATGGCCCTGATGTCCGGCCTGAATTTGGTCTGTCGCGTGGCGATGATTATCAGCAAGACCCTAAGAGAGCAGATGATCCGGAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTCCAGAGGGCGCTGAGGGATCTGACGATCGGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...TGATxGTCCTGATGTCCGGC..............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
........................................................................AGCAGATGCTCCGGAGCAAG.........................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................GATGAGGTTCTTGAAGAAG.......................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................GTCCTGAGGGCGGTGAGG...............	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................GGTCCAGAGGGCGGTGAG................	18	1	1.00	0.00	0.00	0.00	1.00
TCCTCATGGCCCTTATGTC..................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................CGGCGCTGAGGGATCAG.........	17	1	1.00	0.00	0.00	1.00	0.00

dp4

TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTTCGCGACCTCACCATCGGG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................................TTCGCGACTTCACCACCG..	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................TCCATCAAGCGTCTGCGCC.............................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

TGCTGATGGCCATCATGTCGGGCCTCAATCTACTCTGTCGCCTGGCCATGATGCTGAGCAAGAGTGTGCGTGAGCAAATGATTCGCAGTCAATTGCGTTTTATGCCCAAACGGCATATCCAACGAGCTCTCAGGGATCTAACCATTGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................TGTGCGTGAGGAAATGAAT..................................................................	19	1	17.00	16.00	1.00	0.00	0.00
..CTGCTxGCCATCATGTCGG................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................................................CAAGTGGGTGCGTGAGCA.........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................GAGAAAGAGTGTGTGTGAGC..........................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

TGCTGATGGCCTTCATGTCCGGCCTGAACCTGCTCTGCCGTCTGGCCATGATGCTCAGCCGGACGCTGCGTGAGCTGATGATACGCAGCCAATTGCGCTTCATGACCAAGCAGCATGTACAGCGCGTTTTCCGGGATCTAACCATCGGT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................AACGTGCTGTGCCGTCTGG........................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TGCTGATGGCCTTCATGTCCGGCCTGAATCTGCTCTGTCGCCTGGCCATGATGCTCAGCCGGACGCTGCGCGAGCTGATGATACGCAGCCAATTGCGCTATATGACCAAACAGCATGTGCAGCACGTCTTCAGGGATCTGACCATCGGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TCCTCATGGCGATCATCGCTGGCCTAAATCTGCTCTGTCGCCTAACCATGATGGTCAGCCGGACGCTGCGCGAACTGATGATTCGCAGCCAGTTGCGATTCATGACCAAAGAGCATGTGCAGCGCATCTTTAGCCATTTAACCATCGGC

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