dme-mir-4948- 12- and 20-way alignments

dme-mir-4948	chr3R:26876819-26876925 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 26876845-26876866
   star strand at position 26876884-26876902
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:26876804-26876940 -	GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGCT--
droSim1	chr3R:26523820-26523956 -	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGTT--
droSec1	super_4:5701489-5701625 -	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGCT--
droYak2	chr3R:27815996-27816132 -	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGAC-------------------CCTACCTTGCT--
droEre2	scaffold_4820:1105506-1105642 +	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGAC-------------------CCTGCCCTGCT--
droAna3	scaffold_12911:4046748-4046884 +	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAAC-------------------GCGTCCTTGCT--
dp4	chr2:271882-272018 +	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAAT-------------------CCGGCCCAGCT--
droPer1	super_7:3056347-3056483 +	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAAT-------------------CCGGCCCAGCT--
droWil1	scaffold_181108:531799-531935 -	GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCAC-------------------CCGACCCTGTT--
droVir3	scaffold_12855:1470098-1470234 +	GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAG-------------------TCGACCCTGGC--
droMoj3	scaffold_6540:27213622-27213758 +	GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAG-------------------TCGACCCTGGC--
droGri2	scaffold_15074:2330328-2330485 +	GTTCTCCCAGTCACGTTCGGCAGTGTGAGCATAGACACCTGCTGGAGAGGCATGCGTCACACGGGTGGTGGTCACCAGACCCGACCACTTGCCCGCATCCATGGCCCACTTGGCAATGGAATCCACGTAGTTGGTCTTATCCAATATGACCTTGCAGT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:26876804-26876940 -	NA	GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT
droSim1	chr3R:26523820-26523956 -	13	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT
droSec1	super_4:5701489-5701625 -	11	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT
droYak2	chr3R:27815996-27816132 -	12	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT
droEre2	scaffold_4820:1105506-1105642 +	5	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT
droEug1	scf7180000409166:158947-159083 +	2	GCACTCCCAATCTCTGTCGTAGATGTGGGCGTAGGTGGCGGCAGGCGTTGCATGGGTGATCCTGGTGGTGGTGACAATACCAGTGCGCTTGCCCTCCTTTTGGGCCCACTCCATCACGCTTTGAACCCTGCCCTGTT
droBia1	scf7180000302113:442836-442972 +	2	GCACTCCCAATCCCTGTCGTAAATATGGGCGTAGGTGGCCGCAGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACGATTCCCGTGCGCTTGCCCGCCTTCTGGGCCCACTCCATTACGTTCTGGATCCTGCCTTGCT
droTak1	scf7180000415236:217947-218083 -	8	GCACTCCCAATCGCGGTCGTAGATGTGGGCGTAGGTGGCAGCGGGCGTGGCATGAGTGATCCTGGTGGTGGTGACAATTCCAGTGCGCTTGCCCTCCTTTTGTGCCCATTCCATGACGCTTTGGACCCTGCCCTGCT
droEle1	scf7180000491212:972484-972620 -	11	GCATTCCCAATTCCTGTCGTAAATATGGGCGTAAGTGGCGGCGGGCGTGGCATGGGTGATCCTAGTGGTGGTGACTATTCCCGTGCGTTTGCCCAGCTTTTGGGCCCACTCCATGACGCTTTGAACGCGACCTTGCT
droRho1	scf7180000761687:129-265 +	3	GCACTCCCAATCTCTGTCGTAAATGTGGGCGTAGGTGGCGGAGGGCGTGGCATGTGTGATCCTGGTGGTGGTGACTATTCCCGTGCGCTTGCCCTCTTTTTGGGCCCACTCCATGACGCTTTGAACCTGACCTTGCT
droFic1	scf7180000453782:423025-423161 +	1	GCACTCCCAATCCCTGTCGTAGATGTGGGCGTAAGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACAATTCCGGTGCGCTTGCCCGCCTTCTGAGCCCACTCCATGATGCTTTCGACGCGACCTTGCT
droKik1	scf7180000302238:91277-91413 -	5	GCACTCCCAGTCCCGGTTGTATATATGGGCATATGTGGCAGCGGGTGTGGCATGCGTGATCCTGGTCGTGGTGACTACTCCAGTGCGTTTTCCCTCCTTTTGGGCCCAATCCATAATGCTCTGGACGCGACCCGATT
droAna3	scaffold_12911:4046748-4046884 +	1	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT
droBip1	scf7180000396640:894541-894677 +	3	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCATGGGTAATCCGAGTGGTGGTAACTATTCCAGTTCGCTTTTTCTCCTTTTGGGCCCACTCCATGACGCTCGCGACACGTCCTTGCT
dp4	chr2:271882-272018 +	1	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT
droPer1	super_7:3056347-3056483 +	7	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT
droWil1	scaffold_181108:531799-531935 -	13	GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCACCCGACCCTGTT
droVir3	scaffold_12855:1470098-1470234 +	1	GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC
droMoj3	scaffold_6540:27213622-27213758 +	4	GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC
droGri2	scaffold_14624:4037357-4037493 +	2	GCATTCCCAGTCACGATTATAGATATTGGCATAGCTAGATGCCGGTGTGGCATGCGTAATCCTTGTGTTTGTCACCACGCCCGTCCGTTTGCCCACCCGCTGTGCCCAGTCCATGATGGAGTCGAGGCGACCCTGTG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGCT--

Size

Hit Count

Total Norm

droSim1

GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGTT--	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................CGTCGCGTGGGTGGTCCTG..............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGAC-------------------CCTGCCTTGCT--	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......TTGTCGCGGTCGTAGATG.....................................................................................................................................	18	1	1.00	1.00	0.00	0.00
...............................TAGGCGGCGGGGGGCGTGGCG..........................................................................................................	21	1	1.00	0.00	1.00	0.00
..........................................................................CCACGCCGGTGCGCTTGCCCTC..............................................................	22	1	1.00	0.00	1.00	0.00
.................................................................TTCTAGTGACCACGCCGG...........................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGAC-------------------CCTACCTTGCT--	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................ATGGGGGCGTCCGTGGC.......................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................GTGGCGGCAGGTGGGGC...........................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................GTGGCATGGGCGTTCCTGGT............................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................GCATGGATxATCCTGGTGGT.........................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGAC-------------------CCTGCCCTGCT--	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................GCAGGCGTGGCATGGGCT....................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAAC-------------------GCGTCCTTGCT--	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................GGCGTGGGGAATCCGACTGG..........................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................TCCATGAGGCTCTTAAC-------------------G............	18	1	1.00	0.00	0.00	1.00	0.00
.......................TGTGGTCGTAGGTTGGA......................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
............................................................................ATTCCAGTTCGCTTGTGCT...............................................................	19	1	1.00	0.00	0.00	0.00	1.00

dp4

GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAAT-------------------CCGGCCCAGCT--	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...................TAAATGTGGGCGTGGGTGGCC......................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droPer1

GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAAT-------------------CCGGCCCAGCT--	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................TGTGGGCGAAGGTGGACGC....................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
..................GTAGATGTCGGCGTAGGC..........................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................TGGCTGTGGGCGTAGGTGG........................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................TGTGGGCGAAGGTGGACG.....................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCAC-------------------CCGACCCTGTT--	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................AAGTTGAGGCAGACGTGG............................................................................................................	18	1	16.00	11.00	0.00	5.00	0.00
....................................................TGTGTAATTATGGTAGTGGTAAT...................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droVir3

GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAG-------------------TCGACCCTGGC--	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................CGTAATGCGTGTxGTGGCCA....................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................GTTTGCCGTxACGCTGTGCC....................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAG-------------------TCGACCCTGGC--

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GTTCTCCCAGTCACGTTCGGCAGTGTGAGCATAGACACCTGCTGGAGAGGCATGCGTCACACGGGTGGTGGTCACCAGACCCGACCACTTGCCCGCATCCATGGCCCACTTGGCAATGGAATCCACGTAGTTGGTCTTATCCAATATGACCTTGCAGT

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