dme-mir-275-as- 12- and 20-way alignments

dme-mir-275-as	chr2L:7425795-7425892 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 7425812-7425834
   star strand at position 7425851-7425873
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:7425780-7425907 -	ATGGT--GAAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TACAGTCGGGGGAACATCA
droSim1	chr2L:7217350-7217477 -	ATGGC--GGAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droSec1	super_3:2941240-2941367 -	ATGAC--GGAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droYak2	chr2L:5473766-5473897 +	ATATCGTGGAGT--------------T----GGAG----ATATATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTGTTCAGTCGGGGGAACATCA
droEre2	scaffold_4929:16344506-16344633 -	ATGGT--GGAGA--------------T----GGAG----ATATATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droAna3	scaffold_12916:15333988-15334092 -	ATGGC--G--------------------------G----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-----TGCAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG--GAGAGT-------------
dp4	chr4_group1:4175728-4175848 -	ATGAT--G---------CCACACAGAT----G--------TTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAAAAAA-----CCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTG--------
droPer1	super_5:1086441-1086561 +	ATGAT--G---------CCACACAGAT----G--------TTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAAAAAA-----CCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTG--------
droWil1	scaffold_180772:5257564-5257692 +	GTGTC--GTCGTTGT-----CGCCGTCGTCGTGCGATGAATCTTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGT---ATTGAATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC-----------------------
droVir3	scaffold_12963:15419948-15420059 +	ATGGT--A-AGC--------------T----TAAGATGA--ATACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAACCAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------
droMoj3	scaffold_6500:18399371-18399491 +	ATGCT--AGAATTGCTAGCAGAG----------CGTTGA--ATGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGAGATAATCGAAA-----CCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------
droGri2	scaffold_15126:5008401-5008523 -	ATGTT----TG------CTGAGCAGGCGCCGTTTGTTGA--ATGCGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAATCAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC-----------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:7425780-7425907 -	NA	ATGG--TGAA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TA----------CAGTCGGG--GGAACA--T--CA
droSim1	chr2L:7217350-7217477 -	1	ATGG--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droSec1	super_3:2941240-2941367 -	1	ATGA--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droYak2	chr2L:5473766-5473897 +	1	ATATCGTGGA------------------GTTGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTC-TG-------T-TCAGTCGGG--GGAACA--T--CA
droEre2	scaffold_4929:16344506-16344633 -	1	ATGG--TGGA------------------GATGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droEug1	scf7180000409463:614687-614823 -	1	GCGA--TGAAG--------------ACATATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATGT--A-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCAAGGTAGAAGACAT-TTAAGCCTTT-TCA---GGG--AGAACA--T--CA
droBia1	scf7180000302422:9125514-9125641 -	1	GCGG--TGGA------------------TGTGG-AG----ATG--TCTGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAC--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTTT----------AAGCCGGG--GGAACA--T--CA
droTak1	scf7180000415604:142420-142542 +	2	ATGG------------------------GTTGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCCGGG--GGAACA--T--CG
droEle1	scf7180000491028:1624837-1624954 +	4	AAA--------------------------ATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--G-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTTGG---GGAACA-------
droRho1	scf7180000766421:7648-7769 +	2	------TGGA------------------AATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATATGAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCTGG---GGAACA-------
droFic1	scf7180000454115:155668-155793 -	2	GTGC--TGGA------------------TATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGCAGTAGACTT-TT-------TTCCAGC-TGG--GGAACA-------
droKik1	scf7180000302384:54817-54950 +	1	GAGT--TGTT------------------G---GC-GATG-ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAAGAGACTTTTT----------CAGCTGGGAAGGAACACATCCCG
droAna3	scaffold_12916:15333988-15334092 -	1	ATGG--CG---------------------------G----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG-GA----------GAGT-------------------
droBip1	scf7180000396572:1689389-1689508 +	1	ATGT--CGGA------------------TATGGCGG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TG----------GAG---------TACA--T--GG
dp4	chr4_group1:4175727-4175841 -	2	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droPer1	super_5:1086448-1086562 +	1	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droWil1	scaffold_180772:5257564-5257692 +	2	GTGT--CGTCGTTGTCGCCGTCGTC--GT---GC-GATGAATC--TTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGTATTG-AATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC--------------------------------------
droVir3	scaffold_12963:15419953-15420066 +	1	AAGC--TTAA-------------------------GATG-A-A--TACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAACCAAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG-CG----------CAG--------------------
droMoj3	scaffold_6500:18399385-18399491 +	4	GCAG------------------------A---GC-GTTG-A-A--TGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGA---GATAATCGAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC--------------------------------------
droGri2	scaffold_15126:5008401-5008495 -	5	ATG--------------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAATCAAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC--------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATGGT--GAAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TACAGTCGGGGGAACATCA

Size

Hit Count

Total Norm

droSim1

ATGGC--GGAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................CCCCGGTCACTGATTAGCGCGC...................................	22	2	3.50	0.00	2.00	0.00	1.50
..........................................................................................................CCCCGGTCACTGATTAGCGCGCA..................................	23	2	3.50	0.00	1.00	1.50	1.00
............................................................................CTGACTGx---ATATAAAAAA-----G............................................................	18	2	1.00	0.00	1.00	0.00	0.00
............................................................................................................CCGGTCACTGATTAGCGCGCA..................................	21	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................CCCGGTCACTGATTAGCGCG....................................	20	2	0.50	0.00	0.00	0.50	0.00
..........................................................................................................CCCCGGTCACTGATTAGCGC.....................................	20	2	0.50	0.00	0.50	0.00	0.00
...........................................................CGCGCTACTTCAGGTACCTGACT.................................................................................	23	2	0.50	0.00	0.50	0.00	0.00
............................................................................CTGACTGT---CTAxAAAAAA-----C............................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

ATGAC--GGAGA--------------T----GGAG----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................................CCCCGGTCACTGATTAGCGCGC...................................	22	2	0.50	0.00	0.00	0.50
..........................................................................................................CCCCGGTCACTGATTAGCGCG....................................	21	2	0.50	0.00	0.00	0.50

droYak2

ATATCGTGGAGT--------------T----GGAG----ATATATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTGTTCAGTCGGGGGAACATCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................TCTGG-GCCCACGCGCGCTA.................................................................................................	19	2	0.50	0.00	0.00	0.00	0.00	0.50

droEre2

ATGGT--GGAGA--------------T----GGAG----ATATATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................TCAGTCGGTTGAACATCA	18	2	0.50	0.50	0.00	0.00	0.00

droAna3

ATGGC--G--------------------------G----ATATATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-----TGCAAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG--GAGAGT-------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
............................................................................CTGACTGx-----TGCAAAGA-----CCA..........................................................	18	2	0.50	0.00	0.00	0.00	0.50
........................................................................GTACCxGACTGT-----TGGAAAAA-----.............................................................	19	2	0.50	0.00	0.00	0.00	0.50

dp4

ATGAT--G---------CCACACAGAT----G--------TTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAAAAAA-----CCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTG--------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

ATGAT--G---------CCACACAGAT----G--------TTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAAAAAA-----CCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTG--------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................AACAGCT----G--------TTCGTGTCTA.................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................CTAG-CTGCACGCGCGCTA.................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00

droWil1

GTGTC--GTCGTTGT-----CGCCGTCGTCGTGCGATGAATCTTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGT---ATTGAATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC-----------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..GTC--GTCGTCGT-----CGTCGTC........................................................................................................................................	18	7	1.29	0.00	0.00	0.00	1.29
.......GTCGTCGT-----CGTCGTCGTC.....................................................................................................................................	18	7	1.29	0.00	0.00	0.00	1.29
GTGTC--GTAGTCGT-----CGCCGTC........................................................................................................................................	20	2	1.50	1.00	0.50	0.00	0.00
..CTC--GTCGTTGT-----CGTCGTC........................................................................................................................................	18	2	1.50	0.00	0.00	0.00	1.50
.......GTCGTTGT-----CGTCGTCGTC.....................................................................................................................................	18	3	0.67	0.00	0.00	0.00	0.67
..........GTCGT-----CGCCGTCGTCGTC..................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.TGGC--GTCGTTGT-----CGTCGTC........................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..GTA--GTCGTTGT-----CGCTGTC........................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.........CGTCGT-----CGCCGTCGTCGTC..................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.......GTCGTTGT-----CGTCGTCGTCGTC..................................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................TAGCGCGCAAGTTAAGAGT........................	19	2	0.50	0.50	0.00	0.00	0.00
..GTC--GTCGTCGT-----CGTCGTCGTC.....................................................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
..GTC--GTCGTTGT-----CGTCGTC........................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
..GTC--GTCGTCGT-----CGTCGTCG.......................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
........TCGCTGT-----CGCTGTCGTCGT...................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..GTC--GTCGTCGT-----CGCCGTC........................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.......GTCGTCGT-----CGTCGTCGTCG....................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
....C--GTCGTCGT-----CGTCGTCGTC.....................................................................................................................................	19	5	0.20	0.00	0.00	0.00	0.20
....C--GTCGTCGT-----CGTCGTCGT......................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
....A--GTCGCTGT-----CGCCGTCGT......................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.TGTC--GTCGTCGT-----CGTCGTC........................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.ATTC--GTCGTTGT-----CGCCGTC........................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.......GTCGCCGT-----CGCCGTCGTC.....................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
.........CGTCGT-----CGTCGTCGTCGT...................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14

droVir3

ATGGT--A-AGC--------------T----TAAGATGA--ATACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAACCAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................TCTGGGCxCCACGCGCGCT..................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
...................................ATGG--ATGCGTCTGGCCACCAC.........................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00

droMoj3

ATGCT--AGAATTGCTAGCAGAG----------CGTTGA--ATGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGAGATAATCGAAA-----CCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......AGAATTGCTAGCAGAG----------CGTT..............................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
............................................................................CTGACTGTGAGCTAAACGAA...................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droGri2

ATGTT----TG------CTGAGCAGGCGCCGTTTGTTGA--ATGCGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAATCAAAA-----CCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC-----------------------	Size	Hit Count	Total Norm	V109 Male body
...............................................CTGGGCAGCACGCGCGCTA.................................................................................................	19	2	1.00	1.00
...............................................CTGGGCTCCACGCGCGCT..................................................................................................	18	2	1.00	1.00
...............................................CTGGCCTGCACGCGCGCTAC................................................................................................	20	2	0.50	0.50
...............................................CTGGGCAGCACGCGCGCTAC................................................................................................	20	2	0.50	0.50

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