dme-mir-312-as- 12- and 20-way alignments

dme-mir-312-as	chr2R:16471561-16471626 +	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 16471602-16471622
   star strand at position 16471565-16471586
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:16471546-16471641 +	GATTCGTTTTAAAG-------------------TAATCAGGCCGTCTCAAGTGCAATACTAGTTAA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAATCG-CTTCAA--ACTTAATT
droSim1	chr2R:15132834-15132929 +	GATTCTTTTTAAAG-------------------TAATTCGGCCGTCTCAAGTGCAATACAAGTTTA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAAACG-CTTTAA--ACTTAATT
droSec1	super_1:14025748-14025843 +	GATTCTTTTTAAAG-------------------TAATTCGGCCGTCTCAAGTGCAATACAAGTTTA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAAACG-CTTTAA--ACTTAATT
droYak2	chr2R:12724685-12724781 -	GATTCGTTTAAAAG-------------------TAATCCGGCCGTCTCAAGTGCAATACTAGCTTT-AA-TAGTGCAGAATTGCTCCTGGGACGAACCGAAGCG-CTTCAA--ACGCAATT
droEre2	scaffold_4845:10616687-10616785 +	GTTTTGTTTAAAAG-------------------TAATCCGGCCGTCTCAAGTGCAATACTAGCTTAAAAAAAATGCAGAATTGCTCCTGGTACGAACCGAAGCG-CTTCAA--ACTTAATT
droAna3	scaffold_13266:4132669-4132780 -	TTTTCGGTTATAGC----CGCTTAGATCCACTATATTTCGGCCGTCTCAAGTGCAATACTTGTATA-AA-AAACCAAGAGTTGCACTAGAGACGCACCGGAAAA-TTGTAG--ATGTTTTT
dp4	chr3:8679756-8679826 -	TTTGAACCCAGCAGTAGGCA-------------CTTTCAGGCCAGTGGGTGTGCAATACTGGTGAA-ATACAACACAGTATTGCCC-----------------------------------
droPer1	super_4:2566590-2566653 -	TTCGTATTTGCAAG-------------------AACCACGGCCTAC--------------------------------------AAATCAAAGCAGCTCGATGCACCCTTCCGCTTGTACA
droWil1	scaffold_180700:3453141-3453235 -	TGTTTAACTTGAAC-------------------TTTTCCGGCCGTGAAGTGTGCAATTATTTTCGT-AT--ATTACA-ATTTGCAGACTAAACGAACCTAAAAAATTTTCG--AGTTTATG
droVir3	scaffold_12875:13669041-13669063 +	GACACGGCCTGAA------------------------------------------------------------------------------------------------AA--ATATAGCT
droMoj3	scaffold_6496:9090603-9090622 +	AAGAAG---------------------------------------------------------------------------------------------------CTTAAA--TTGCAGAC
droGri2	scaffold_15245:17564268-17564296 -	ACCACA-----------------------------------------------------------------------------------------GCCGAAAAA-CTGAAG--ATTTGCTT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:16471546-16471641 +	NA	GATTCGT-----------------------------------------TTTAAAGTAATCAGGCCGTC--------------TCAAGTGCAATACTAGTTAAAA----AATGCAGAATTGCCCTTGTGACGAACCAAATCGCTTCAAACTTAATT---------
droSim1	chr2R:15132834-15132929 +	1	GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droSec1	super_1:14025748-14025843 +	1	GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droYak2	chr2R:12724685-12724781 -	1	GATTCGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTTAA---TAGTGCAGAATTGCTCCTGGGACGAACCGAAGCGCTTCAAACGCAATT---------
droEre2	scaffold_4845:10618147-10618242 +	3	GTTTTGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTAAA----AATGCAGAATTGCTCCTGGTACGAACCGAAGCGCTTCAAACTTAATT---------
droEug1	scf7180000409474:1490038-1490133 -	1	GTTTTGT----------------------------------------ATTTCAAGTCATCCGGCCGTC--------------TGAAGTGCAATTTTCTATT--G----ACTCTAAAATTGCACAAAAGGCGAACCGAAATACTAGAAATTTTATTT--------
droBia1	scf7180000302291:2816211-2816324 -	1	AGTTTCT----------------ATGCACT----------TTCCTTGTTTTCAAGCACTCCGGCCGTC--------------TCAAGTGCAATTCTAGTCGGA-----AATACAGGATTGCTCCTGGGACGGACCGAAACGCCAAAAATATGCCTA--TAT---
droTak1	scf7180000415401:99973-100067 +	1	GTTTCGT----------------------------------------ATTTAAAGTATTCCGGCCGTC--------------TCAAGTGCAATACTAGGTGAA-----AATTCAGAATTGCGCCTGAGACGGACCGGAACACCAGAAATAT-GTT---------
droEle1	scf7180000491201:736234-736328 +	1	TTTTTAT-----------------------------------------TCCAAAGTGTTGCGGCCGTC--------------TCAAGTGCAATGCTAACCAGAA----AACGCAGAATTGCCCCATAGACGTACCGAAACACCAGAAAT-TAGTA---------
droRho1	scf7180000780104:82286-82422 +	1	AATGCAAAAATAACTTTTT--CAATAAACTTGCTTAAATGTT-TTAAATCCAAAGTATTGCGGCCGTC--------------TCAAGTGCAATGCTAGCCAAGA--AAAACGAAGAATTGCTTTTGAGACGAGCCGAAACACCAGAAATTTGTTCG--------
droFic1	scf7180000454039:1776269-1776366 +	1	ATA--AA-----------------------------------------TTTAAAGCATTTCGGCCGTC--------------TCAAGTGCAATGCTAGCCATAAAGTTAATTTAGTATTGCCACCCAAGACGACCGAAACACTCGAAATTGGTTT---------
droKik1	scf7180000302471:941817-941912 +	3	GTTTTGG-----------------------------------------GCCGCCTTGATCTGGCCGTT--------------TCAAGTGCAATTCTGGCTATTA----ACCACAGATTTGCACCTCAAACAGCACAGACCTTTACGGCCGGAGCT---------
droAna3	scaffold_13266:4132676-4132765 -	1	GCTTAGA-----------------------------------------TCCACTATATTTCGGCCGTC--------------TCAAGTGCAATACTTGTATAAA---AAACCAAGAGTTGCACTAGAGACGCACCGGAAAATTGTAGA----------------
droBip1	scf7180000396427:2575377-2575498 -	1	CTTTCGGC---------TTG----------------TAGCTGCATAGATCCACAATATTCTGGCCGTC--------------TCGAGTGCAATTCTTGTTGGAA---AAACCAAGATTTGCACTGGAGATGACCCCGAAAATTGTAGACATAAATCCAAACACA
dp4	chr3:8679756-8679828 -	2	TGTTGAAC---------CCA----------------GC---------AGTAGGCACTTTCAGGCCAGT--------------GGGTGTGCAATACTGGTGAAAT--ACAACACAGTATTGCCC-----------------------------------------
droPer1	super_4:2566585-2566655 -	1	ATTCGTAT----------------------------------------TTGCAAGAACCACGGCCTACAAATCAAAGCAGCTCG--------------------------------------------ATGCACCCTTCCGCTTGTA-CACTAAT---------
droWil1	Unknown	NA	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:13669092-13669193 +	2	CTTGTGTT---------TTAA--ATGGA-------------------ATCTCAATTTTTCCGGCCGTG--------------AAAAGTGCAATACTTGTAAAAATAAAAAAAAAGAATTGACACTGACCACAGCCGAAAAACTAGC------------------
droMoj3	Unknown	NA	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15245:17564268-17564358 -	1	AGACCC---------------------------------------------TCATTTATCCGGCCGTG--------------AAGAGTGCAATGCTTGTCAAAT-----AAAAAGAATTGACACTAACCACAGCCGAAAAACTGAAGATTTGCTT---------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GATTCGTTTTAAAG-------------------TAATCAGGCCGTCTCAAGTGCAATACTAGTTAA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAATCG-CTTCAA--ACTTAATT

Size

Hit Count

Total Norm

droSim1

GATTCTTTTTAAAG-------------------TAATTCGGCCGTCTCAAGTGCAATACAAGTTTA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAAACG-CTTTAA--ACTTAATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................AATTGCCCTTGTGACGAACTT......................	21	2	0.50	0.00	0.50	0.00	0.00

droSec1

GATTCTTTTTAAAG-------------------TAATTCGGCCGTCTCAAGTGCAATACAAGTTTA-AA--AATGCAGAATTGCCCTTGTGACGAACCAAAACG-CTTTAA--ACTTAATT

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

GATTCGTTTAAAAG-------------------TAATCCGGCCGTCTCAAGTGCAATACTAGCTTT-AA-TAGTGCAGAATTGCTCCTGGGACGAACCGAAGCG-CTTCAA--ACGCAATT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GTTTTGTTTAAAAG-------------------TAATCCGGCCGTCTCAAGTGCAATACTAGCTTAAAAAAAATGCAGAATTGCTCCTGGTACGAACCGAAGCG-CTTCAA--ACTTAATT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
GTTTTATTAAAAAG-------------------TAAT....................................................................................	18	2	1.50	1.00	0.00	0.00	0.50

droAna3

TTTTCGGTTATAGC----CGCTTAGATCCACTATATTTCGGCCGTCTCAAGTGCAATACTTGTATA-AA-AAACCAAGAGTTGCACTAGAGACGCACCGGAAAA-TTGTAG--ATGTTTTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................................................AGTTGCACTAGAGACGCACCGGAAA..................	25	2	0.50	0.00	0.00	0.00	0.50
...........................................ATATCAAGTGCAATACTTG...........................................................	19	2	0.50	0.00	0.00	0.00	0.50

dp4

TTTGAACCCAGCAGTAGGCA-------------CTTTCAGGCCAGTGGGTGTGCAATACTGGTGAA-ATACAACACAGTATTGCCC-----------------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......................................GGCCAGTGGGTGCGCAATACTG............................................................	22	2	0.50	0.00	0.00	0.50	0.00

droPer1

TTCGTATTTGCAAG-------------------AACCACGGCCTAC--------------------------------------AAATCAAAGCAGCTCGATGCACCCTTCCGCTTGTACA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TGTTTAACTTGAAC-------------------TTTTCCGGCCGTGAAGTGTGCAATTATTTTCGT-AT--ATTACA-ATTTGCAGACTAAACGAACCTAAAAAATTTTCG--AGTTTATG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................ATTTTTGT-AT--ATTATA-AT.........................................	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

GACACGGCCTGAA------------------------------------------------------------------------------------------------AA--ATATAGCT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AAGAAG---------------------------------------------------------------------------------------------------CTTAAA--TTGCAGAC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ACCACA-----------------------------------------------------------------------------------------GCCGAAAAA-CTGAAG--ATTTGCTT

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										None	None
UNAFold Image										None	None	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																	None		None
UNAFold Image																	None		None