dme-mir-983-1-as- 12- and 20-way alignments

dme-mir-983-1-as	chrX:4262342-4262432 +	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 4262358-4262379
   star strand at position 4262396-4262416
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:4262327-4262447 +	TAC-GCCAGCGAGTTGAATGTTTACAACAACTAGATAATGCGTAACTACCTAATGAATGAACTGAAAATCATTAGTTCGAAACGT-ATTATTTAATTATTGCAATATAATAGCATATGCATAT
droSim1	chrX:3277334-3277447 +	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTGACGAACTCATGAATGA-CTGAAAATCATGTGTTCGAAAGGT-ATTACTAAATTACTGCAAGATATCA---TATGC---A
droSec1	super_4:2462216-2462328 -	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTAACGAACTCATGAATGA-CTGAAAATCATATGTTCGAAAGGT-ATTACTAAATTACTGCAACATATCA---TATGC----
droYak2	Unknown	---------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:1633112-1633231 +	CAC-GCCAACGAGTTGAATGTTAACAATAACTTAATAATCCGTTTCGCATTTATGAATGA-TTAAAGCACATAACTTCGAATCGA-ATTATTAAATCACTGTAACATAATATCACACAATTCC
droAna3	Unknown	---------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	---------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	---------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	---------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	---------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:31109889-31110001 +	TATCATGAGCTTTTCAAGTACTTAA---AGCTAGATAACAAATTT------CGTTTATTG-ATTAAATTGATAGGTTTTGGTTTTAATTATTTAGTTATTTTAATATAGTAACATACGTTGTT
droGri2	Unknown	---------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:4262327-4262447 +	NA	TAC-GCCAGCGAGTTGAATGTTTACAACAACTAGATAATG---------------------------------------CGTAACTACCTAATGAATGA---ACTGAAAAT-CATTAGTTC----------GAA----------AC-GTATTATTTAATTATTGCAATATAAT------------AGCATATG---------------------------CATAT
droSim1	chrX:3277334-3277447 +	1	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTGACGAACTCATGAATGA----CTGAAAAT-CATGTGTTC----------GAA----------AG-GTATTACTAAATTACTGCAAGATATC---------------ATAT------------------------------GCA
droSec1	super_4:2462215-2462328 -	3	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTAACGAACTCATGAATGA----CTGAAAAT-CATATGTTC----------GAA----------AG-GTATTACTAAATTACTGCAACATATC---------------ATAT------------------------------GCA
droYak2	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:1633112-1633231 +	1	CAC-GCCAACGAGTTGAATGTTAACAATAACTTAATAATC---------------------------------------CGTTTCGCATTTATGAATGA----TTAAAGCA-CATAACTTC----------GAA----------TC-GAATTATTAAATCACTGTAACATAAT------------ATCACACA---------------------------ATTCC
droEug1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301703:495454-495597 -	2	AAA-TCCGACACG----------------------------------TACTATTTGTT-TTTAAACCGAGCAAATAGTACGTAACGAACTTTCTAATGA----TTGGAAA----TGCGTTT----------GAA----------AC-A-------------CTACACACA---ATTTAAGATGGCAATATGTACCCTTAATTTAATAATGAAAAACCTTTTATAA
droTak1	scf7180000415394:1160785-1160887 -	2	GA------------TGTTTGTTAACAATAATTGAATAATCCGAAACGCACTACTGCATTTTCAAAATAAGCAC-----------------------------------------TAAGAAC----------GAA----------TC-GGACTATTAAATGATTGGAAATTTC-------------------------------------------------CTTT
droEle1	scf7180000491011:2112374-2112507 -	1	GAC-A-------------------------------------ATGCGAACAAGTTGATTTTAAAAAGGAGTGCATA---GTCAACAAAATGTTAAAAGAGAACTTGAAAATTCACTTGTTTTTATATCTATTCA----------CT-TTATTATATATTTTTTGTAATATGTA------------TGTATGTA---------------------------TGTCG
droRho1	scf7180000779334:415671-415796 -	2	CTA-AGCAGTGTGCTATTTATTAATTCGAACTATTTTAAT---------------------------------------ATTGATTAGGTAATAGATAT----CTAAAACT-AATATTTTA----------GGAGCAACTTATGAT-ATGTTACTATACAACTACACAAC---TTTT-------------AAG---------------------------CAGAT
droFic1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:31109889-31110001 +	3	TATCATGAGCTTTTCAAGTACTTAA---AGCTAGATAACA---------------------------------------AATTT------CGTTTATTG----ATTAAATT-GATAGGTTT----------TGG----------TTTTAATTATTTAGTTATTTTAATATAGT------------AACATACG---------------------------TTGTT
droGri2	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TAC-GCCAGCGAGTTGAATGTTTACAACAACTAGATAATGCGTAACTACCTAATGAATGAACTGAAAATCATTAGTTCGAAACGT-ATTATTTAATTATTGCAATATAATAGCATATGCATAT

Size

Hit Count

Total Norm

droSim1

TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTGACGAACTCATGAATGA-CTGAAAATCATGTGTTCGAAAGGT-ATTACTAAATTACTGCAAGATATCA---TATGC---A	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................AGATAATACCTGACGAACTCA......................................................................	21	3	1.67	0.00	1.33	0.33	0.00
........................................................................GTGTTCGAAAGGT-ATTACT...............................	19	3	0.67	0.00	0.67	0.00	0.00
.......................................................................TGTGTTCGAAAGGT-ATTACT...............................	20	3	0.33	0.00	0.00	0.33	0.00
...............................................................................................TTAATGCAAGATATCA---TATGA---.	21	2	0.50	0.50	0.00	0.00	0.00
................................AGATAATACCTGACGGACTCA......................................................................	21	3	0.33	0.00	0.33	0.00	0.00

droSec1

TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTAACGAACTCATGAATGA-CTGAAAATCATATGTTCGAAAGGT-ATTACTAAATTACTGCAACATATCA---TATGC----	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................TATGTTCGAAAGGT-ATTACTAA.............................	22	3	0.33	0.00	0.33	0.00

droYak2

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CAC-GCCAACGAGTTGAATGTTAACAATAACTTAATAATCCGTTTCGCATTTATGAATGA-TTAAAGCACATAACTTCGAATCGA-ATTATTAAATCACTGTAACATAATATCACACAATTCC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................ACTTCGAATCGA-ATTATTAAAT...........................	22	2	8.50	0.50	0.00	0.00	8.00
.........................................................................ACTTCGAATCGA-ATTATTA..............................	19	2	1.50	0.00	0.00	0.00	1.50
.......................................................................TAACTTCGAATCGA-ATTATT...............................	20	2	0.50	0.00	0.00	0.00	0.50
.......................................................................TAACTTCGAATCGA-ATTATTAA.............................	22	2	0.50	0.00	0.00	0.00	0.50
.........................................................................ACTTCGAATCGA-ATTATT...............................	18	2	0.50	0.00	0.00	0.00	0.50
................................TAATAATCCGTTTCGCATTTATG....................................................................	23	3	0.33	0.00	0.00	0.00	0.33
.........................................................................ACTTCGAATCGA-ATTATTAAAC...........................	22	2	0.50	0.00	0.50	0.00	0.00
.........................................................................ACTTCGAATCGA-ATTATTAAATG..........................	23	2	0.50	0.00	0.00	0.00	0.50

droAna3

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

---------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TATCATGAGCTTTTCAAGTACTTAA---AGCTAGATAACAAATTT------CGTTTATTG-ATTAAATTGATAGGTTTTGGTTTTAATTATTTAGTTATTTTAATATAGTAACATACGTTGTT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

---------------------------------------------------------------------------------------------------------------------------

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