sblock181387- Best orthologs

sblock181387	chrX:9538471-9538556 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 9538521-9538543
   star strand at position 9538500-9538519
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:9538456-9538571 -		1	TTTTCAGATCTCCAAGATATTTGCAAAG-----ATACTGAATTTATGCGATAAACTTGCAC-TGTCATAGT---------------------------------AGT-----AGTTCTTTCCATAAATTCGTAATGTAATGG----AAA----------------------------------------------------------------------------------------------------------------CGAAT-------TA--------------------AAAA---TC--TG
droSim1	chrX:7590585-7590703 -	MAF	4	TTTTCAGATCTCCAAGATATTTGCGAAG-----ATACTGAATTTATGCGATAAACTTGCAC-TGTCATAGT---------------------------------AGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGAAT-------TA--------------------AAAA---TC--GG
droSec1	super_15:302161-302279 -	LASTZ	3	TTTTCAGATCTCCAAGATATTTGCAAAG-----ATACTGAATTTATGCGATAAGCTTGCAC-TGTCATAGT---------------------------------AGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGAAT-------TA--------------------AAAA---TC--GG
droYak2	chrX:18128934-18129060 -	LASTZ	4	TTTTCAGATCTCCAAGATATTGACAAAG-----ATACTGGATTCATGCGATAAACTCGTAC-CGTCGGAAC---------------------------------TGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------TGAATCACTCTTTA--------------------AAGA---TC---T
droEre2	scaffold_4690:5579674-5579800 +	LASTZ	4	TCTTCAGATCTCCAAGATATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTAT-TGTCAGGGT-----------------------------------------ACTTGTTCTCATAAATTCGTAATGTCATGG----AAT----------------------------------------------------------------------------------------------------------------TGAATCACTCTTTA--------------------AGAG---TCTTGG
droEug1	scf7180000409032:387239-387428 +	LASTZ	5	TTTTCAGATCTCCAAGATATTTGTTAAG-----ATACTGGACTTAAGCGGTTAACTTGTAC-TGTCAGATA-----------------------------------------AATATTTCCCATAAATTCAAAGTGTTATGGCTGAAATTGATTTTCTAAAAGCAATCTA-ATC-----GAAGATTATATATCCCATAAAT------------------------------------------------------------TGGATTAATATCTATGAAATGGAAGGGCTGAAAAGGGG---GC--TT
droBia1	scf7180000301760:5525605-5525707 -	LASTZ	4	TTTCAGGATCTCCGAGGTACT-GCACAG-----ACACTTGACGCAAGCGCTAAACCTGTGC-TGTCCCAGT-----------------------------------------GCTATTTCACATAAACTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGATT-------T----------------------------------
droTak1	scf7180000415872:166233-166330 -	LASTZ	4	TTTCAAGATCTCGAAGATATTTGTACAGAT---ATACTGGATTTAAGCGATAAACTTGTACTTGTCACAGT-----------------------------------------ACTATTTCCCATAAAATCGCAAAATAATCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000491013:359530-359622 -	LASTZ	5	TTTTAAGATCTCGAACATATTGCAAGAG-----ATACTGAACTTAAGCGATTAACTTCGAC-TGTCAGAAT-----------------------------------------CATATTTTTCATTAGCTCGTAAAGCAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000780080:558549-558656 +	LASTZ	5	TTTTAAGATCTCGAAGATATT----AAA-----ACAACGCACTCTTGCGATAAAATTGAAC-TGTCAGAGT-----------------------------------------ACTATTTTCTATAAA-TCGTATTGTAATGG----TTT----------------------------------------------------------------------------------------------------------------TAAAA-------TG--------------------GAAT---CC--AG
droFic1	scf7180000454076:123635-123714 -	LASTZ	4	TGATG------------------------------------------CGTAAATTATACAT-TTTTGCTTT---------------------------------AGT-----AGTTCT-TGAAAGATTTCGCAAAGAAGTGT-----AC----------------------------------------------------------------------------------------------------------------CGATT-------TA--------------------AGATTTTCT--AG
droKik1	scf7180000302395:626782-626857 -	LASTZ	5	CATATCTT------------TCGCAATG-----AGACTTGTCTTCTGAGAGAAAAC----------------------------------------------------------------------------------------------------------------TTA-CCAAATAGTTTGGAAT-----ATATGAAAT-----------------------------------------------------------CTTTT-------------------------------------G--AA
droAna3	Unknown		0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396571:278436-278548 +	LASTZ	0	TGC--AGACCTCTAAAAAATTTCAAAAT-----AAAATGACTTTAA--AATTA------TC-TGCCAACATAATATATCCTTTTGTTACTAATTGAAGTTAAAAAATA---------------------------------------------------------------------------------------------------------------------------------------------------------TTAATTATTACTTT---------------------AAA---TT--TA
dp4	chr4_group1:5095426-5095542 -	LASTZ	0	CTTCGAAAACA-----------------------------------------AATC----------------------------------------------------------------------------------------------------------------TTC-CCTTTTTTTTTCAAGG-----GTATCAAACACTCGACTCCCCTTGCCAGGGTGCTTTTTTGTTGCCTTCTTCTTTTATTTTGACTTGAGCCAAG-------TC--------------------AAGT---TG--TG
droPer1	super_7:3845924-3845978 -	LASTZ	0	ATTTGAAGTATTGGAGGAGC--------------------------------------------------------------------------------------------GCATAGTTCAATGAACCGGAAATCTAATTA--------------------------------------------------------------------------------------------------------------------------A-------------------------------------TT--AA
droWil1	scaffold_181096:3465786-3465827 +	LASTZ	0	AAATTCATTTA------------TA----------------------------------------------------------------------------------------------------AATTTA----------------------------------------ATA-----GATTA-----------------------------------------------------------------------------TTAAA-------TA--------------------GTAT---AT--AG
droVir3	Unknown		0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:12829321-12829420 -	LASTZ	0	TTCATTGATAACT--GATACTAGCCAAG-----CCCTCGATAGCACGTGAGCAA--AGTCT-TGTCAGA-------------------------------------------AATGCATTTCATAAATTTGTAGTGTAGAAT----ATA----------------------------------------------------------------------------------------------------------------TGAAT-------------------------------------G--AA
droGri2	scaffold_14853:2001546-2001618 -	LASTZ	0	GCGGGAAAAAT----------------------ATACTACAATAAAACATGTATTTTTTATATGCCAT-------------------------------------------------TCTTTT----------------TGT----GTT----------------------------------------------------------------------------------------------------------------CTCGT-------TG--------------------TAAA---TT--TG

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	TTTTCAGATCTCCAAGATATTTGCAAAGA-----TACTGAATTTATGCGATAAACTTGCAC-TGTCATAGTAGT-----AGTTCTTTCCATAAATTCGTAATGTAATGG----AAACGA--------------------------------------ATT----------------AAAAATC----------------------TG
droSim1	TTTTCAGATCTCCAAGATATTTGCGAAGA-----TACTGAATTTATGCGATAAACTTGCAC-TGTCATAGTAGTAGT--AGTTATTTCCATAAATTCGTAATGTAATGG----AATCGA--------------------------------------ATT----------------AAAAATC----------------------GG
droSec1	TTTTCAGATCTCCAAGATATTTGCAAAGA-----TACTGAATTTATGCGATAAGCTTGCAC-TGTCATAGTAGTAGT--AGTTATTTCCATAAATTCGTAATGTAATGG----AATCGA--------------------------------------ATT----------------AAAAATC----------------------GG
droYak2	TTTTCAGATCTCCAAGATATTGACAAAGA-----TACTGGATTCATGCGATAAACTCGTAC-CGTCGGAACTGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGG----AATTGA--------------------------------------AT---------CACTCTTTAAAGATC----------------------T-
droEre2	TCTTCAGATCTCCAAGATATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTAT-TGTCAGGGT--------ACTTGTTCTCATAAATTCGTAATGTCATGG----AATTGA--------------------------------------AT---------CACTCTTTAAGAGTC-T-------------------TGG
droEug1	TTTTCAGATCTCCAAGATATTTGTTAAGA-----TACTGGACTTAAGCGGTTAACTTGTAC-TGTCAGATA--------AATATTTCCCATAAATTCAAAGTGTTATGGCTGAAATTGATTTTCTAAAAGCAATCTAATCGAAGATTATATATCCCATA-AATTGGATTAATATCTATGAAAT--GGAAGGGCTGAAAAGGGGGCTT
droBia1	TTTCAGGATCTCCGAGGTACT-GCACAGA-----CACTTGACGCAAGCGCTAAACCTGTGC-TGTCCCAGT--------GCTATTTCACATAAACTCGTAATGTAATGG----AATCGA--------------------------------------TTT-----------------------------------------------
droTak1	TTTCAAGATCTCGAAGATATTTGTACAGATA---TACTGGATTTAAGCGATAAACTTGTACTTGTCACAGT--------ACTATTTCCCATAAAATCGCAAAATAATCG--------------------------------------------------------------------------------------------------
droEle1	TTTTAAGATCTCGAACATATTGCAAGAGA-----TACTGAACTTAAGCGATTAACTTCGAC-TGTCAGAAT--------CATATTTTTCATTAGCTCGTAAAGCAAT----------------------------------------------------------------------------------------------------
droRho1	TTTTAAGATCTCGAAGATATT----AAAA-----CAACGCACTCTTGCGATAAAATTGAAC-TGTCAGAGT--------ACTATTTTCTATAAA-TCGTATTGTAATGG----TTTTAA--------------------------------------AAT----------------GGAATCC----------------------AG
droFic1	TGA------------------------------------------TGCGTAAATTATACAT-TTTTGCTTTAGT-----AGTTCT-TGAAAGATTTCGCAAAGAAGTGT-----ACCGA--------------------------------------TTT----------------AAGATTTTC-------------------TAG
droKik1	CATAT------------CTTTCGCAATGA-----GACTTGTCTTCTGAGAGAAAACTT----------------------------ACCA---------AATAGTTTGG----AATATA--------------------------------------TG---------AAATCTTTTG---------------------------AA

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			None

Small RNA-seq read pileup

Species

Alignment

droSim1

TTTTCAGATCTCCAAGATATTTGCGAAG-----ATACTGAATTTATGCGATAAACTTGCAC-TGTCATAGT---------------------------------AGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGAAT-------TA--------------------AAAA---TC--GG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................................................AATGG----ACT----------------------------------------------------------------------------------------------------------------CGAAT-------GA--------------------AAA..........	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

TTTTCAGATCTCCAAGATATTTGCAAAG-----ATACTGAATTTATGCGATAAGCTTGCAC-TGTCATAGT---------------------------------AGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGAAT-------TA--------------------AAAA---TC--GG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................ATTTAAGCGATAAGCGTGC.........................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

TTTTCAGATCTCCAAGATATTGACAAAG-----ATACTGGATTCATGCGATAAACTCGTAC-CGTCGGAAC---------------------------------TGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------TGAATCACTCTTTA--------------------AAGA---TC---T

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TCTTCAGATCTCCAAGATATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTAT-TGTCAGGGT-----------------------------------------ACTTGTTCTCATAAATTCGTAATGTCATGG----AAT----------------------------------------------------------------------------------------------------------------TGAATCACTCTTTA--------------------AGAG---TCTTGG

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TTTTCAGATCTCCAAGATATTTGTTAAG-----ATACTGGACTTAAGCGGTTAACTTGTAC-TGTCAGATA-----------------------------------------AATATTTCCCATAAATTCAAAGTGTTATGGCTGAAATTGATTTTCTAAAAGCAATCTA-ATC-----GAAGATTATATATCCCATAAAT------------------------------------------------------------TGGATTAATATCTATGAAATGGAAGGGCTGAAAAGGGG---GC--TT

Size

Hit Count

Total Norm

droBia1

TTTCAGGATCTCCGAGGTACT-GCACAG-----ACACTTGACGCAAGCGCTAAACCTGTGC-TGTCCCAGT-----------------------------------------GCTATTTCACATAAACTCGTAATGTAATGG----AAT----------------------------------------------------------------------------------------------------------------CGATT-------T----------------------------------

Size

Hit Count

Total Norm

droTak1

TTTCAAGATCTCGAAGATATTTGTACAGAT---ATACTGGATTTAAGCGATAAACTTGTACTTGTCACAGT-----------------------------------------ACTATTTCCCATAAAATCGCAAAATAATCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droEle1

TTTTAAGATCTCGAACATATTGCAAGAG-----ATACTGAACTTAAGCGATTAACTTCGAC-TGTCAGAAT-----------------------------------------CATATTTTTCATTAGCTCGTAAAGCAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droRho1

TTTTAAGATCTCGAAGATATT----AAA-----ACAACGCACTCTTGCGATAAAATTGAAC-TGTCAGAGT-----------------------------------------ACTATTTTCTATAAA-TCGTATTGTAATGG----TTT----------------------------------------------------------------------------------------------------------------TAAAA-------TG--------------------GAAT---CC--AG

Size

Hit Count

Total Norm

droFic1

TGATG------------------------------------------CGTAAATTATACAT-TTTTGCTTT---------------------------------AGT-----AGTTCT-TGAAAGATTTCGCAAAGAAGTGT-----AC----------------------------------------------------------------------------------------------------------------CGATT-------TA--------------------AGATTTTCT--AG

Size

Hit Count

Total Norm

droKik1

CATATCTT------------TCGCAATG-----AGACTTGTCTTCTGAGAGAAAAC----------------------------------------------------------------------------------------------------------------TTA-CCAAATAGTTTGGAAT-----ATATGAAAT-----------------------------------------------------------CTTTT-------------------------------------G--AA

Size

Hit Count

Total Norm

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TGC--AGACCTCTAAAAAATTTCAAAAT-----AAAATGACTTTAA--AATTA------TC-TGCCAACATAATATATCCTTTTGTTACTAATTGAAGTTAAAAAATA---------------------------------------------------------------------------------------------------------------------------------------------------------TTAATTATTACTTT---------------------AAA---TT--TA

Size

Hit Count

Total Norm

dp4

CTTCGAAAACA-----------------------------------------AATC----------------------------------------------------------------------------------------------------------------TTC-CCTTTTTTTTTCAAGG-----GTATCAAACACTCGACTCCCCTTGCCAGGGTGCTTTTTTGTTGCCTTCTTCTTTTATTTTGACTTGAGCCAAG-------TC--------------------AAGT---TG--TG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................TC----------------------------------------------------------------------------------------------------------------TTC-CGTTTTTTTTTCAAGA-----GT.................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droPer1

ATTTGAAGTATTGGAGGAGC--------------------------------------------------------------------------------------------GCATAGTTCAATGAACCGGAAATCTAATTA--------------------------------------------------------------------------------------------------------------------------A-------------------------------------TT--AA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AAATTCATTTA------------TA----------------------------------------------------------------------------------------------------AATTTA----------------------------------------ATA-----GATTA-----------------------------------------------------------------------------TTAAA-------TA--------------------GTAT---AT--AG

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

TTCATTGATAACT--GATACTAGCCAAG-----CCCTCGATAGCACGTGAGCAA--AGTCT-TGTCAGA-------------------------------------------AATGCATTTCATAAATTTGTAGTGTAGAAT----ATA----------------------------------------------------------------------------------------------------------------TGAAT-------------------------------------G--AA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................TCAGT-------------------------------------------AAAGCATTTCATA.......................................................................................................................................................................................	18	1	6.00	0.00	3.00	3.00	0.00
..............................................................................................................................ATTTGTAxTGTAGAAT----ATA----------------------------------------------------------------------------------------------------------------CG.............................................	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

GCGGGAAAAAT----------------------ATACTACAATAAAACATGTATTTTTTATATGCCAT-------------------------------------------------TCTTTT----------------TGT----GTT----------------------------------------------------------------------------------------------------------------CTCGT-------TG--------------------TAAA---TT--TG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:12:31 EDT

sblock181387

chrX:9538471-9538556 -

Candidate

intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup