sblock147574- Best orthologs

sblock147574	chr3R:12058990-12059092 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 12059006-12059027
   star strand at position 12059057-12059077
   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	chr3R:12058975-12059107 +		1	CTTTGAT--AAAGCAATAATTAAATAATTACAAAATG----------------------------------------------------------------------------------------------------------------------------------------------TTAGTTATATTTACAAATTAGTTTTTAGTACTAGAAAACTACCTAGATTTGTAAATATCTCTAACAAA------------------CAT------------------------------------------------------------------------GTTGTTATAAGATA--------------------------C--------------------------------------------------ACA--TTTCCAGTG
droSim1	chr3R:9407157-9407279 -	LASTZ	3	CAGTAAT--TAA-----------TTAATTACAAAATG----------------------------------------------------------------------------------------------------------------------------------------------TAGGTTATACTTAGAAAATAGTTGTTAGTACTACAAAACTACGTAGATTTGTAAATATCTCTAACAAA------------------CAT------------------------------------------------------------------------GTTGTTATAAGATA--------------------------C--------------------------------------------------ACA--TTTCCAGTG
droSec1	super_219:5788-5910 -	LASTZ	3	CAGTAAT--TAA-----------TTAATTACAAAATG----------------------------------------------------------------------------------------------------------------------------------------------TAGGTTATATTTAGAAAATAGTTGTTAGTACTACAAAACCACCTAGTTTTGTAAATATCTCTAGCAAA------------------CAT------------------------------------------------------------------------TTGGTTATAAGATA--------------------------C--------------------------------------------------ACA--TTTCCAGTG
droYak2	chr3R:14371434-14371609 -	LASTZ	4	TTCACAC--AGAAAAATCAGTAATTAACTTAAATATT----------------------------------------------------------------------------------------------------------------------------------------------ACATTTAAATTTAGAAATTGGGTG----TAAAACAGAAGTACCTCAATTTGCAAATAACTTTAAAAAA------------------GGTTTATTTTC-----GAACTATCGATCATTT----------------------------------------------------------------------------------------------CGTAAGCCTTGATTTAACCCT--AGCTGTT-GCGAAAAGTTAA-TTTTCCAGTG
droEre2	scaffold_4770:11583141-11583230 +	LASTZ	5	TTGTTTT--TA------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA-----------------------------------------------------------------------------------GGTTGATTTTG-----GAACTAGCGATCAGTT----------------------------------------------------------------------------------------------CGTTTGCCTAGATTTGTACTT--AACTGTT-GCGAAAAATAAA-TTTTCCAGTG
droEug1	scf7180000409797:1457960-1458053 -	LASTZ	0	CTTCAAG--AGGA-------AACT---TAACAATATT----------------------------------------------------------------------------------------------------------------------------------------------TAAGTTTT---------------------------------------------------------------------------------------CCC-----TGTTAAT---CA---------------------------------------------------------------------------------------------------TTAACTATCACTTATTCCT--AACACTTACCAAAATATCCA-TTTTCCAGTA
droBia1	scf7180000302075:3196702-3196832 +	LASTZ	0	AATCTAA--TTTGTAATAAAAAA-----------GTT-----------------------TGTATATTTTTAT--------------------------------------------------------------------------------------------------------------ATATTTTAGTGAAGTAACTTAT------------------------------------------------------------GGATAATTTCC-----CACCTAAC---CATTT----------------------------------------------------------------------------------------------AGTAAGCCTCTCTGAATTCCT--AACACCT---AAAAAATACG-TTTTCCAGTG
droTak1	scf7180000413892:95434-95602 -	LASTZ	0	CATTCCT--AAAA--A----TACT---TTACTGAATGTACTACGTTTTGCAATAATTTTAAGCAAATTTCTTTCCATTTCTATTCAGGAAGCTTTTCAGTTAATTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCAAAGGAATTAGCGATCATAT----------------------------------------------------------------------------------------------AGTTAGCCTCAATATATTCCC--AGCACTT-GCCAAAAATACA-TTTTCCAGTG
droEle1	scf7180000491080:1872815-1873041 +	LASTZ	0	AAATTAA--AAGGTAAA---AACT---TTACAAAATT---------------------------------------------------------------------------AAAACTGGAAATGTCATGATAAAGTCAAATGATACTTATGTATATTACATTTTAATTATAAAAAACA-------------------------------------C------TAT---------------------TTTTTAATGAGCTTTA-----------------------------------------------TTTTCGTCACAAAAACA--------------TTTTAATAAAATAATATTATTGTATATTGCTGCTTATAAAAAGTTCGATCCTTTAGCTTAAATCCAT---C--AAC-ACA-GCT-AAAATAAA-TTTTCCAGT-
droRho1	scf7180000767081:47281-47442 -	LASTZ	0	GCCTTAC--TAAACAAGAAAAACT---TCGCGAAA--------------------------------------------------------------------------------------------------AAGTCA-----------------------TTTAAAAGTAACTAACA-------------------------------------CAT----------------------------ATTTTAATGGGCTT-A-----------------------------------------------TTAACGTTAGACAAATACTTTTACGAGACTG---T-------TA--------------------------TAAGTCC----TC-TACCTGTTGTTTATATCCACAA-CCTA-GCAAAAAGTACA-TTTTTCAGTG
droFic1	scf7180000453829:1362214-1362328 -	LASTZ	0	ATTTCCT--ATATAGATAATAACT----TGTCAAATG----------------------------------------------------------------------------------------------------------------------------------------------TTAACTACA-----------ATTT--------------------------------------------TTTTTATTGTGTTG-AGA-------------------------------TATTTATCATCCAATAT-----------------TTCCAAGCCTTTCACTAAATTTGG--------------------------A--------------------------------------------------ATA--TTTTGAATG
droKik1	scf7180000302706:1039140-1039238 -	LASTZ	0	CAAATCAACAGAA-------AACT------------------------------------AGTATACTATTAC------------------CTTTTCAG--AATATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCATAAAA---CACAATCATAT---------------------------------TTAAAAACACTTCA----AACAT---------------------------------------------------------------------------GTTAAA-CTTTCCAGT-
droAna3	scaffold_12911:2484085-2484206 -	LASTZ	0	TTTCTTC--AAAAGATTGGTCCAATAAT----------------------------------------------------------------------------TTT-------------------------------------------------------------------------------CACATAGAAAAAGGGAC----TACAGCCGAACTTAATCTATACTCCCA----------------------------------------------------------------------------CTATTATCTGAAACTTTTATTTCAGAGATTA---T-------CA--------------------------C--------------------------------------------------AAATTCTAACAGTG
droBip1	scf7180000396714:624067-624177 +	LASTZ	0	TTTAAGA--GAAG-------TTC-----------------------------------------------------------------------------------TCACTCAGAAATGGGTGTTTC---------------------------------------------------------------------------------ACA-----ACCAATGAGA---------------------------------------------------------ACTTATAATCCAT--------------TATTTATCTAAAACTTTAAATGCACAGAT--------TGAGACA--------------------------C--------------------------------------------------AAATTCTAGCAGT-
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	CTTTGATAAAGCAATAATTAAATAATTACAAAATGTTAGTTATATTTACAAATTAGTTTTTAGTACTAGAAAACTACCTAGATTTGTAAATATCTCTAACAAACAT-------------------------------------------------GTTGTTATAAGATACACATTTCCAGTG
droSim1	C-----------AGTAATTAATTAATTACAAAATGTAGGTTATACTTAGAAAATAGTTGTTAGTACTACAAAACTACGTAGATTTGTAAATATCTCTAACAAACAT-------------------------------------------------GTTGTTATAAGATACACATTTCCAGTG
droSec1	C-----------AGTAATTAATTAATTACAAAATGTAGGTTATATTTAGAAAATAGTTGTTAGTACTACAAAACCACCTAGTTTTGTAAATATCTCTAGCAAACAT-------------------------------------------------TTGGTTATAAGATACACATTTCCAGTG
droYak2	TTCACACAGAAAAATCAGTAATTAACTTAAATATTACATTTAAATTTAGAAATTGGGTG----TAAAACAGAAGTACCTCAATTTGCAAATAACTTTAAAAAAGGTTTATTTTCGAACTATCGATCATTTCGTAAGCCTTGATTTAACCCTAGCTGTTGCGAAAAGTT--AATTTTCCAGTG
droEre2	T-----------TGTTTT--------------------------------------------------------------------------------TATAAGGTTGATTTTGGAACTAGCGATCAGTTCGTTTGCCTAGATTTGTACTTAACTGTTGCGAAAAATA--AATTTTCCAGTG

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
UNAFold Image															None	None	None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

CAGTAAT--TAA-----------TTAATTACAAAATG----------------------------------------------------------------------------------------------------------------------------------------------TAGGTTATACTTAGAAAATAGTTGTTAGTACTACAAAACTACGTAGATTTGTAAATATCTCTAACAAA------------------CAT------------------------------------------------------------------------GTTGTTATAAGATA--------------------------C--------------------------------------------------ACA--TTTCCAGTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...................................................................................................................................................................................................AATTGTGGTTAGTACTAC........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................AAAATTGTGGTTAGTACT..........................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

CAGTAAT--TAA-----------TTAATTACAAAATG----------------------------------------------------------------------------------------------------------------------------------------------TAGGTTATATTTAGAAAATAGTTGTTAGTACTACAAAACCACCTAGTTTTGTAAATATCTCTAGCAAA------------------CAT------------------------------------------------------------------------TTGGTTATAAGATA--------------------------C--------------------------------------------------ACA--TTTCCAGTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................................................................................................................ACAATTGTTGTTAGTACT..........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TTCACAC--AGAAAAATCAGTAATTAACTTAAATATT----------------------------------------------------------------------------------------------------------------------------------------------ACATTTAAATTTAGAAATTGGGTG----TAAAACAGAAGTACCTCAATTTGCAAATAACTTTAAAAAA------------------GGTTTATTTTC-----GAACTATCGATCATTT----------------------------------------------------------------------------------------------CGTAAGCCTTGATTTAACCCT--AGCTGTT-GCGAAAAGTTAA-TTTTCCAGTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................................................................................................................................................................................GGTG----TAAAACAGGAGTAC................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................................AGCTAGAAATTGGGTG----TA............................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

TTGTTTT--TA------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA-----------------------------------------------------------------------------------GGTTGATTTTG-----GAACTAGCGATCAGTT----------------------------------------------------------------------------------------------CGTTTGCCTAGATTTGTACTT--AACTGTT-GCGAAAAATAAA-TTTTCCAGTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCCAGCG	18	2	0.50	0.00	0.00	0.00	0.50

droEug1

CTTCAAG--AGGA-------AACT---TAACAATATT----------------------------------------------------------------------------------------------------------------------------------------------TAAGTTTT---------------------------------------------------------------------------------------CCC-----TGTTAAT---CA---------------------------------------------------------------------------------------------------TTAACTATCACTTATTCCT--AACACTTACCAAAATATCCA-TTTTCCAGTA

Size

Hit Count

Total Norm

droBia1

AATCTAA--TTTGTAATAAAAAA-----------GTT-----------------------TGTATATTTTTAT--------------------------------------------------------------------------------------------------------------ATATTTTAGTGAAGTAACTTAT------------------------------------------------------------GGATAATTTCC-----CACCTAAC---CATTT----------------------------------------------------------------------------------------------AGTAAGCCTCTCTGAATTCCT--AACACCT---AAAAAATACG-TTTTCCAGTG

Size

Hit Count

Total Norm

droTak1

CATTCCT--AAAA--A----TACT---TTACTGAATGTACTACGTTTTGCAATAATTTTAAGCAAATTTCTTTCCATTTCTATTCAGGAAGCTTTTCAGTTAATTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCAAAGGAATTAGCGATCATAT----------------------------------------------------------------------------------------------AGTTAGCCTCAATATATTCCC--AGCACTT-GCCAAAAATACA-TTTTCCAGTG

Size

Hit Count

Total Norm

droEle1

AAATTAA--AAGGTAAA---AACT---TTACAAAATT---------------------------------------------------------------------------AAAACTGGAAATGTCATGATAAAGTCAAATGATACTTATGTATATTACATTTTAATTATAAAAAACA-------------------------------------C------TAT---------------------TTTTTAATGAGCTTTA-----------------------------------------------TTTTCGTCACAAAAACA--------------TTTTAATAAAATAATATTATTGTATATTGCTGCTTATAAAAAGTTCGATCCTTTAGCTTAAATCCAT---C--AAC-ACA-GCT-AAAATAAA-TTTTCCAGT-

Size

Hit Count

Total Norm

droRho1

GCCTTAC--TAAACAAGAAAAACT---TCGCGAAA--------------------------------------------------------------------------------------------------AAGTCA-----------------------TTTAAAAGTAACTAACA-------------------------------------CAT----------------------------ATTTTAATGGGCTT-A-----------------------------------------------TTAACGTTAGACAAATACTTTTACGAGACTG---T-------TA--------------------------TAAGTCC----TC-TACCTGTTGTTTATATCCACAA-CCTA-GCAAAAAGTACA-TTTTTCAGTG

Size

Hit Count

Total Norm

droFic1

ATTTCCT--ATATAGATAATAACT----TGTCAAATG----------------------------------------------------------------------------------------------------------------------------------------------TTAACTACA-----------ATTT--------------------------------------------TTTTTATTGTGTTG-AGA-------------------------------TATTTATCATCCAATAT-----------------TTCCAAGCCTTTCACTAAATTTGG--------------------------A--------------------------------------------------ATA--TTTTGAATG

Size

Hit Count

Total Norm

droKik1

CAAATCAACAGAA-------AACT------------------------------------AGTATACTATTAC------------------CTTTTCAG--AATATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCATAAAA---CACAATCATAT---------------------------------TTAAAAACACTTCA----AACAT---------------------------------------------------------------------------GTTAAA-CTTTCCAGT-

Size

Hit Count

Total Norm

droAna3

TTTCTTC--AAAAGATTGGTCCAATAAT----------------------------------------------------------------------------TTT-------------------------------------------------------------------------------CACATAGAAAAAGGGAC----TACAGCCGAACTTAATCTATACTCCCA----------------------------------------------------------------------------CTATTATCTGAAACTTTTATTTCAGAGATTA---T-------CA--------------------------C--------------------------------------------------AAATTCTAACAGTG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................................................................................................................................................................................................................................................................AGGGATTT---T-------CA--------------------------C--------------------------------------------------AAATTC........	18	1	1.00	0.00	1.00	0.00	0.00

droBip1

TTTAAGA--GAAG-------TTC-----------------------------------------------------------------------------------TCACTCAGAAATGGGTGTTTC---------------------------------------------------------------------------------ACA-----ACCAATGAGA---------------------------------------------------------ACTTATAATCCAT--------------TATTTATCTAAAACTTTAAATGCACAGAT--------TGAGACA--------------------------C--------------------------------------------------AAATTCTAGCAGT-

Size

Hit Count

Total Norm

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

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:11:21 EDT

sblock147574

chr3R:12058990-12059092 +

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