sblock179483- Best orthologs

sblock179483	chrX:7824544-7824616 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 7824585-7824604
   star strand at position 7824555-7824576
   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:7824529-7824631 -		1	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTTAAAGAACTGCC---CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTCCCC------CAC---------T-TCG--TCCGACC
droSim1	chrX:6274364-6274467 -	LASTZ	4	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTCCCA------CAC---------T-TCG--TCCGACC
droSec1	super_50:111506-111609 -	LASTZ	3	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTTCCA------CAC---------T-TCG--TCTGACC
droYak2	chrX:13488072-13488176 +	LASTZ	3	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCACTCCCCCTTTTC--AT-------------------CA-TTCCGTAACTAA-GTCCCA------CCC---------C-TCG--GCC--CC
droEre2	scaffold_4690:16736830-16736927 -	LASTZ	3	TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTGA-GTCCCA------CCC---------T-TCG--T----CC
droEug1	scf7180000409830:75845-75947 -	LASTZ	5	TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGTTA-------GTGGGTGGGTGGTAAAACCGATCC-CCGCCCTAT--------------GCCTGTCAA-A-CTC-AAAAATAAAAAAAAA------CAC---------C-T---------CT
droBia1	scf7180000302198:25129-25216 -	LASTZ	5	T-G---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGTTA--CCGCCCTCC---C--T-----TTGCCT---------------------------------------AT----C-CAG--TCCAGCC
droTak1	scf7180000415262:139383-139482 -	LASTZ	4	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGCCC---CTCTCT--------------CGGCCTATCCCCC-TTC-TAAATTAA-CTCCCC------CTC------------CG---------
droEle1	scf7180000491044:620034-620139 +	LASTZ	4	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAAGTTGTGGGTGGGTGGGTGGTGGAACCGCCCGG-CCGTCTTC--AT-------------------TC-TGC-CAAAGCAA-CCCCCC------T----------GATC-------TATC
droRho1	scf7180000776942:301298-301369 +	LASTZ	5	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAA-------GTGGGTGGGTGGTGGAACCGCCC--CCGCTCTTC-------------------------------------------------------------------------GGCC
droFic1	scf7180000454077:2195920-2195996 +	LASTZ	5	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGATA-------GTGGGTGGGCAATGGAACCGCCCCC-CTCTCT--------------CTGCTC-------------------------------------------------------ATCC
droKik1	scf7180000302696:1693213-1693329 -	LASTZ	4	TCG-CTGCCGCTGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGGTG-------GCGGATAGGTGGTTGGCC-------CTGCTTCTCCTGTCATC-------------------CC-GAGCCCCA-GTTCAAGTCTCCCTGTCGAGCACGTTT----------C
droAna3	scaffold_13117:2045785-2045865 -	LASTZ	3	CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TC-TGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT
droBip1	scf7180000396425:26892-26973 +	LASTZ	4	CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TCTTGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT
dp4	chrXL_group1a:2469610-2469680 +	LASTZ	2	--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------
droPer1	super_28:903934-904004 +	LASTZ	2	--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------
droWil1	scaffold_180777:545832-545921 -	MAF	5	TTTGCTGTT-TTGCGATGCTCTATTGATTTTTTTTtTTTTtTTTTTTTTTTTTTTATATATGTATATATTTGGTGGTGG---------------------GAGGAAGAGA----------------------------------------------------------------------------------------AG
droVir3	scaffold_12970:10151308-10151337 +	LASTZ	5	CTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTTGCG-----------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:11301064-11301096 -	LASTZ	5	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTATTTGCG--------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_14853:6560969-6560993 +	LASTZ	5	CTG---------GCGATGCTGTATTGATTTTTT-------------------------------------T---------------------------------------------------------------------------------------------------------------------------------

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	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTTAAAGAACTGCC---CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTCCCC------CAC---------T-TCG--TCCGACC
droSim1	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTCCCA------CAC---------T-TCG--TCCGACC
droSec1	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTTCCA------CAC---------T-TCG--TCTGACC
droYak2	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCACTCCCCCTTTTC--AT-------------------CA-TTCCGTAACTAA-GTCCCA------CCC---------C-TCG--GCC--CC
droEre2	TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTGA-GTCCCA------CCC---------T-TCG--T----CC
droEug1	TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGTTA-------GTGGGTGGGTGGTAAAACCGATCC-CCGCCCTAT--------------GCCTGTCAA-A-CTC-AAAAATAAAAAAAAA------CAC---------C-T---------CT
droBia1	T-G---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGTTA--CCGCCCTCC---C--T-----TTGCCT---------------------------------------AT----C-CAG--TCCAGCC
droTak1	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGCCC---CTCTCT--------------CGGCCTATCCCCC-TTC-TAAATTAA-CTCCCC------CTC------------CG---------
droEle1	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAAGTTGTGGGTGGGTGGGTGGTGGAACCGCCCGG-CCGTCTTC--AT-------------------TC-TGC-CAAAGCAA-CCCCCC------T----------GATC-------TATC
droRho1	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAA-------GTGGGTGGGTGGTGGAACCGCCC--CCGCTCTTC-------------------------------------------------------------------------GGCC
droFic1	TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGATA-------GTGGGTGGGCAATGGAACCGCCCCC-CTCTCT--------------CTGCTC-------------------------------------------------------ATCC
droKik1	TCG-CTGCCGCTGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGGTG-------GCGGATAGGTGGTTGGCC-------CTGCTTCTCCTGTCATC-------------------CC-GAGCCCCA-GTTCAAGTCTCCCTGTCGAGCACGTTT----------C
droAna3	CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TC-TGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT
droBip1	CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TCTTGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT
dp4	--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------
droPer1	--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------
droWil1	TTTGCTGTT-TTGCGATGCTCTATTGATTTTTTTTtTTTTtTTTTTTTTTTTTTTATATATGTATATATTTGGTGGTGG---------------------GAGGAAGAGA----------------------------------------------------------------------------------------AG
droVir3	CTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTTGCG-----------------------------------------------------------------------------------------------------------------------------
droMoj3	TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTATTTGCG--------------------------------------------------------------------------------------------------------------------------
droGri2	CTG---------GCGATGCTGTATTGATTTTTT-------------------------------------T---------------------------------------------------------------------------------------------------------------------------------

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

Small RNA-seq read pileup

Species

Alignment

droSim1

TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTCCCA------CAC---------T-TCG--TCCGACC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................ATTGATTTTCT------------------------------------TCGGTGC............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................TTGAxTTTTT------------------------------------TGGGTGGTGGC........................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------TTGGGTGGGTGAAAGAACTGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTAA-GTTCCA------CAC---------T-TCG--TCTGACC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................GTGGTGGCxA-------GTGGGTGGG......................................................................................................	18	1	1.00	0.00	0.00	1.00
.........................................................................TGGTGGCGA-------xTGGGTGGGT.....................................................................................................	18	1	1.00	0.00	1.00	0.00
........................TGTTTTTTT------------------------------------TCGGGGGTG..........................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCACTCCCCCTTTTC--AT-------------------CA-TTCCGTAACTAA-GTCCCA------CCC---------C-TCG--GCC--CC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................GTGGTGGCTA-------GTGGGTGGGT.....................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................A-------GTGGGTGGGCGATGGAG..............................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................TGGGTGGTGGCTG-------GTGGGTGG.......................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGCTA-------GTGGGTGGGTGATGGAACCGCCC--CCGCTCTTC--AC-------------------CA-TTC-GAAACTGA-GTCCCA------CCC---------T-TCG--T----CC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................GTGGGTG-------GTGGGTGGGTGA...................................................................................................	19	1	13.00	0.00	0.00	0.00	13.00
...........................................................................GTGGGTG-------GTGGGTGGGTG....................................................................................................	18	2	3.00	0.00	0.00	0.00	3.00
...........................................................................GTGGAAA-------GTGGGTGGGTG....................................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
............................................................................TGGGTG-------GTGGGTGGGTGA...................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
...........................................................................GTGGGTC-------GTGGGTGGGTG....................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................GTCGGTA-------GTGGGTGGGTG....................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................GGTGGTGGxAA-------GTGGGTGGG......................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................GGTGGCTA-------GTGGGTGGGTGATGGAA..............................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
TTA---------GCGATTCTGTATTGAT............................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................GTGGCTA-------GTGGGTGGGTGATGGAA..............................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
........................................................................GTGGTGTGTA-------GTGGGTGGGT.....................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................................................................................................TAC--AC-------------------Cx-TTC-GAAACTGA-GT....................................	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

TTG---------GCGATGCTGTATTGATTTTT--------------------------------------CGGTGGTGGTTA-------GTGGGTGGGTGGTAAAACCGATCC-CCGCCCTAT--------------GCCTGTCAA-A-CTC-AAAAATAAAAAAAAA------CAC---------C-T---------CT

Size

Hit Count

Total Norm

droBia1

T-G---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGTTA--CCGCCCTCC---C--T-----TTGCCT---------------------------------------AT----C-CAG--TCCAGCC

Size

Hit Count

Total Norm

droTak1

TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGCTA-------GTGGGTGGGTGGTGGAACCGCCC---CTCTCT--------------CGGCCTATCCCCC-TTC-TAAATTAA-CTCCCC------CTC------------CG---------

Size

Hit Count

Total Norm

droEle1

TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAAGTTGTGGGTGGGTGGGTGGTGGAACCGCCCGG-CCGTCTTC--AT-------------------TC-TGC-CAAAGCAA-CCCCCC------T----------GATC-------TATC

Size

Hit Count

Total Norm

droRho1

TTG---------GCGATGCTGTATTGATTTTT-------------------------------------CCGGTGGTGGAAA-------GTGGGTGGGTGGTGGAACCGCCC--CCGCTCTTC-------------------------------------------------------------------------GGCC

Size

Hit Count

Total Norm

droFic1

TTG---------GCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGATA-------GTGGGTGGGCAATGGAACCGCCCCC-CTCTCT--------------CTGCTC-------------------------------------------------------ATCC

Size

Hit Count

Total Norm

droKik1

TCG-CTGCCGCTGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGGGTG-------GCGGATAGGTGGTTGGCC-------CTGCTTCTCCTGTCATC-------------------CC-GAGCCCCA-GTTCAAGTCTCCCTGTCGAGCACGTTT----------C

Size

Hit Count

Total Norm

droAna3

CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TC-TGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................GTTGGTGG----------GTGGGT----GG--------------------------CC.......................................................................	18	1	130.00	0.00	130.00	0.00	0.00
.......................................................................GTGGGTGG----------GTGGGT----GT--------------------------CC.......................................................................	18	3	23.00	0.33	22.67	0.00	0.00
.........................GATTTTT-------------------------------------TGGGTGGTGG----------T..............................................................................................................	18	1	15.00	12.00	2.00	0.00	1.00
...............................T-------------------------------------CGGGTGGTGG----------GTGGGT----G....................................................................................................	18	1	8.00	0.00	8.00	0.00	0.00
.......................................................................GGGGGTGG----------GTGGGT----GG--------------------------CC.......................................................................	18	1	5.00	0.00	4.00	1.00	0.00
...............................T-------------------------------------CGGGTGGTGG----------GTGGGT----.....................................................................................................	17	1	3.00	0.00	0.00	3.00	0.00
.......................................................................GTTGGTGG----------GTGGGT----GT--------------------------CC.......................................................................	18	1	3.00	0.00	3.00	0.00	0.00
........................TGATTTTT-------------------------------------TGGGTGGTGG----------T..............................................................................................................	19	1	3.00	2.00	1.00	0.00	0.00
.......................TTGATTTTG-------------------------------------TGGGTGGTGG----------G..............................................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
.......................TTGATTTTT-------------------------------------TGGGTGGTGG----------T..............................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
...............................T-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCT......................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.....................................................................TCGGTGGTGG----------GTGGGT----GT--------------------------C........................................................................	19	1	2.00	0.00	2.00	0.00	0.00
...............................G-------------------------------------TGGGTGGTGG----------GTGGGT----G....................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.......................................................................GGTGGTGG----------GCGGGT----GG--------------------------CC.......................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................TT-------------------------------------TCGGTGGTGG----------GxGGGT----GC--------------------------.........................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.......................TTGATTTTG-------------------------------------TCGGTGGTGG----------T..............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................................................................TCGGTGGTGG----------GTGGGT----GT--------------------------CAA......................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................T-------------------------------------TCGGGGGTGG----------GTxGGT----GT--------------------------C........................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.........................GATTTTG-------------------------------------TGGGTGGTGG----------GT.............................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTGGGTGG----------GTGGGT----GT--------------------------CCT......................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................ACCCGGGTTCGAT----ACC	16	1	1.00	0.00	0.00	1.00	0.00
.......................................................................GGTTGTGG----------GTGCGT----GT--------------------------CC.......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................GATTTTG-------------------------------------TCGGTGGTGG----------T..............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................CTTGATTTTT-------------------------------------TGGGTGGTG..........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................TGGGTGGTGG----------GTGGGT----GG--------------------------.........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTTGGTGG----------GTGGGT----GT--------------------------CG.......................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................GTGGGTG----------GTGGGT----GT--------------------------CC.......................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.....................................................................TCGGTGGTGG----------GTGGGT----GT--------------------------CA.......................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...............................G-------------------------------------TGGGTGGTGG----------GTGGGT----.....................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
...............................T-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CC.......................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................TCGGTGGTGG----------GTGGGT----GT--------------------------A........................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTTGGTGT----------GTGGGT----GT--------------------------CC.......................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............................TT-------------------------------------GCGGTxGTGG----------GTGGGT----G....................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
.......................................................................GCTGGTGG----------GTGGGT----GG--------------------------CC.......................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droBip1

CCG--------TGCGATGCTGTATTGATTTTT-------------------------------------TCGGTGGTGG----------GTGGGT----GT--------------------------CCTCCGAC-----------TCTTGT-TACG-----------GTCTCC------ACCCGGTTTCGAT----ACT

Size

Hit Count

Total Norm

dp4

--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................GTGGTGG----------GTGGGTTCGGG....................................................................................................	18	1	5.00	5.00	0.00	0.00	0.00
.......................................................................CGTGGTGG----------GTGGGTTCGGG....................................................................................................	19	1	2.00	1.00	0.00	1.00	0.00
...........................................................................GTGG----------GTGGGTGGGGGATG.................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.......................................................................CGTGGTGG----------GTGGGTTCGGGATGCA...............................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
......................................................................CCGTGGTGG----------GTGGGTTCGGG....................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00

droPer1

--A---------GCGATGCTGTATTGATTTTTTC-----------------------------------TCCGTGGTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------AACCTGA-GCCACA------CGC---------T-T-----------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................GTGGTGG----------GTGGGTTCGGG....................................................................................................	18	1	6.00	6.00	0.00	0.00	0.00	0.00
..........................................................................GCTGG----------ATGGGTTCGGGAT..................................................................................................	18	1	4.00	4.00	0.00	0.00	0.00	0.00
.......................................................................CGTGGTGG----------GTGGGTTCGGG....................................................................................................	19	1	3.00	3.00	0.00	0.00	0.00	0.00
...........................................................................GTGG----------GTGGGTTCGGGATGCGGTC----------------------------------------------..............................................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
.......................................................................CGTGGTGG----------GTGGGTTCGGGAT..................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................GGTGG----------GTGGGATCGGGAT..................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................GTGGTGG----------GTGGGTTCGGGAT..................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................GTGGTGG----------GAGGGTTCGGG....................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................GTGG----------GTGGGTTCGGGATGCGGTA----------------------------------------------..............................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

TTTGCTGTT-TTGCGATGCTCTATTGATTTTTTTTtTTTTtTTTTTTTTTTTTTTATATATGTATATATTTGGTGGTGG---------------------GAGGAAGAGA----------------------------------------------------------------------------------------AG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................TTTTTTTTTTTTTTTTTTT........................................................................................................................................................	19	89	0.08	0.00	0.08	0.00	0.00
.................................ATTTTTTTTTTTTTTTTTTTTT.................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
.............................ATTTTTTTTTTTTTTTTTTTTT.....................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
...........................ATTTTTTTTTTTTTTTTTTTTT.......................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..............................ATTTTTTTTTTTTTTTTTTTTT....................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
................................ATTTTTTTTTTTTTTTTTTTTT..................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
...............................ATTTTTTTTTTTTTTTTTTTTT...................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
............................ATTTTTTTTTTTTTTTTTTTTT......................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..........................ATTTTTTTTTTTTTTTTTTTTT........................................................................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..................................TTTTTTTTTTTTTTTTTTT...................................................................................................................................................	19	89	0.04	0.00	0.00	0.04	0.00
............................TTTTTTTTTTTTTTTTTTTTTT......................................................................................................................................................	22	58	0.07	0.00	0.00	0.07	0.00
...........................ATTTTTTTTTTTTTTTTTTTT........................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
................................TTTTTTTTTTTTTTTTTTTTTTT.................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..........................TTTTTTTTTTTTTTTTTTTTTTT.......................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..............................TTTTTTTTTTTTTTTTTTTTTTT...................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
.............................ATTTTTTTTTTTTTTTTTTTTTTTT..................................................................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
..............................TTTTTTTTTTTTTTTTTTTTT.....................................................................................................................................................	21	68	0.04	0.00	0.00	0.00	0.04
...............................TTTTTTTTTTTTTTTTTTTTTTT..................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..........................ATTTTTTTTTTTTTTTTTTTTTTTT.....................................................................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
..................................ATTTTTTTTTTTTTTTTTTTT.................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.................................TTTTTTTTTTTTTTTTTTTTTTT................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
............................ATTTTTTTTTTTTTTTTTTTT.......................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
................................ATTTTTTTTTTTTTTTTTTTT...................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
..............................ATTTTTTTTTTTTTTTTTTTTTTTT.................................................................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
............................ATTTTTTTTTTTTTTTTTTTTTTTT...................................................................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
...............................ATTTTTTTTTTTTTTTTTTTT....................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
..............................ATTTTTTTTTTTTTTTTTTTT.....................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
..........................ATTTTTTTTTTTTTTTTTTTT.........................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.................................ATTTTTTTTTTTTTTTTTTTT..................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
...........................ATTTTTTTTTTTTTTTTTTTTTTTT....................................................................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
............................TTTTTTTTTTTTTTTTTTTTTTT.....................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
.............................ATTTTTTTTTTTTTTTTTTTT......................................................................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.............................TTTTTTTTTTTTTTTTTTTTTTT....................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
...........................TTTTTTTTTTTTTTTTTTTTTTT......................................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..................................TTTTTTTTTTTTTTTTTTTTTTT...............................................................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00

droVir3

CTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTTGCG-----------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............AGTGCTGTATTGATTTTT........................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TTG---------GCGATGCTGTATTGATTTTTT------------------------------------TTATTTGCG--------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CTG---------GCGATGCTGTATTGATTTTTT-------------------------------------T---------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:00 EDT

sblock179483

chrX:7824544-7824616 -

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