sblock180544- Best orthologs

sblock180544	chrX:8914206-8914441 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 8914213-8914235
   star strand at position 8914374-8914396
   mutations
   read mismatches

Notes: LASTZ cannot bridge the long gap between orthologs.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:8914191-8914456 -		1	TTCACGCTTTCAG--TT-------------------------------------------------------------------GTTGTGG-CC-AACGCGGCGTATGAGTAATTTTTACGATTCGAAATAATATTGCTCATACGCACGGTTGGCAGAAACAATAAC---------------------------------------------------------ATTTCG-----TTGCCATTATTTTACTTAGACTTCACTTCA-------T-ATTACT-CTTCTTGCTGACTCGATAGTTTAGG------CTTTCAGTAGATTATGTGGCTAACGCGGCGTATGAGTAATTTTTACGATTCGCA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAAAACC-----------------------------------------AAAATGTA------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A
droSim1	chrX_random:2620992-2621142 -	LASTZ	5	CAGTATGTTTTT-AT-T-------------------------------------------------------------------GT-----------------------------------------------------------------------------------------------------------------------------------------------T-----TTACCATTATTTTA-----------------------TTC---------------TACTCAAGAATTTAGG------CTTTCACGAG---TTGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA----------------------------------------TGTA------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A
droSec1	super_34:276860-277014 -	LASTZ	5	TTCACGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACAGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA----------------------------------------TTTAAAATTTACAACTAACTAGTTTCTT---AATATTTC-------------------------------AAATTCAATTGAACTGTTACTTCTTGCTG----------------------------------------------------
droYak2	chrX:12398475-12398645 +	LASTZ	5	ATTTTTTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTACTTTACTTAGACTTTACTTTA-------TTAAGGCT-GGACTTGCGGACTCAAGAATTGAAG------CTTTCAGTAGTTGTTGTGGCCAACGAGGCGTATGCGTATTTTTTGCAATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ATGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACC-----------------------------------------GAAATTGT------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A
droEre2	scaffold_4690:6199366-6199555 +	LASTZ	5	TTTAAGCTTTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAGTTGTTGTGGCTAACAGGGCGTATGAGTATTT-TTACGATTCGTA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA------------------------------------------TCAAATTTATAGCTAACTAGTTTTTTTTGAGTATTTC-------------------------------AAATTTAATTAGACTGTTGGTACTTTCTTCTCAAGTATT----AA--ACA-----------------GTTTGTACT-TT-C
droEug1	scf7180000408176:352475-352750 -	LASTZ	0	CTCAAATTATGA------------------------------------------------------------ATTAAAAGATTCTTTGCGG-CT-ACCTACTCGTATGAGCAATCTTTAAGGCTTCA-ACCATGTTACCCATACGCACTGTAAGCACACTTAATGTA----TTTTTAAATAC-AATATTAATTTAACATTAAACTCTTATTTT-----------------------------------------------------------TCAGACTCAGTTCTTGCAGT-TCTCAAACTATTA------ATTTCAAAATTCTTTGTGGCCACCTAGCCGTATGAGCAATCTTTAAGGCCTCAA--TCCATATTACTCATACGC-----------------------------------------------------------------------------------------------ACTGT---------------------------------------------------------------------------------------------------------------------------------------------------------AAGCACTTTA---AA----------------------------------------TGTA------------------------------------------------------------------------------------------------------------------------------------------TTA---T-T
droBia1	scf7180000301760:2643053-2643260 -	LASTZ	0	TTATAGCTTTCT-TT-TCCATAATGGAAAAATAGTAAATAGATCCTCTATTCCTTACAAAACTTTATTATAACTTTTCAATTTTTGTGTGA-CT-AACAGGTCGTATGGGTAATTTTACT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGCGGCTAACTAGTCGTATGGGTTATTTTAACAGCTTAAA--ACCAAATTGCTCATACGT-----------------------------------------------------------------------------------------------TCCGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCCTCACG-----------------------------------------AAAATGTT------------------------------------------------------------------------------------------------------------------------------------------AAATTTTCA
droTak1	scf7180000415169:1006936-1007095 +	LASTZ	0	TTG-------------------------------------------------------------------------------------GTGGC--AACAGGTCGTATGCGCAATTTTCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTATGA--AAAAAATTGCTCATACGT-----------------------------------------------------------------------------------------------AACGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCAA----------------------------------------------------------------------TTTTTTCTTGTATATTTTAAGCCAATGGAAGCTATATTTTGAATGGCTC----------------------TCATGTTTATAAA------------AAAA-----TGCATATTTATATTTATAAT-TT-A
droEle1	scf7180000491006:2420273-2420533 -	LASTZ	0	TTTTTCTGT------TT-------------------------------------------------------------------AATTTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCACAATTCGTATGTGTCGTTTTTGGGAAACCAT--GTAAAAGCTGTGTTTAAA-----------------------------------------------------------------------------------------------ACAATAGTCAAAAGCCCATATAAACCCATTAATATTATTGAATTTGTTATATTTTATGAATAAAACTATTTTAAAGATCT----GT------------------------------------------------------------------------TTAT--------------------------------------------------------------------------------------------TTTAACGGA----ATATTTTGAACTTTTCTAGCTTCTTTTAATTGTGGTAATCATTTTTACAAATATGTTTTGAACACAGCTTATTGAAAAAAAATAATTCCAAC-TT-A
droRho1	scf7180000779841:432485-432767 -	LASTZ	0	TGCAAAACTTCAT--TGA---A--------------------------------------------------ATTGAAAGA---------A-CTCAAAATG------------TCATCAAGCATTCTCAAAATATTACTCATACGCACCGTAGCCAGGGTTAAAATATATATTTTGCAAAAGTAT----------------------------------------TATTAGTCCCT--TAATT-ATTTATTTAGGTTAAAGTTAATTATTTATTTAGGTTAACTAAAGAAGT-TCCGAAA----------------AAATACTGAATCTGGCTAACATGTCGTATGGTTAATTTAAGCGTGTTCAAATATAATATTACTCATACGT-----------------------------------------------------------------------------------------------ACGAC---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCACTGTT---CC------------------------------T-----GTACTAAT------------------------------------------------------------------------------------------------------------------------------------------AAATATT-C
droFic1	scf7180000453829:885009-885260 -	LASTZ	0	GCATTGATTTTT-TG-T-------------------------------------------------------------------AAGTCGG-CT-AACAGGTCGTATGCTTAATTTAAATGGCTACGCAATATATTACTCATACGCGCGGTTGCCATAT-----GCG----TTTTTGAAAAG-GCT--TGAA--TATATTAAACTAAAATTTAGAGGAATTATAATATCG-----T---------------------------------------------------------TCCCAATTTGAAGCCATTGAT-TCTTTTGGTAAGCCGGCTAACAGGTCGTATGCTTAATTTAAATGGCTACAC--AATATATTACTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCATAAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000302698:163589-163660 +	LASTZ	0	ATC-------------------------------------------------------------------------------------TGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTACGTGTCGTATGAGTGTAATTTTCATCTCAA-----------------AC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGAAGCAGACTTATATCAA---GATATA---------------------------------------------------------------------------------------------------------CAA-----A
droAna3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	chrXR_group6:5402738-5402996 +	LASTZ	0	TACACCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGAAAAAAGCGCTGCAGTTGTATTATTTTCAATTAGAT--TTAAATATACATATATGCCATAAATTTGGTACCAAGAAAGAAAATATTAAAATTCAATTGGAAACATTAAAAATATGTTTTCATATTTAAAATTTAAATTTCATAATTCAAATATAAA-------------------------ATTTAAA------------------------------------------------------------------------------------TTTCATGCATAAAACTTAAATTTCA----------------GAAAAAAAAAATTTTATTTCATATTAAAAATTGAAAGTTTCATAATTAAAATATA------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A
droPer1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181108:619867-620118 +	LASTZ	0	TTG-------------------------------------------------------------------------------------TGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAATGCGGCGTATGCGCAATTCTTT------AAA--AAAATATT----------------------------------------AAAGCCTACTTTCAGTTGTTTGAATGT--------TGCCCATCATTTATATCATATCACACAGACACAGC-------------------------ACTTTCTC-----------------------------------------TGTGTGTGTGTTTGAATACTTTACCTTATTATTTATCTTTGTGTCCATGCACATAATTTATGTTTTATGCTTTTGTGTTTTGCAAAAACAAAAATA-------ATACAAAAAAATAAAAG---------------------------------------------------------------------------------------------TTAACAGA----------------AACACC----AA--ACA----------------------ATTT-CC-A
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	TTCACGCTTTCAGTTGTTGTGGCCAACGCGGCGTATGAGTAATTTTTACGATTCGAAATAATATTGCTCATACGCACGGTTGGCAGAAACAATAACATTTCGTT-----------GCCATTATTTTACTTAGACTTCACTTCAT-ATTACTCTTCTTGCTGACTCGATAGTTTAGGCTTTCAGTAGATTATGTGGCTAACGCGGCGTATGAGTAATTTTTACGATTCGCAATAATATTGCTCATACGCACGGTTGGCAAAACCAAAA-TGTAAAATTTA------------------------------------------------------------------------------------
droSim1	C-----------------------------------------------------------------------------------------------AGTATGTTTTTATTGTTTTACCATTATTTT----------------ATTC--------------TACTCAAGAATTTAGGCTTTCACGAGT---TGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAAATAATATTGCTCATACGCACGGTTGGCAGAACCAAAAATGTAAAATTTA------------------------------------------------------------------------------------
droSec1	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACGAGTTGTTGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAAATAATATTGCTCATACGCACAGTTGGCAGAACCAAAAATTTAAAATTTACAACTAACTAGTTTCTT---AATATTTCAAATTCAATTGAACTGTTACTTCTTGCTG---------------------------
droYak2	------------------------------------------------------------------------------------------------ATTTTTTT-----------TTGGTTACTTTACTTAGACTTTACTTTATTAAGGCTGGACTTGCGGACTCAAGAATTGAAGCTTTCAGTAGTTGTTGTGGCCAACGAGGCGTATGCGTATTTTTTGCAATTCGAAATAATATTGCTCATACGCATGGTTGGCAGAACCGAAATTG-TAAATTTA------------------------------------------------------------------------------------
droEre2	T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAAGCTTTCAGTAGTTGTTGTGGCTAACAGGGCGTATGAGTATT-TTTACGATTCGTAATAATATTGCTCATACGCACGGTTGGCAGAACCAAAAAT--CAAATTTATAGCTAACTAGTTTTTTTTGAGTATTTCAAATTTAATTAGACTGTTGGTACTTTCTTCTCAAGTATTAAACAGTTTGTACTTTC

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

CAGTATGTTTTT-AT-T-------------------------------------------------------------------GT-----------------------------------------------------------------------------------------------------------------------------------------------T-----TTACCATTATTTTA-----------------------TTC---------------TACTCAAGAATTTAGG------CTTTCACGAG---TTGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA----------------------------------------TGTA------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................................................................................................................................................................................................................................................GCCAACGCGGCGGATGCGTA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................................................................................................................ATGTTACTCATACGC-----------------------------------------------------------------------------------------------ACGG........................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................................................................................................................GCCAACGCGTCGTATGAG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................CGC-----------------------------------------------------------------------------------------------AGGGC---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACC....................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

TTCACGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGTGGCCAACGCGGCGTATGAGTATTTTTTACGATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACAGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA----------------------------------------TTTAAAATTTACAACTAACTAGTTTCTT---AATATTTC-------------------------------AAATTCAATTGAACTGTTACTTCTTGCTG----------------------------------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................................................................................................................................................................................................................................................................GCCAACGCTGCGTATGCGT................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00

droYak2

ATTTTTTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTACTTTACTTAGACTTTACTTTA-------TTAAGGCT-GGACTTGCGGACTCAAGAATTGAAG------CTTTCAGTAGTTGTTGTGGCCAACGAGGCGTATGCGTATTTTTTGCAATTCGAA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ATGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACC-----------------------------------------GAAATTGT------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTTAAGCTTTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAGTTGTTGTGGCTAACAGGGCGTATGAGTATTT-TTACGATTCGTA--ATAATATTGCTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGGCAGAACCAAAAA------------------------------------------TCAAATTTATAGCTAACTAGTTTTTTTTGAGTATTTC-------------------------------AAATTTAATTAGACTGTTGGTACTTTCTTCTCAAGTATT----AA--ACA-----------------GTTTGTACT-TT-C	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................................................................................................................................................................................................................................................................AACAGGGCGTATGAGTAAT.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00

droEug1

CTCAAATTATGA------------------------------------------------------------ATTAAAAGATTCTTTGCGG-CT-ACCTACTCGTATGAGCAATCTTTAAGGCTTCA-ACCATGTTACCCATACGCACTGTAAGCACACTTAATGTA----TTTTTAAATAC-AATATTAATTTAACATTAAACTCTTATTTT-----------------------------------------------------------TCAGACTCAGTTCTTGCAGT-TCTCAAACTATTA------ATTTCAAAATTCTTTGTGGCCACCTAGCCGTATGAGCAATCTTTAAGGCCTCAA--TCCATATTACTCATACGC-----------------------------------------------------------------------------------------------ACTGT---------------------------------------------------------------------------------------------------------------------------------------------------------AAGCACTTTA---AA----------------------------------------TGTA------------------------------------------------------------------------------------------------------------------------------------------TTA---T-T

Size

Hit Count

Total Norm

droBia1

TTATAGCTTTCT-TT-TCCATAATGGAAAAATAGTAAATAGATCCTCTATTCCTTACAAAACTTTATTATAACTTTTCAATTTTTGTGTGA-CT-AACAGGTCGTATGGGTAATTTTACT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGCGGCTAACTAGTCGTATGGGTTATTTTAACAGCTTAAA--ACCAAATTGCTCATACGT-----------------------------------------------------------------------------------------------TCCGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCCTCACG-----------------------------------------AAAATGTT------------------------------------------------------------------------------------------------------------------------------------------AAATTTTCA

Size

Hit Count

Total Norm

droTak1

TTG-------------------------------------------------------------------------------------GTGGC--AACAGGTCGTATGCGCAATTTTCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTATGA--AAAAAATTGCTCATACGT-----------------------------------------------------------------------------------------------AACGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCAA----------------------------------------------------------------------TTTTTTCTTGTATATTTTAAGCCAATGGAAGCTATATTTTGAATGGCTC----------------------TCATGTTTATAAA------------AAAA-----TGCATATTTATATTTATAAT-TT-A

Size

Hit Count

Total Norm

droEle1

TTTTTCTGT------TT-------------------------------------------------------------------AATTTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCACAATTCGTATGTGTCGTTTTTGGGAAACCAT--GTAAAAGCTGTGTTTAAA-----------------------------------------------------------------------------------------------ACAATAGTCAAAAGCCCATATAAACCCATTAATATTATTGAATTTGTTATATTTTATGAATAAAACTATTTTAAAGATCT----GT------------------------------------------------------------------------TTAT--------------------------------------------------------------------------------------------TTTAACGGA----ATATTTTGAACTTTTCTAGCTTCTTTTAATTGTGGTAATCATTTTTACAAATATGTTTTGAACACAGCTTATTGAAAAAAAATAATTCCAAC-TT-A

Size

Hit Count

Total Norm

droRho1

TGCAAAACTTCAT--TGA---A--------------------------------------------------ATTGAAAGA---------A-CTCAAAATG------------TCATCAAGCATTCTCAAAATATTACTCATACGCACCGTAGCCAGGGTTAAAATATATATTTTGCAAAAGTAT----------------------------------------TATTAGTCCCT--TAATT-ATTTATTTAGGTTAAAGTTAATTATTTATTTAGGTTAACTAAAGAAGT-TCCGAAA----------------AAATACTGAATCTGGCTAACATGTCGTATGGTTAATTTAAGCGTGTTCAAATATAATATTACTCATACGT-----------------------------------------------------------------------------------------------ACGAC---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCACTGTT---CC------------------------------T-----GTACTAAT------------------------------------------------------------------------------------------------------------------------------------------AAATATT-C

Size

Hit Count

Total Norm

droFic1

GCATTGATTTTT-TG-T-------------------------------------------------------------------AAGTCGG-CT-AACAGGTCGTATGCTTAATTTAAATGGCTACGCAATATATTACTCATACGCGCGGTTGCCATAT-----GCG----TTTTTGAAAAG-GCT--TGAA--TATATTAAACTAAAATTTAGAGGAATTATAATATCG-----T---------------------------------------------------------TCCCAATTTGAAGCCATTGAT-TCTTTTGGTAAGCCGGCTAACAGGTCGTATGCTTAATTTAAATGGCTACAC--AATATATTACTCATACGC-----------------------------------------------------------------------------------------------ACGGT---------------------------------------------------------------------------------------------------------------------------------------------------------TGCCATAAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droKik1

ATC-------------------------------------------------------------------------------------TGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTACGTGTCGTATGAGTGTAATTTTCATCTCAA-----------------AC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGAAGCAGACTTATATCAA---GATATA---------------------------------------------------------------------------------------------------------CAA-----A

Size

Hit Count

Total Norm

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

Size

Hit Count

Total Norm

dp4

TACACCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGAAAAAAGCGCTGCAGTTGTATTATTTTCAATTAGAT--TTAAATATACATATATGCCATAAATTTGGTACCAAGAAAGAAAATATTAAAATTCAATTGGAAACATTAAAAATATGTTTTCATATTTAAAATTTAAATTTCATAATTCAAATATAAA-------------------------ATTTAAA------------------------------------------------------------------------------------TTTCATGCATAAAACTTAAATTTCA----------------GAAAAAAAAAATTTTATTTCATATTAAAAATTGAAAGTTTCATAATTAAAATATA------------------------------------------------------------------------------------------------------------------------------------------AAAT-TT-A	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATAAG-------------------------ATTTAAA------------------------------------------------------------------------------------TTTCAG.............................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TTG-------------------------------------------------------------------------------------TGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAATGCGGCGTATGCGCAATTCTTT------AAA--AAAATATT----------------------------------------AAAGCCTACTTTCAGTTGTTTGAATGT--------TGCCCATCATTTATATCATATCACACAGACACAGC-------------------------ACTTTCTC-----------------------------------------TGTGTGTGTGTTTGAATACTTTACCTTATTATTTATCTTTGTGTCCATGCACATAATTTATGTTTTATGCTTTTGTGTTTTGCAAAAACAAAAATA-------ATACAAAAAAATAAAAG---------------------------------------------------------------------------------------------TTAACAGA----------------AACACC----AA--ACA----------------------ATTT-CC-A	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCCC-----------------------------------------TGTGTGTGTGTGTG...............................................................................................................................................................................................................................................................................	19	16	0.13	0.00	0.13	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCCC-----------------------------------------TGTGTGTGTGTGTG...............................................................................................................................................................................................................................................................................	18	41	0.05	0.00	0.05	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAATTAAAG---------------------------------------------------------------------------------------------TTAACGGA----------------A...............................................	18	1	2.00	0.00	2.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CATTCTA-----------------------------------------TGTGTGTGTGTT.................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G-----------------------------------------TGTGTGTTTGTTTGAAT............................................................................................................................................................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAAAAAGA-------ATACAAAAA.............................................................................................................................................................................	18	10	0.10	0.00	0.10	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G-----------------------------------------TGTGTGTGTGTTTGAAA............................................................................................................................................................................................................................................................................	18	15	0.07	0.07	0.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCTC-----------------------------------------TGTGTGTGTGTGTG...............................................................................................................................................................................................................................................................................	18	28	0.04	0.00	0.04	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCTC-----------------------------------------TGTCTGTGTGTGTG...............................................................................................................................................................................................................................................................................	18	49	0.02	0.00	0.02	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAxA----------------AACAGC----AA--ACA----------------------ATT......	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAATA-------ATGTAAAAAAA...........................................................................................................................................................................	18	11	0.09	0.00	0.09	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTCTT-----------------------------------------TGTGTGTGTGTGT................................................................................................................................................................................................................................................................................	19	31	0.03	0.03	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTGAATGC--------GGCCCATCAT................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTC-----------------------------------------TGTGTGTGTGTGGGA..............................................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACGTCCTC-----------------------------------------TGTGTGTGTG...................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTGTCTC-----------------------------------------TGTGTGTGTGT..................................................................................................................................................................................................................................................................................	18	34	0.03	0.00	0.03	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................TGTGCAATTCGTT------AAA--AA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAACAAGAAAATAAAAG---------------------------------------------------------------------------------------------T.......................................................................	18	5	0.20	0.00	0.20	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCATGCACTTAAxTTATGT..............................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAGAAATTAAAG---------------------------------------------------------------------------------------------TTAACA..................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTGAATGT--------TGACCACCA.................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A-------AAACAAGAAAATAAAAG---------------------------------------------------------------------------------------------T.......................................................................	19	3	0.33	0.00	0.33	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCTG-----------------------------------------TGTGTGTGTGTTTGA..............................................................................................................................................................................................................................................................................	20	8	0.13	0.00	0.13	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTT-----------------------------------------TGTGTGTGTGTTTG...............................................................................................................................................................................................................................................................................	19	9	0.11	0.11	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTTATATCAGATCGCACA...............................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTCTCTC-----------------------------------------CGTGTGTGTGT..................................................................................................................................................................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTCTC-----------------------------------------AGTGTGTGTGTG.................................................................................................................................................................................................................................................................................	18	13	0.08	0.00	0.00	0.08	0.00

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 05:12:28 EDT

sblock180544

chrX:8914206-8914441 -

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