sblock53978- Best orthologs

sblock53978	chr2R:1252139-1252239 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1252194-1252217
   star strand at position 1252162-1252183
   mutations
   read mismatches

Notes: Many paralogs exists.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:1252124-1252254 +		1	TTGA--ACTTACTGTTT--AATAA--TGTTAAATACA------------GAT----------------------------------------------------------------ATAT------------AA-TTAAA---------------------------------------------------------GT------------TGCCTTGGCTACGACTTGCTGGCTC------------------------------GTCGGT-ATGGCTGCGATTGAG-----------------------CTATGATCTGCATTTAA-----T-----TATG-------------------GTC---CC---CGCCATATTCC
droSim1	chr3R:1415632-1415763 +	LASTZ	5	TTGA--ACTCACTGTTT--ATAAT--TTTCAAACAGA------------GAT----------------------------------------------------------------ATAT------------AATTTCAA---------------------------------------------------------AT------------TGCCTTGGCTGTGTTCTGCTGGCTC------------------------------GTCGGT-ATGGCTGCGATTGAG-----------------------CTACGAATTCCATTTAA-----T-----CATG-------------------GTC---CC---TGCCATATTCC
droSec1	super_6:1494904-1495035 +	LASTZ	5	TTGA--ACTCACTGTTT--ATAAT--TTTCAAACAGA------------GAT----------------------------------------------------------------ATAT------------AATTTCAA---------------------------------------------------------AT------------TGCCTTGGCTGTGTCCTGCTGGCTC------------------------------GTCGGT-ATGGCTGCGATTGAG-----------------------CTACGAATTCCATTTAA-----T-----CATG-------------------GTC---CC---TGCCATATTCC
droYak2	chr2h_random:1463679-1463807 +	LASTZ	4	TTAA--ACTCACTGTTT--ATTAA--TTTCACACACA------------GAT----------------------------------------------------------------AGAA------------AAATTAAA---------------------------------------------------------GT------------TGCCCGAGCTGCAACTTAATGGCTC------------------------------ATTAGT-AGGGCTGCGATTGAG-----------------------CTATGATTTGCATTTCA-----T-----G----------------------CTG---CC---CGCTATATTCC
droEre2	scaffold_4845:1016186-1016313 -	LASTZ	4	TCTA--ACTCACTGTTT--TTTAA--TTTCCCGCACA------------GAT----------------------------------------------------------------ATAT------------AAAGTTAT---------------------------------------------------------GT------------TACCCTAGCTGCAACTTC--AACTC------------------------------GTCGGT-ATGGCTACGATTGA------------------------CTATGATTATAATTTTA-----A-----TTTG-------------------CTC---CC---CG-CATATTCC
droEug1	scf7180000407524:9378-9509 -	LASTZ	0	TTCT-----CAGTGATT--AATGC--AATCACTTTGT------------GAA----------------------------------------------------------------ATTT------------G-----------------------------------------------------------------T------------TTCGCGAGCTCGGTTTCACT--TTG------------------------------ATCAT--CCGAATCCG----CAATATGACAGCTACTGAT------TAGTAGTTTGGCCTACA-----T-----ATCG-----------------TAGGC---CT---CGCCAT-TTTC
droBia1	scf7180000301469:14871-15004 -	LASTZ	0	TACC--ACTCACTTTTA--TTTTA--TTTTTGGCACA------------AAA----------------------------------------------------------------TTTA------------A--CTTAG---------------------------------------------------------GC------------T--TCTAGCTGCATCTGTCTGGTTC------------------------------GGCAAT-ATGGCTGCGACGATA-----------------------CCCATATCTGCTGATCA-----T-----TTTT-------------ATTTCTGCC---CC---CGCCATATTAC
droTak1	scf7180000410435:1249-1378 +	LASTZ	0	TAAC--ACTCACTTCTT--TCTGT--TTTTTTGCACA------------AAC----------------------------------------------------------------ACTT------------A--TTTAA---------------------------------------------------------GT------------AACTCCCGCTGCGTCCAGCTTCTGG------------------------------GTCAAT-ATGGCTGCGACTATT-----------------------CTA--ATCTGCCTATCA-----T-----CATG-----------------ACGAT---AT---CGCCATATTCC
droEle1	scf7180000490995:30198-30325 -	LASTZ	0	TTCA--AATGGCTTTGT--ACGTT--TTTTTGTAA----------------------------------------------------------------------------------TTT------------A--TTAAA------------------------------ATCGCCCA--------------------C------------TGACG-AGGTTTGATTTTCTCCCTA------------------------------GGCTCT-ATTACTGTGTTTATG-----------------------CTATGAATTTCATGAAT-----T-----ATT--------------------GAA---TA---CA-TGAAATCA
droRho1	scf7180000780189:8752-8880 -	LASTZ	0	TCTACCACTCACTTTTT--TTTGA--TTTC-GGCACA------------AAC----------------------------------------------------------------AGTA------------A-TTTAAA---------------------------------------------------------AA------------C--TCCCGCTCCGTCTAGCTTCCTG------------------------------GACAAT-ATGGCTGCGACCATC-----------------------CCATTATCTGCCTATCA-----T-----TGC--------------------CAT---AT---CGCCATATTCC
droFic1	scf7180000453278:52662-52792 +	LASTZ	0	TCTA--ACTCACTTTTT--ACAAA--ATTTACACAAA------------ATT----------------------------------------------------------------AA-T------------ACT--CGG----------------------TTAA---A---------------------------AT------------TGTC-CGTCTACCACT------TTT------------------------------GCCTTT-TCGGGTACAACTGAA-----------------------CGGTGATCCGTA--TGATCACGC-----CATG-------------------TTC---CCT--AACATCTTTTC
droKik1	scf7180000302639:2558577-2558706 +	LASTZ	0	TCCA--GCTTATGTAAT--TA--G--CTCGA-CTCCA------------GAC----------------------------------------------------T-----------ATAT------------AA-TCACG---------------------------------------------------------CT---TT-------TGCCTTAGATTCAATTAGCTAGTGA------------------------------GGCGTT-AAGCTTGTTCAGGTT-----------------------CCAATTGCTGCATTTAC-----T-----TTC--------------------GGC---AT---CGCATTACCGT
droAna3	scaffold_13337:22759501-22759624 +	LASTZ	0	TTAA--CTTATTTG-CT--CCGTTTATTTCCCGCAG--------------AT----------------------------TCACCTACGCATGACATTAAAGATGGTCTTTTTACGTCAA------------CA-CTAG------------------------------------------------------------------------------------AATT------------------------------------------GGA-TTGGTTA---------------------------------------------TTATCACGT-----GAAG-------------------ATCTGGCT---CAAGAT-ATAG
droBip1	scf7180000395368:41128-41264 +	LASTZ	0	TTGA--ATTTTCTGTAT--CA--------------AA------------AAT----------------------------------------------------------------TTAA------------AA-TTAAA----------------------------------------------ATATGTTTTTCTTATTATTAATTTT-------------------------TACTAAATTATCTTATTCTTATCATTTCATAG-------------------------------------------CCATTTTTCTGTTTTCA-----TTTTATTTGTTGCATATGCGATA------GAC---------------ATCT
dp4	Unknown_group_9:35228-35362 -	LASTZ	0	TCAA--GCCCAGCC-TGATAA--T--CGTTA-TTCTAGATTTCTAAAAAATA------ATTTCCTTATTTATGAGTTAAGTT--------------------------------------------------------------------------TCCTACC-------------------------------------------------------------------------CGCTATTTTATACGGTTCTTAGTGGTTTTCAA-------------------------------------------TCT-----CCTATTTAC-----T-----ACTA-------------------TTT-----------TCCGCCCT
droPer1	super_3:1090211-1090335 -	LASTZ	0	TTTA--CCATATAGCTT--GCATA--TGCTACATACA------------TAT----------------------------------------------------------------ATGT------------AGTTTCGA---------------------------------------------------------AG------------AAATTT----ACAATTTT--AAAAA------------------------------GCTGATGAATGCTGTCCTTGGG-----------------------CTCTAAATATCCTTAAA-----T-----ATCC-------------------GTA---TC---C--TTTATATT
droWil1	scaffold_180935:22520-22643 +	LASTZ	0	ATAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTACATGTACAAAATTTG-------T------------T-----TTCTGCAACTC---AATTC------------------------------ATCAGA-ATACAAACAATTTTA-----------------------CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---TCCCTCATTCC
droVir3	scaffold_12963:2382868-2383002 +	LASTZ	0	TGTA--CTGGGGGA-TGCTGA--A--CTTGA-ACTTGGGCGGGCATA--AAT----------------------------------------------------------------ACAGATTGATGTATAAGCTTTAAT---------------------------------------------------------AA------------TACCTCCACTGGAACCTGCCG----------------------------------CACAGC-TTGGCCGTAAAGTGA-----------------------GTGTATTTAACATTTTA-----T-----TTT--------------------------------------GTTC
droMoj3	scaffold_6680:16275074-16275209 -	LASTZ	0	ACTT--GTCTGT----A--AATGA--TGTTAAATCAG------------AAC----------------------------------------------------------------ACAA------------AA-TTAAAATTGAATTGTTGCATTTTGTGGCA---------------------------------------------------------GC------------A------------------------------ATCATA-TTGACTGCGAGTTGA----------------TTTGAAGCTGAAATTTCCATTTTA-----C-----TTTA-------------------AAT---GC-TTTACTGTATCAA
droGri2	scaffold_14853:628777-628885 -	LASTZ	0	TACA--ATTTCAAGTTG---TAAA--GTATATATATA------------TATATATAGTGTTGTTGGCTTGGACGTGGAAGC--------------------------------------------------------------------------------------------------------------------------------------------------GCTTACGC------------------------------GTGTGT-ATATATAATATATAG-----------------------C----------ATATAA-----T-----A------------------------------------TACATATA

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	TTGAACTTACTGTTTAATAATGTTAAATACAGATATATAAT-TAAAGTTGCCTTGGCTACGACTTGCTGGCTCGTCGGTATGGCTGCGATTGAGCTATGATCTGCATTTAATTATGGTCCCCGCCATATTCC
droSim1	TTGAACTCACTGTTTATAATTTTCAAACAGAGATATATAATTTCAAATTGCCTTGGCTGTGTTCTGCTGGCTCGTCGGTATGGCTGCGATTGAGCTACGAATTCCATTTAATCATGGTCCCTGCCATATTCC
droSec1	TTGAACTCACTGTTTATAATTTTCAAACAGAGATATATAATTTCAAATTGCCTTGGCTGTGTCCTGCTGGCTCGTCGGTATGGCTGCGATTGAGCTACGAATTCCATTTAATCATGGTCCCTGCCATATTCC
droYak2	TTAAACTCACTGTTTATTAATTTCACACACAGATAGAAAAATTAAAGTTGCCCGAGCTGCAACTTAATGGCTCATTAGTAGGGCTGCGATTGAGCTATGATTTGCATTT---CATGCTGCCCGCTATATTCC
droEre2	TCTAACTCACTGTTTTTTAATTTCCCGCACAGATATATAAAGTTATGTTACCCTAGCTGCAACTTC--AACTCGTCGGTATGGCTACGATTGA-CTATGATTATAATTTTAATTTGCTCCCCGC-ATATTCC

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

TTGA--ACTCACTGTTT--ATAAT--TTTCAAACAGA------------GAT----------------------------------------------------------------ATAT------------AATTTCAA---------------------------------------------------------AT------------TGCCTTGGCTGTGTTCTGCTGGCTC------------------------------GTCGGT-ATGGCTGCGATTGAG-----------------------CTACGAATTCCATTTAA-----T-----CATG-------------------GTC---CC---TGCCATATTCC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........TTGTTT--ATAAT--TTTCAGAC..............................................................................................................................................................................................................................................................................................................................................................	19	3	0.67	0.00	0.00	0.00	0.67
.........................................................................................................................................................................................................................GGCTGxGTTCTGCTGGCTG------------------------------......................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
...............................................................................................................................................................................................................................GTTCTGCTTGCTC------------------------------ATCGG.................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00

droSec1

TTGA--ACTCACTGTTT--ATAAT--TTTCAAACAGA------------GAT----------------------------------------------------------------ATAT------------AATTTCAA---------------------------------------------------------AT------------TGCCTTGGCTGTGTCCTGCTGGCTC------------------------------GTCGGT-ATGGCTGCGATTGAG-----------------------CTACGAATTCCATTTAA-----T-----CATG-------------------GTC---CC---TGCCATATTCC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................................................................................................................................................................................................CTGGCTC------------------------------GTCGGT-ATGGCTGC.......................................................................................................	21	9	0.11	0.11	0.00	0.00
..............................AAACAGA------------GAT----------------------------------------------------------------ATTG------------AATT........................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00

droYak2

TTAA--ACTCACTGTTT--ATTAA--TTTCACACACA------------GAT----------------------------------------------------------------AGAA------------AAATTAAA---------------------------------------------------------GT------------TGCCCGAGCTGCAACTTAATGGCTC------------------------------ATTAGT-AGGGCTGCGATTGAG-----------------------CTATGATTTGCATTTCA-----T-----G----------------------CTG---CC---CGCTATATTCC

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TCTA--ACTCACTGTTT--TTTAA--TTTCCCGCACA------------GAT----------------------------------------------------------------ATAT------------AAAGTTAT---------------------------------------------------------GT------------TACCCTAGCTGCAACTTC--AACTC------------------------------GTCGGT-ATGGCTACGATTGA------------------------CTATGATTATAATTTTA-----A-----TTTG-------------------CTC---CC---CG-CATATTCC

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TTCT-----CAGTGATT--AATGC--AATCACTTTGT------------GAA----------------------------------------------------------------ATTT------------G-----------------------------------------------------------------T------------TTCGCGAGCTCGGTTTCACT--TTG------------------------------ATCAT--CCGAATCCG----CAATATGACAGCTACTGAT------TAGTAGTTTGGCCTACA-----T-----ATCG-----------------TAGGC---CT---CGCCAT-TTTC

Size

Hit Count

Total Norm

droBia1

TACC--ACTCACTTTTA--TTTTA--TTTTTGGCACA------------AAA----------------------------------------------------------------TTTA------------A--CTTAG---------------------------------------------------------GC------------T--TCTAGCTGCATCTGTCTGGTTC------------------------------GGCAAT-ATGGCTGCGACGATA-----------------------CCCATATCTGCTGATCA-----T-----TTTT-------------ATTTCTGCC---CC---CGCCATATTAC

Size

Hit Count

Total Norm

droTak1

TAAC--ACTCACTTCTT--TCTGT--TTTTTTGCACA------------AAC----------------------------------------------------------------ACTT------------A--TTTAA---------------------------------------------------------GT------------AACTCCCGCTGCGTCCAGCTTCTGG------------------------------GTCAAT-ATGGCTGCGACTATT-----------------------CTA--ATCTGCCTATCA-----T-----CATG-----------------ACGAT---AT---CGCCATATTCC

Size

Hit Count

Total Norm

droEle1

TTCA--AATGGCTTTGT--ACGTT--TTTTTGTAA----------------------------------------------------------------------------------TTT------------A--TTAAA------------------------------ATCGCCCA--------------------C------------TGACG-AGGTTTGATTTTCTCCCTA------------------------------GGCTCT-ATTACTGTGTTTATG-----------------------CTATGAATTTCATGAAT-----T-----ATT--------------------GAA---TA---CA-TGAAATCA

Size

Hit Count

Total Norm

droRho1

TCTACCACTCACTTTTT--TTTGA--TTTC-GGCACA------------AAC----------------------------------------------------------------AGTA------------A-TTTAAA---------------------------------------------------------AA------------C--TCCCGCTCCGTCTAGCTTCCTG------------------------------GACAAT-ATGGCTGCGACCATC-----------------------CCATTATCTGCCTATCA-----T-----TGC--------------------CAT---AT---CGCCATATTCC

Size

Hit Count

Total Norm

droFic1

TCTA--ACTCACTTTTT--ACAAA--ATTTACACAAA------------ATT----------------------------------------------------------------AA-T------------ACT--CGG----------------------TTAA---A---------------------------AT------------TGTC-CGTCTACCACT------TTT------------------------------GCCTTT-TCGGGTACAACTGAA-----------------------CGGTGATCCGTA--TGATCACGC-----CATG-------------------TTC---CCT--AACATCTTTTC

Size

Hit Count

Total Norm

droKik1

TCCA--GCTTATGTAAT--TA--G--CTCGA-CTCCA------------GAC----------------------------------------------------T-----------ATAT------------AA-TCACG---------------------------------------------------------CT---TT-------TGCCTTAGATTCAATTAGCTAGTGA------------------------------GGCGTT-AAGCTTGTTCAGGTT-----------------------CCAATTGCTGCATTTAC-----T-----TTC--------------------GGC---AT---CGCATTACCGT

Size

Hit Count

Total Norm

droAna3

TTAA--CTTATTTG-CT--CCGTTTATTTCCCGCAG--------------AT----------------------------TCACCTACGCATGACATTAAAGATGGTCTTTTTACGTCAA------------CA-CTAG------------------------------------------------------------------------------------AATT------------------------------------------GGA-TTGGTTA---------------------------------------------TTATCACGT-----GAAG-------------------ATCTGGCT---CAAGAT-ATAG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................A------------CA-CTAG------------------------------------------------------------------------------------AATT------------------------------------------GGA-TTGGTTA---------------------------------------------TTAT.......................................................	25	1	1.00	1.00	0.00	0.00	0.00

droBip1

TTGA--ATTTTCTGTAT--CA--------------AA------------AAT----------------------------------------------------------------TTAA------------AA-TTAAA----------------------------------------------ATATGTTTTTCTTATTATTAATTTT-------------------------TACTAAATTATCTTATTCTTATCATTTCATAG-------------------------------------------CCATTTTTCTGTTTTCA-----TTTTATTTGTTGCATATGCGATA------GAC---------------ATCT

Size

Hit Count

Total Norm

dp4

TCAA--GCCCAGCC-TGATAA--T--CGTTA-TTCTAGATTTCTAAAAAATA------ATTTCCTTATTTATGAGTTAAGTT--------------------------------------------------------------------------TCCTACC-------------------------------------------------------------------------CGCTATTTTATACGGTTCTTAGTGGTTTTCAA-------------------------------------------TCT-----CCTATTTAC-----T-----ACTA-------------------TTT-----------TCCGCCCT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................................................................................................................................................................................................................................TTAGTGTTTTTCCA-------------------------------------------TCT-----CCTAT............................................................	22	1	1.00	0.00	1.00	0.00	0.00

droPer1

TTTA--CCATATAGCTT--GCATA--TGCTACATACA------------TAT----------------------------------------------------------------ATGT------------AGTTTCGA---------------------------------------------------------AG------------AAATTT----ACAATTTT--AAAAA------------------------------GCTGATGAATGCTGTCCTTGGG-----------------------CTCTAAATATCCTTAAA-----T-----ATCC-------------------GTA---TC---C--TTTATATT

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ATAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTACATGTACAAAATTTG-------T------------T-----TTCTGCAACTC---AATTC------------------------------ATCAGA-ATACAAACAATTTTA-----------------------CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---TCCCTCATTCC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTACA..............................................................................................................................................................................................................	28	5	2.80	0.00	2.80	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTAC...............................................................................................................................................................................................................	27	5	1.20	0.20	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................T-----------------------CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---...........	25	2	2.50	0.00	2.50	0.00	0.00
......................................................................................................................................................................................CAAGATTTG-------T------------T-----CTCTGCAACT.............................................................................................................................................................	21	4	0.75	0.00	0.00	0.00	0.75
...............................................................................................................................................................................................................................................................................................T-----------------------CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---TCT........	28	2	1.00	0.00	1.00	0.00	0.00
................T--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAATTTTACATGT...........................................................................................................................................................................................................	26	6	0.33	0.00	0.33	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTA................................................................................................................................................................................................................	26	5	0.40	0.00	0.40	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................TTTACAATTTG-----T-----T----------------------CTT---CT---TCCCGCAT...	26	2	1.00	0.00	1.00	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAATTTTACA..............................................................................................................................................................................................................	28	5	0.40	0.00	0.40	0.00	0.00
..............................................................................................................................................................................TACATGTTCAAAATTTG-------T------------T-----TTCTGCAAC..............................................................................................................................................................	28	4	0.50	0.00	0.50	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATA......................................................................................................................................................................................................................	21	5	0.40	0.00	0.40	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................TTTACAATTTG-----C-----T----------------------CTT---CT---TCCCTTA....	25	2	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................TTTTACAATTTG-----T-----T----------------------CTT---CT---TCCCT......	24	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................................................................................................................................................................................................TCTACTTTACAATTTG-----T-----T----------------------CTT---CT---TCCCG......	28	2	0.50	0.00	0.50	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAA.....................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................TATTTTACAATTTG-----T-----T----------------------CTT---CT---T..........	22	2	0.50	0.00	0.50	0.00	0.00
.....................................................................................................................................................................................TCAAAATTTG-------T------------T-----TTATGCAACTC---AAT......................................................................................................................................................	26	4	0.25	0.00	0.25	0.00	0.00
..CT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGC.............................................................................................................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00
...T--ACCCTTGCAGT--CG-----------------------------------------------------------------------------------------------------------------------------------------TTGGCA............................................................................................................................................................................................................................	20	4	0.25	0.00	0.00	0.00	0.25
.........................................................................................................................................................................................................................................................................................................................CTATTTTACAATTTG-----C-----T----------------------CTT---CT---TCCCT......	27	2	0.50	0.00	0.50	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTAGTAATAATAGT....................................................................................................................................................................................................................	28	4	0.25	0.00	0.25	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGATAATAATAATTTTACA..............................................................................................................................................................................................................	28	5	0.20	0.00	0.20	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................TACAATTTG-----T-----T----------------------CTT---CT---TCCCGCAT...	24	2	0.50	0.00	0.50	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAAGT......................................................................................................................................................................................................................	28	4	0.25	0.00	0.25	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGT.............................................................................................................................................................................................................................	21	4	0.25	0.00	0.25	0.00	0.00
.................................................................................................................................................................TTAATAATAATTTTACATGTT..........................................................................................................................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
.....................................................................................................................................................................TAATAATTTTACATGTTCAAAATT...................................................................................................................................................................................................	24	4	0.25	0.00	0.25	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGGAATAATATTTT..................................................................................................................................................................................................................	25	5	0.20	0.20	0.00	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGAAATAATAATTTTACA..............................................................................................................................................................................................................	28	5	0.20	0.00	0.20	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................TACAATTTG-----C-----T----------------------CTT---CT---TCCCTTAT...	24	2	0.50	0.00	0.50	0.00	0.00
..........TTGCAGC--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAAT.......................................................................................................................................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTAGTAATAATAG.....................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAAT.......................................................................................................................................................................................................................	19	5	0.20	0.00	0.00	0.20	0.00
.....................................................................................................................................................................TAATAATTTTACATGTTCAAAATTGG-------T------------.............................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
............GCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTAC...............................................................................................................................................................................................................	26	5	0.20	0.00	0.20	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAATATTTT..................................................................................................................................................................................................................	24	5	0.20	0.00	0.20	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAATTTTA................................................................................................................................................................................................................	26	5	0.20	0.00	0.20	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................TTACAATTTG-----T-----T----------------------CTT---CT---TCTT.......	21	3	0.33	0.00	0.33	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAATAT.....................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTA.................................................................................................................................................................................................................	26	5	0.20	0.00	0.20	0.00	0.00
................T--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTACGTGTT..........................................................................................................................................................................................................	27	5	0.20	0.00	0.20	0.00	0.00
.............................................................................................................................................................................................TG-------T------------T-----TTCTGCAACTC---AATTC------------------------------AT....................................................................................................................	22	6	0.17	0.00	0.17	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---TC.........	26	2	0.50	0.00	0.50	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATA.........................................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAA........................................................................................................................................................................................................................	24	4	0.25	0.00	0.25	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTCATAATATTTT..................................................................................................................................................................................................................	24	5	0.20	0.00	0.20	0.00	0.00
ATAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCA............................................................................................................................................................................................................................	23	4	0.25	0.00	0.25	0.00	0.00
..............AGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAATATT....................................................................................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
................T--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTATATGTT..........................................................................................................................................................................................................	27	5	0.20	0.00	0.20	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCCATAAT.......................................................................................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAATTT..................................................................................................................................................................................................................	25	5	0.20	0.00	0.20	0.00	0.00
..............................................................................................................................................................................TACATGTTCAAAATTGG-------T------------T-----TTCTGCAAC..............................................................................................................................................................	28	4	0.25	0.00	0.25	0.00	0.00
........TCTTGCGGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTT..................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................TATTTTACAATTTG-----T-----T----------------------CTT---CT---TCCC.......	25	2	0.50	0.00	0.50	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTG...............................................................................................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
...............GT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTTTACATGT...........................................................................................................................................................................................................	27	5	0.20	0.00	0.20	0.00	0.00
...............................................................................................................................................................................ACATGTTCCAAATTTG-------T------------T-----TTCTGCAACT.............................................................................................................................................................	28	4	0.25	0.00	0.25	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCCAT..........................................................................................................................................................................................................................	24	4	0.25	0.00	0.25	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTAATAATAATTT..................................................................................................................................................................................................................	24	5	0.20	0.00	0.20	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAATAATTGTA................................................................................................................................................................................................................	26	5	0.20	0.00	0.20	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................TATTTTACAATTTG-----T-----T----------------------CTT---CT---TCTT.......	25	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................................................................................................T-----------------------CTCTATTTTACAATTTG-----T-----T----------------------CTT---CT---TC.........	27	2	0.50	0.00	0.50	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGC.............................................................................................................................................................................................................................	21	4	0.25	0.25	0.00	0.00	0.00
.............CAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGCAATAATATTTTTACA..............................................................................................................................................................................................................	26	5	0.20	0.00	0.20	0.00	0.00
.TAC--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAAT.......................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
.............................................................................................................................................................................TTACATGTTCAAAATCTG-------T------------T-----TTCTGCA................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
...T--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAA.....................................................................................................................................................................................................................	27	4	0.25	0.00	0.25	0.00	0.00
..........TTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATTT..................................................................................................................................................................................................................	25	5	0.20	0.00	0.20	0.00	0.00
..............................................................................................................................................................................TACATGTTCAAAATTTG-------T------------T-----TTCTGCA................................................................................................................................................................	26	4	0.25	0.00	0.25	0.00	0.00
..................................................................................................................................................................................TGTTCAAAATTGG-------T------------T-----TTCTGCAAC..............................................................................................................................................................	24	4	0.25	0.00	0.25	0.00	0.00
...........TGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGTTAATAATAA.....................................................................................................................................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
...........TGCAGT--GC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAACAATAATTT..................................................................................................................................................................................................................	24	5	0.20	0.00	0.20	0.00	0.00
........CCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAATAATAATT...................................................................................................................................................................................................................	26	4	0.25	0.00	0.25	0.00	0.00
..AT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGAAA...........................................................................................................................................................................................................................	22	4	0.25	0.00	0.25	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................CTATTTTACAATTTG-----T-----T----------------------CTT---CT---TCT........	25	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................CTC---AATTC------------------------------ATCAAT-ATACAAACAAT....................................................................................................	25	7	0.14	0.00	0.14	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................TATTTTACAATTTG-----T-----T----------------------CTT---CT---TCT........	24	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................................................TAATTTTACATGTTCAAAATTTG-------T------------T-----.......................................................................................................................................................................	25	4	0.25	0.00	0.25	0.00	0.00
............GCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TTGGTAGTAATAATT...................................................................................................................................................................................................................	22	5	0.20	0.00	0.20	0.00	0.00
.TAT--ACCCTTGCAGT--CC-----------------------------------------------------------------------------------------------------------------------------------------TAGGTC............................................................................................................................................................................................................................	22	4	0.25	0.25	0.00	0.00	0.00

droVir3

TGTA--CTGGGGGA-TGCTGA--A--CTTGA-ACTTGGGCGGGCATA--AAT----------------------------------------------------------------ACAGATTGATGTATAAGCTTTAAT---------------------------------------------------------AA------------TACCTCCACTGGAACCTGCCG----------------------------------CACAGC-TTGGCCGTAAAGTGA-----------------------GTGTATTTAACATTTTA-----T-----TTT--------------------------------------GTTC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ACTT--GTCTGT----A--AATGA--TGTTAAATCAG------------AAC----------------------------------------------------------------ACAA------------AA-TTAAAATTGAATTGTTGCATTTTGTGGCA---------------------------------------------------------GC------------A------------------------------ATCATA-TTGACTGCGAGTTGA----------------TTTGAAGCTGAAATTTCCATTTTA-----C-----TTTA-------------------AAT---GC-TTTACTGTATCAA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TACA--ATTTCAAGTTG---TAAA--GTATATATATA------------TATATATAGTGTTGTTGGCTTGGACGTGGAAGC--------------------------------------------------------------------------------------------------------------------------------------------------GCTTACGC------------------------------GTGTGT-ATATATAATATATAG-----------------------C----------ATATAA-----T-----A------------------------------------TACATATA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:34 EDT

sblock53978

chr2R:1252139-1252239 +

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