sblock36967- Best orthologs

sblock36967	chr2R:2948548-2948660 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2948554-2948576
   star strand at position 2948634-2948655
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:2948533-2948675 -		1	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TCT-------------------------------GTTTGTTTTGAC---AT-
droSim1	chr2R:1748656-1748798 -	LASTZ	4	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droSec1	super_1:616417-616559 -	LASTZ	1	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droYak2	chr2L:15661832-15661981 -	LASTZ	3	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCT----TGGGTTTCT-------------------------------GTTTGTTTTGCC---AT-
droEre2	scaffold_4929:19619112-19619253 +	LASTZ	1	TATTGCACAAC--------TTCCC-CTGGGGCCCAAATA------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTGT-GCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTTGATTTGGGTCTTGAGTC-----------TCT-------------------------------GTTTGTTTTGCC---AT-
droEug1	scf7180000409672:4966061-4966186 -	LASTZ	4	GATTGCACAAC--------TTCCCTTTGGGGCCCC----------AGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGCCTCCGCGT----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droBia1	scf7180000302292:3194465-3194584 +	LASTZ	4	GATTGCCCAAC--------TTCCCTTCGGGGCCCC----------GGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGC------------------T-----------------------T------CGATT----------GCGCGGAGGCACTTTGCATTCGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTGGCC---AT-
droTak1	scf7180000415382:187919-188034 -	LASTZ	4	GATTGCACAAC--------TTCCC-CGC------A----------GGTTGCCAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGT------------------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCTCGTCTCT------------T-------------------------------GTTTGTTTGGCC---CT-
droEle1	scf7180000491265:55250-55375 -	LASTZ	4	GATTGCACAAC--------TTCCCTTTGGGGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droRho1	scf7180000780072:208014-208139 +	LASTZ	4	GATTGCACAAT--------TTCCCTTTGGCGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droFic1	scf7180000453955:317044-317167 +	LASTZ	4	GATTGCCCAAC--------TTCCT-TGGGGGCTCG----------AGTTGCAAAA-------TGCAAGAGTTCCACTCGAGCGAACCGCCTCCGCGT----------T-----------------------T------CGATT----------GC---GGGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droKik1	scf7180000302640:45649-45757 -	LASTZ	5	AGTTGCCCAACGAAGGCTGTGCCT-TCGGGGCGCG----------TGTTGCAATC-------TGCAAGAGTTCCACTCGAGTGCCTC---------------------------------------------------------------------------CACTCCGCATTGGATGTGGGGCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droAna3	scaffold_13266:3185126-3185263 -	LASTZ	3	AATTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCGTCCG--TCCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTT---------------------------G------CTAGT----------GC--C-AAGTGTTTTGCATTTTATTTGGGTCT-----CTGTTTTGGTT-TTC-------------------------------GTTTGTTT----------
droBip1	scf7180000396427:1655567-1655694 -	LASTZ	4	AGTTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCG------TTTTGGAGTTCCAGTCGAGTGCCTCGCCTCCGCATT--TTT-----------------------------------TGCTT----------GC--C-AAGTGTTTTGCATTTTATTTGGATTT-----CT-----------GT-------------------------------TTTTGTTTTCGC---TT-
dp4	chr3:1224831-1224985 -	LASTZ	5	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droPer1	super_2:1392971-1393125 -	LASTZ	5	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droWil1	scaffold_180700:2520193-2520301 -	LASTZ	5	C-----------------------------------------------------------------------------------CTGGCCTCGGCTTT-----TGATT-----------------------T------TGATT--------------TAAACCACTTTGCATTTAATTTATTTTT-----TTT---------TGTTTTTATTTTATGCGTTTGGGCATTTCTTCTTATTTGTTTACCTCGTATA
droVir3	scaffold_10324:1098530-1098634 -	LASTZ	5	CTT-------------------------------GAGTG------GGCCGCTGGC-------TGGA-----------CGGGTATCTCTCATCTCCAG---------------------CCTTGCTT-----T------CGATT----------TTG-CTGGCTACTTTGCATTTTTTTACGGCAT-----T-----------TCT-------------------------------ACTTGTTTTGCT---GC-
droMoj3	scaffold_6496:4946449-4946566 +	LASTZ	5	G----------------------------------------------TTGCAAGT-------GGCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATT------TTTTT----------CC--GTAGCTATTTTGCATT-----------------------------TCC-------------------------------ACTTGTATTGTT---A--
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	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TCT-------------------------------GTTTGTTTTGAC---AT-
droSim1	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droSec1	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droYak2	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCT----TGGGTTTCT-------------------------------GTTTGTTTTGCC---AT-
droEre2	TATTGCACAAC--------TTCCC-CTGGGGCCCAAATA------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTGT-GCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTTGATTTGGGTCTTGAGTC-----------TCT-------------------------------GTTTGTTTTGCC---AT-
droEug1	GATTGCACAAC--------TTCCCTTTGGGGCCCC----------AGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGCCTCCGCGT----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droBia1	GATTGCCCAAC--------TTCCCTTCGGGGCCCC----------GGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGC------------------T-----------------------T------CGATT----------GCGCGGAGGCACTTTGCATTCGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTGGCC---AT-
droTak1	GATTGCACAAC--------TTCCC-CGC------A----------GGTTGCCAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGT------------------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCTCGTCTCT------------T-------------------------------GTTTGTTTGGCC---CT-
droEle1	GATTGCACAAC--------TTCCCTTTGGGGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droRho1	GATTGCACAAT--------TTCCCTTTGGCGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droFic1	GATTGCCCAAC--------TTCCT-TGGGGGCTCG----------AGTTGCAAAA-------TGCAAGAGTTCCACTCGAGCGAACCGCCTCCGCGT----------T-----------------------T------CGATT----------GC---GGGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droKik1	AGTTGCCCAACGAAGGCTGTGCCT-TCGGGGCGCG----------TGTTGCAATC-------TGCAAGAGTTCCACTCGAGTGCCTC---------------------------------------------------------------------------CACTCCGCATTGGATGTGGGGCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droAna3	AATTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCGTCCG--TCCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTT---------------------------G------CTAGT----------GC--C-AAGTGTTTTGCATTTTATTTGGGTCT-----CTGTTTTGGTT-TTC-------------------------------GTTTGTTT----------
droBip1	AGTTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCG------TTTTGGAGTTCCAGTCGAGTGCCTCGCCTCCGCATT--TTT-----------------------------------TGCTT----------GC--C-AAGTGTTTTGCATTTTATTTGGATTT-----CT-----------GT-------------------------------TTTTGTTTTCGC---TT-
dp4	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droPer1	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droWil1	C-----------------------------------------------------------------------------------CTGGCCTCGGCTTT-----TGATT-----------------------T------TGATT--------------TAAACCACTTTGCATTTAATTTATTTTT-----TTT---------TGTTTTTATTTTATGCGTTTGGGCATTTCTTCTTATTTGTTTACCTCGTATA
droVir3	CTT-------------------------------GAGTG------GGCCGCTGGC-------TGGA-----------CGGGTATCTCTCATCTCCAG---------------------CCTTGCTT-----T------CGATT----------TTG-CTGGCTACTTTGCATTTTTTTACGGCAT-----T-----------TCT-------------------------------ACTTGTTTTGCT---GC-
droMoj3	G----------------------------------------------TTGCAAGT-------GGCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATT------TTTTT----------CC--GTAGCTATTTTGCATT-----------------------------TCC-------------------------------ACTTGTATTGTT---A--

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
UNAFold Image																				None

Small RNA-seq read pileup

Species

Alignment

droSim1

GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................CTTTGCATTCGATTTGGGTCTT....................................................................	22	1	2.00	0.00	1.00	1.00	0.00
.........................................................................................CTCCGCGTT--TTTTCGCT-----------------------G------....................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
....................................................................................................................................................................CTTTGCATTCGATTTGGGTCTTG...................................................................	23	1	3.00	3.00	0.00	0.00
....................................................................................................................................................................CTTTGCATTCGATTTGGGTCT.....................................................................	21	1	1.00	0.00	0.00	1.00
....................................................................................................................................................................CTTTGCATTCGATTTGGGTCTT....................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................................................................................ACTTTGCATTCGATTTGGGT.......................................................................	20	1	1.00	0.00	1.00	0.00

droYak2

GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCT----TGGGTTTCT-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................TGTGTCT----TGGGTTTCG-------------------------------GAT...............	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................GTGTCT----TGGGTTTCG-------------------------------GAT...............	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................GTT--TTTTGGCT-----------------------T------CGATT----------GA--.................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TATTGCACAAC--------TTCCC-CTGGGGCCCAAATA------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTGT-GCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTTGATTTGGGTCTTGAGTC-----------TCT-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................................................................................................................................................TGCATTTGATTTGGGTCTTGAG.................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

GATTGCACAAC--------TTCCCTTTGGGGCCCC----------AGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGCCTCCGCGT----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-

Size

Hit Count

Total Norm

droBia1

GATTGCCCAAC--------TTCCCTTCGGGGCCCC----------GGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGC------------------T-----------------------T------CGATT----------GCGCGGAGGCACTTTGCATTCGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTGGCC---AT-

Size

Hit Count

Total Norm

droTak1

GATTGCACAAC--------TTCCC-CGC------A----------GGTTGCCAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGT------------------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCTCGTCTCT------------T-------------------------------GTTTGTTTGGCC---CT-

Size

Hit Count

Total Norm

droEle1

GATTGCACAAC--------TTCCCTTTGGGGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-

Size

Hit Count

Total Norm

droRho1

GATTGCACAAT--------TTCCCTTTGGCGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-

Size

Hit Count

Total Norm

droFic1

GATTGCCCAAC--------TTCCT-TGGGGGCTCG----------AGTTGCAAAA-------TGCAAGAGTTCCACTCGAGCGAACCGCCTCCGCGT----------T-----------------------T------CGATT----------GC---GGGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-

Size

Hit Count

Total Norm

droKik1

AGTTGCCCAACGAAGGCTGTGCCT-TCGGGGCGCG----------TGTTGCAATC-------TGCAAGAGTTCCACTCGAGTGCCTC---------------------------------------------------------------------------CACTCCGCATTGGATGTGGGGCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-

Size

Hit Count

Total Norm

droAna3

AATTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCGTCCG--TCCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTT---------------------------G------CTAGT----------GC--C-AAGTGTTTTGCATTTTATTTGGGTCT-----CTGTTTTGGTT-TTC-------------------------------GTTTGTTT----------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......CAAC--------TTGCG-CGGAGTTGC............................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................TT-TTC-------------------------------GTTTTTAT----------	18	5	0.20	0.00	0.00	0.00	0.20

droBip1

AGTTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCG------TTTTGGAGTTCCAGTCGAGTGCCTCGCCTCCGCATT--TTT-----------------------------------TGCTT----------GC--C-AAGTGTTTTGCATTTTATTTGGATTT-----CT-----------GT-------------------------------TTTTGTTTTCGC---TT-

Size

Hit Count

Total Norm

dp4

CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................................................................TTTT-----CGGTT-----------------------TTCGGTGTCTT................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.......................................TGGCCATGTTGCGGGTGACTG..................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00

droPer1

CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................GGCCATGTTGCAAGTGACTG..................................................................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
......................................................................................CGCCTCGACTTT-----CGGTT-----------------------TTCG.......................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................GCCATGTTGTAAGGGACT...................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................CT-----AGGTT-----------------------TTCGGTGTTTT................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................CAAGxGACTGGATGTTGTTGT.......................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

C-----------------------------------------------------------------------------------CTGGCCTCGGCTTT-----TGATT-----------------------T------TGATT--------------TAAACCACTTTGCATTTAATTTATTTTT-----TTT---------TGTTTTTATTTTATGCGTTTGGGCATTTCTTCTTATTTGTTTACCTCGTATA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................................................................................................................................TTT---------TGTGTTTATTATATGC....................................	19	1	29.00	0.00	29.00	0.00	0.00
........................................................................................................................................................................................T-----TTT---------TGTGTTTATTATATGC....................................	20	1	19.00	0.00	18.00	1.00	0.00
...............................................................................................................................................................................................TT---------TGTGTTTATTATATGC....................................	18	1	7.00	0.00	7.00	0.00	0.00
........................................................................................................................................................................................T-----TTT---------TGTGTTTATTATATG.....................................	19	1	7.00	0.00	7.00	0.00	0.00
...........................................................................................................................................................................................................................TTCGGGCATTTCTTCTTT.................	18	1	4.00	0.00	2.00	0.00	2.00
................................................................................................TT-----TGAAT-----------------------T------TGATT--------------TAAAA............................................................................................	18	6	0.50	0.00	0.00	0.00	0.50
..................................................................................................................................................................................TATTTTT-----TTT---------TGTTTTTTTGT.........................................	21	18	0.06	0.00	0.00	0.06	0.00
..............................................................................................ATTT-----TGAAT-----------------------T------TGATT--------------TAAA.............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................GAATGTATTTTT-----TTT---------TGT.................................................	18	3	0.33	0.00	0.33	0.00	0.00
...............................................................................................TTT-----TGAAT-----------------------T------TGATT--------------TAAAA............................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................TGTTTTTACTTTATGAGT..................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................CATTTATTTTATTTTG-----TT..............................................................	18	11	0.09	0.00	0.09	0.00	0.00
...................................................................................................................................................................................ATTTTT-----TTT---------TATTTGTATT..........................................	19	18	0.06	0.00	0.06	0.00	0.00
..........................................................................................................................................................................ATTCAATTTATTTTT-----GTT---------....................................................	18	3	0.33	0.00	0.33	0.00	0.00
..........................................................................................................................................................................ATTTAATTTATGTTT-----TTG---------T...................................................	19	4	0.25	0.00	0.00	0.00	0.25
............................................................................................................................................................................................................................................ATTTGTTTACCCCGTTTA	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................ATTTTT-----TTT---------TGTTTGAAT...........................................	18	14	0.07	0.00	0.07	0.00	0.00
........................................................................................................................................................................................T-----TTC---------TGTTTTTATTATATGCG...................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................TAATTTTTTTTT-----TTG---------TGTTTTT.............................................	22	10	0.10	0.00	0.10	0.00	0.00
..............................................................................................................................................................................CATTTATTTTA-----TTT---------TGTT................................................	18	11	0.09	0.00	0.09	0.00	0.00
..............................................................................................................................................................................AATTTATTTTT-----TTG---------TGAT................................................	18	2	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................................................TTGTT-----TTT---------TGTTTTTGTTTT........................................	20	40	0.03	0.00	0.03	0.00	0.00
.................................................................................................................................................................................TTATTTTG-----TTT---------TGTTTCT.............................................	18	13	0.08	0.00	0.08	0.00	0.00
...............................................................................................................................................................................ATTTATTTTT-----TTT---------TGCATT..............................................	19	5	0.20	0.00	0.20	0.00	0.00

droVir3

CTT-------------------------------GAGTG------GGCCGCTGGC-------TGGA-----------CGGGTATCTCTCATCTCCAG---------------------CCTTGCTT-----T------CGATT----------TTG-CTGGCTACTTTGCATTTTTTTACGGCAT-----T-----------TCT-------------------------------ACTTGTTTTGCT---GC-	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................................................................................................................................................................T-----T-----------TCT-------------------------------ACATGTTTGGCT---G..	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................TTTGTATTTTTTTATGGCA......................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00

droMoj3

G----------------------------------------------TTGCAAGT-------GGCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATT------TTTTT----------CC--GTAGCTATTTTGCATT-----------------------------TCC-------------------------------ACTTGTATTGTT---A--

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 05:20:33 EDT

sblock36967

chr2R:2948548-2948660 -

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