sblock221622- Best orthologs

sblock221622	chr3R:19094949-19095044 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_CDS

Legend:

   mature strand at position 19095007-19095027
   star strand at position 19094968-19094987
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:19094934-19095059 +		1	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCTGATGGGTTAGCCGCT------GA-GGT
droSim1	chr3R:18910498-18910623 +	LASTZ	3	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCT------GA-GGT
droSec1	super_0:19459752-19459877 +	LASTZ	4	GGACAGTTG------AGAGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGTT------GA-GGT
droYak2	chr3R:19969866-19969991 +	LASTZ	3	GGACAATTG------AACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCGGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCC------GA-TGG
droEre2	scaffold_4820:8959323-8959448 -	LASTZ	3	GGACAGTTG------GACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCAACCG-A---------AGCTGGCGGATGGGTTGGCCGCC------GA-GGT
droEug1	scf7180000409473:254972-255094 -	LASTZ	4	GGACAGTTG------AACGCCATCACCGGC------------------GGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGTAGA----TTATTGACGTCGCTACT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGAGTTGACCGCCGGATGGGA-GTT
droBia1	scf7180000302075:4604033-4604149 +	LASTZ	4	GGACAGTTG------GACGCCATCACCGGCGGCAGCGG---------CAGCAGC---AGCGGCTG------CGG------------CCGCACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droTak1	scf7180000414295:164513-164629 +	LASTZ	4	GGACAGTTG------AACGCCATCGCCGGCGGCAGCGG---------C------------AGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTATTGACATCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTT-------------------
droEle1	scf7180000491280:209279-209416 +	LASTZ	4	GGACAGTTG------AGCGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGAAGCAGC------------AGCGGCTGCCGCATTGGCGAGCAGCAGA----TTGTTGACGTCGCCGCT---GCTGCCGTTGCCCCCG-A---------AGCTGGCGGATGGGTTGCCCGCC------GG-GCT
droRho1	scf7180000780140:23288-23411 -	LASTZ	4	AGCCGCAGT------AGCAGCAGCATCGGCAGCAGCAG---------CAGCAGC---A------------GCAGCAGCAGCGGCTGCAGCAGCGGGATCCAG------------CAGCGGCGCCGGC---TTGGATGTGGCCA--------------GTCTGGTGGGTCTGG--TGCGCG------GC-GGT
droFic1	scf7180000453906:760202-760324 -	LASTZ	4	GGACAGTTG------AACGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACTTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droKik1	scf7180000302307:473329-473451 -	LASTZ	4	GGAAAGTTG------GATGCCATCACCGGCAGACGCGG---------CGACAGC---GGCAGCGG------CAG------------CAGCGCTGGCGAGCAGCAGA----TTGTTGACGCCGCTGCT---GCTGCCGTTGCCACCA-A---------AGCTGCCGGG-GGTTT--------------G-GCT
droAna3	scaffold_13340:8296287-8296436 -	LASTZ	4	CGACAGTTGGACGCCAACACCATCGCCAGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACGCCGCTGCT---ACTGCCGTTGCCACCA-ACGCCGA---CGCTGGCCGATGCGTGGCTCGCG------GG-GCT
droBip1	scf7180000396691:1677356-1677480 +	LASTZ	4	TGGCCTCCA------CGCTG----CCCAACGGCGG------------CGCCAGC---ACCAGCCTG------------AGCGGCACCAGCGTTGGCTCGC---AGA----GCGTGGCTGCCGCTGCT---GCTGCCGCTGCCGCCG-C---------CTCTGCCGGATCGGGGG---GCG------GA-GGC
dp4	chrXR_group6:8583769-8583897 +	LASTZ	3	CAACAGCCA------ACGGCTATAACCAACAACCGCAG---------CAGCAGC---GGCAGCAG------------CAGCAGCGGC------AGC-AGCAGCA-A----TTGTTGCCATTGTCGTAGTTGTTGCCGCTGCTTGTATA---------CCCTGGCGCAGAGGGTAGT-----------A-TGA
droPer1	super_0:10926574-10926696 +	LASTZ	3	CGACAGTTG------GACACCAACGCCAACGCCCACAC---------CATCGCCAGAGGCGGCGGCAACGGCAGTAGT------------AGCGGCATTCAGACGA----TTCGTGCTGCCACTGCT---GATGCCGTTGTCTCCG-T---------TGCTC------------------------TG-GAT
droWil1	scaffold_181089:723997-724131 -	LASTZ	4	GGACAATTG------GACGCCGTCTCCAGCAGCGGCGG---------CGGCAGC---GGCAGCAGC------AG------------CCGCACTGGCGAGCAGCAAG----TTGTTGACTCCGCCGCTGCTGCTGCCGTTGCCGCTG-A---------CGCAGACGCTACTGTTGGTCATA------TT-GTT
droVir3	scaffold_12932:1166920-1167036 +	LASTZ	3	---------------------ATCGCCAGCGGCGGCGG---------CGGCGGC---GGCAGCGAC------AA------CTGC------TGCG----GCAGCATTTGCATTGTTGACCTCGCTGCT---GCTGCC--CGCCGCGA-------CAGCAGCCG-CCGTTGAGTTGGCGGCG------AC-GGC
droMoj3	scaffold_6328:387888-388007 +	LASTZ	3	C----------------------CGCCAGCAGCCGGAACAGGGACAGCAGCGCTT--------GA---------------CG---------GCGGCG-ACAGCGGA----CTGGCGCCGCTGCTGCT---GCTGCCGCTGCCACCG-CTGCTAA---AGTAGTTCATTGTGTTTGCCGCC------GACGTT
droGri2	scaffold_14906:4290741-4290869 -	LASTZ	3	CGTCAATTG------ACCGCAATCGTCAGGGGCAGCGA---------CAGCGGC------AGTTGC------------AACAGTCGCCGAATTGCCAAGTAGCAAG----TTATTAACGCCGCTGCTGCTGCTGCTGCTGCCGTTA-CCTCCGG---CGCCG---------------CTT------GC-AAT

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	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCTGATGGGTTAGCCGCT------GA-GGT
droSim1	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCT------GA-GGT
droSec1	GGACAGTTG------AGAGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGTT------GA-GGT
droYak2	GGACAATTG------AACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCGGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCC------GA-TGG
droEre2	GGACAGTTG------GACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCAACCG-A---------AGCTGGCGGATGGGTTGGCCGCC------GA-GGT
droEug1	GGACAGTTG------AACGCCATCACCGGC------------------GGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGTAGA----TTATTGACGTCGCTACT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGAGTTGACCGCCGGATGGGA-GTT
droBia1	GGACAGTTG------GACGCCATCACCGGCGGCAGCGG---------CAGCAGC---AGCGGCTG------CGG------------CCGCACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droTak1	GGACAGTTG------AACGCCATCGCCGGCGGCAGCGG---------C------------AGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTATTGACATCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTT-------------------
droEle1	GGACAGTTG------AGCGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGAAGCAGC------------AGCGGCTGCCGCATTGGCGAGCAGCAGA----TTGTTGACGTCGCCGCT---GCTGCCGTTGCCCCCG-A---------AGCTGGCGGATGGGTTGCCCGCC------GG-GCT
droRho1	AGCCGCAGT------AGCAGCAGCATCGGCAGCAGCAG---------CAGCAGC---A------------GCAGCAGCAGCGGCTGCAGCAGCGGGATCCAG------------CAGCGGCGCCGGC---TTGGATGTGGCCA--------------GTCTGGTGGGTCTGG--TGCGCG------GC-GGT
droFic1	GGACAGTTG------AACGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACTTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droKik1	GGAAAGTTG------GATGCCATCACCGGCAGACGCGG---------CGACAGC---GGCAGCGG------CAG------------CAGCGCTGGCGAGCAGCAGA----TTGTTGACGCCGCTGCT---GCTGCCGTTGCCACCA-A---------AGCTGCCGGG-GGTTT--------------G-GCT
droAna3	CGACAGTTGGACGCCAACACCATCGCCAGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACGCCGCTGCT---ACTGCCGTTGCCACCA-ACGCCGA---CGCTGGCCGATGCGTGGCTCGCG------GG-GCT
droBip1	TGGCCTCCA------CGCTG----CCCAACGGCGG------------CGCCAGC---ACCAGCCTG------------AGCGGCACCAGCGTTGGCTCGC---AGA----GCGTGGCTGCCGCTGCT---GCTGCCGCTGCCGCCG-C---------CTCTGCCGGATCGGGGG---GCG------GA-GGC
dp4	CAACAGCCA------ACGGCTATAACCAACAACCGCAG---------CAGCAGC---GGCAGCAG------------CAGCAGCGGC------AGC-AGCAGCA-A----TTGTTGCCATTGTCGTAGTTGTTGCCGCTGCTTGTATA---------CCCTGGCGCAGAGGGTAGT-----------A-TGA
droPer1	CGACAGTTG------GACACCAACGCCAACGCCCACAC---------CATCGCCAGAGGCGGCGGCAACGGCAGTAGT------------AGCGGCATTCAGACGA----TTCGTGCTGCCACTGCT---GATGCCGTTGTCTCCG-T---------TGCTC------------------------TG-GAT
droWil1	GGACAATTG------GACGCCGTCTCCAGCAGCGGCGG---------CGGCAGC---GGCAGCAGC------AG------------CCGCACTGGCGAGCAGCAAG----TTGTTGACTCCGCCGCTGCTGCTGCCGTTGCCGCTG-A---------CGCAGACGCTACTGTTGGTCATA------TT-GTT
droVir3	---------------------ATCGCCAGCGGCGGCGG---------CGGCGGC---GGCAGCGAC------AA------CTGC------TGCG----GCAGCATTTGCATTGTTGACCTCGCTGCT---GCTGCC--CGCCGCGA-------CAGCAGCCG-CCGTTGAGTTGGCGGCG------AC-GGC
droMoj3	C----------------------CGCCAGCAGCCGGAACAGGGACAGCAGCGCTT--------GA---------------CG---------GCGGCG-ACAGCGGA----CTGGCGCCGCTGCTGCT---GCTGCCGCTGCCACCG-CTGCTAA---AGTAGTTCATTGTGTTTGCCGCC------GACGTT
droGri2	CGTCAATTG------ACCGCAATCGTCAGGGGCAGCGA---------CAGCGGC------AGTTGC------------AACAGTCGCCGAATTGCCAAGTAGCAAG----TTATTAACGCCGCTGCTGCTGCTGCTGCTGCCGTTA-CCTCCGG---CGCCG---------------CTT------GC-AAT

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

GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCT------GA-GGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................................................CCGAxxG-A---------AGCTGGCGGATGG......................	19	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................GTCACCG-A---------AGCTxGCGGAT........................	18	2	0.50	0.00	0.00	0.50	0.00
..................................................................................................................TGACGTCGTTGCT---GCTGA.........................................................	18	4	0.25	0.00	0.25	0.00	0.00
...........................................................................................................................................CCGAxxG-A---------AGCTGGCGGATG.......................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................GTCATCG-A---------AGCTGGCGGATG.......................	20	2	0.50	0.00	0.00	0.50	0.00

droSec1

GGACAGTTG------AGAGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGTT------GA-GGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................................................CGCTGCT---GCTGCCGCCGCC..................................................	19	36	0.03	0.00	0.03	0.00
..............................................................................................................................................ATCG-A---------AGCTGGCGGATGGTT....................	20	2	0.50	0.50	0.00	0.00
...........................GGCAGCGGCGG---------CAGCAGC---G------------..........................................................................................................................	19	31	0.03	0.00	0.03	0.00
...............................................CGGCAGC---G------------GCAGCAGG------------AC....................................................................................................	18	10	0.10	0.10	0.00	0.00
..........................................................................................................................CTGCT---GCTGCCGCCGCCA.................................................	18	31	0.03	0.00	0.03	0.00
........................................................................................................................CGATGCC---GCTGCCGTTGC...................................................	18	4	0.25	0.00	0.25	0.00
...................................................................................................................GACGTCGCTGTG---GCTGCC........................................................	18	2	0.50	0.50	0.00	0.00
................................CAGCGG---------CGGCAGC---G------------ACAGCAG...................................................................................................................	21	13	0.08	0.00	0.00	0.08
......TTG------GGAGCGATCACCGGC..................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00
................................CTGCGG---------CGGCAAC---G------------GCAGCA....................................................................................................................	20	8	0.13	0.13	0.00	0.00
.......................................................................CAGCAGC------------AACGGCGAGCAGC.........................................................................................	20	2	0.50	0.50	0.00	0.00

droYak2

GGACAATTG------AACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCGGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCC------GA-TGG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................GAGCAGCAGA----TTATAGAGG.........................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
..................................GCAG---------TGGCAGC---G------------GCAGCGGC------------......................................................................................................	20	32	0.03	0.00	0.00	0.03	0.00	0.00
.........................................................................................................................GCTGCT---GCTCCCGTCGCC..................................................	18	5	0.20	0.00	0.20	0.00	0.00	0.00
..................................................CCAC---G------------GCAGCGGC------------ACTGGC................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
.....................................G---------CGGCAGC---G------------GCAGCCGC------------G.....................................................................................................	18	33	0.03	0.00	0.03	0.00	0.00	0.00
...........................GGCAGCGGCGG---------CAGCAGC---G------------GCA.......................................................................................................................	22	9	0.11	0.00	0.00	0.11	0.00	0.00
............................GCAGCAGCGG---------CGGCAGC---G------------GA........................................................................................................................	20	28	0.04	0.00	0.04	0.00	0.00	0.00
................................................................................................GAGCAACAGA----TTATTGGCGT........................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................................CGAGCAGCAGA----TTATAGAG..........................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
................................................................................................................................................................TGGCGGACGGGTTAGCTGCC------......	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GGACAGTTG------GACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCAACCG-A---------AGCTGGCGGATGGGTTGGCCGCC------GA-GGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................TCGGCGG---------CGGCAGC---G------------GCAGC.....................................................................................................................	20	12	0.17	0.00	0.00	0.00	0.17
.....................................................................................................................CGGCGCTGCT---GCTTCCGT......................................................	18	3	0.33	0.00	0.00	0.00	0.33
..................................................CAGT---G------------GCAGxAGC------------ACTGGC................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
........................................................................................................................CGCTGCA---GCTGCCGTTGGA..................................................	19	2	0.50	0.00	0.00	0.00	0.50

droEug1

GGACAGTTG------AACGCCATCACCGGC------------------GGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGTAGA----TTATTGACGTCGCTACT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGAGTTGACCGCCGGATGGGA-GTT

Size

Hit Count

Total Norm

droBia1

GGACAGTTG------GACGCCATCACCGGCGGCAGCGG---------CAGCAGC---AGCGGCTG------CGG------------CCGCACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------

Size

Hit Count

Total Norm

droTak1

GGACAGTTG------AACGCCATCGCCGGCGGCAGCGG---------C------------AGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTATTGACATCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTT-------------------

Size

Hit Count

Total Norm

droEle1

GGACAGTTG------AGCGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGAAGCAGC------------AGCGGCTGCCGCATTGGCGAGCAGCAGA----TTGTTGACGTCGCCGCT---GCTGCCGTTGCCCCCG-A---------AGCTGGCGGATGGGTTGCCCGCC------GG-GCT

Size

Hit Count

Total Norm

droRho1

AGCCGCAGT------AGCAGCAGCATCGGCAGCAGCAG---------CAGCAGC---A------------GCAGCAGCAGCGGCTGCAGCAGCGGGATCCAG------------CAGCGGCGCCGGC---TTGGATGTGGCCA--------------GTCTGGTGGGTCTGG--TGCGCG------GC-GGT

Size

Hit Count

Total Norm

droFic1

GGACAGTTG------AACGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACTTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------

Size

Hit Count

Total Norm

droKik1

GGAAAGTTG------GATGCCATCACCGGCAGACGCGG---------CGACAGC---GGCAGCGG------CAG------------CAGCGCTGGCGAGCAGCAGA----TTGTTGACGCCGCTGCT---GCTGCCGTTGCCACCA-A---------AGCTGCCGGG-GGTTT--------------G-GCT

Size

Hit Count

Total Norm

droAna3

CGACAGTTGGACGCCAACACCATCGCCAGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACGCCGCTGCT---ACTGCCGTTGCCACCA-ACGCCGA---CGCTGGCCGATGCGTGGCTCGCG------GG-GCT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.................................................GCGGT---GGCAGCAGC------------AGCGGC............................................................................................................	20	28	0.29	0.00	0.29	0.00	0.00
....................................GG---------CGGCxGC---GGCAGCAGG------------AGC...............................................................................................................	20	4	0.75	0.25	0.50	0.00	0.00
................................................GGCAGC---GGCAGTAGC------------AGCGGC............................................................................................................	21	13	0.23	0.00	0.23	0.00	0.00
.................................................GCAGA---GGCAGCAGC------------AGCGGC............................................................................................................	20	67	0.03	0.00	0.03	0.00	0.00
.....................................G---------CGGCAGC---GGTAGCGGC------------AGC...............................................................................................................	20	18	0.06	0.00	0.06	0.00	0.00
..................................GCGG---------CGGCAGC---GGCAGCATC------------AC................................................................................................................	22	2	0.50	0.00	0.50	0.00	0.00
.........................................................GGCAGCAGC------------AGCGTCGGC.........................................................................................................	18	32	0.03	0.00	0.03	0.00	0.00
...................................CGG---------CGGCxGC---GGCAGCAGG------------AGC...............................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
.................................................................C------------AGCGGCAGCGGCACTGGC................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
..........................CAGCAGCAGCGG---------CGGCAGC---GGGAGC.................................................................................................................................	25	6	0.17	0.00	0.17	0.00	0.00
.....................................G---------CAGCAGC---GGCAGCAGC------------AGCG..............................................................................................................	21	49	0.02	0.00	0.02	0.00	0.00
............................GCAGCGGCGG---------CGGCAGC---GGCA...................................................................................................................................	21	9	0.11	0.11	0.00	0.00	0.00
...................................CGG---------CGGTAGC---AGCAGCAGC------------AGC...............................................................................................................	22	40	0.03	0.00	0.03	0.00	0.00
.....................................G---------CGGCGGC---GGCAGCATC------------AGC...............................................................................................................	20	38	0.03	0.00	0.03	0.00	0.00
.................................................................C------------AGCGGGTGCCGCGCTGGC................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..................................GCGG---------CGGCCGC---GGCAGCGGC------------..................................................................................................................	20	10	0.10	0.10	0.00	0.00	0.00
............................GCAGCGGCGG---------CGGCAGC---GTCAGC.................................................................................................................................	23	5	0.20	0.20	0.00	0.00	0.00
..................AACTTCGCCAGCAGCCGC............................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
......ATGGACGCCAACAGCATC........................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droBip1

TGGCCTCCA------CGCTG----CCCAACGGCGG------------CGCCAGC---ACCAGCCTG------------AGCGGCACCAGCGTTGGCTCGC---AGA----GCGTGGCTGCCGCTGCT---GCTGCCGCTGCCGCCG-C---------CTCTGCCGGATCGGGGG---GCG------GA-GGC

Size

Hit Count

Total Norm

dp4

CAACAGCCA------ACGGCTATAACCAACAACCGCAG---------CAGCAGC---GGCAGCAG------------CAGCAGCGGC------AGC-AGCAGCA-A----TTGTTGCCATTGTCGTAGTTGTTGCCGCTGCTTGTATA---------CCCTGGCGCAGAGGGTAGT-----------A-TGA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................................................................................................................................G	22	27	0.07	0.00	0.07	0.00	0.00
.....................................................C---GGCAGCAG------------CAGCAGCGGG------G..................................................................................................	20	46	0.04	0.04	0.00	0.00	0.00
...................................................AGC---GGTAGCAG------------CAGCAGCGGC------C..................................................................................................	22	13	0.08	0.00	0.08	0.00	0.00
.....................................................C---GGCAGCAG------------CAGCAGCGGG------GG.................................................................................................	21	39	0.03	0.03	0.00	0.00	0.00
....................................AG---------CAGCAGC---GGCAGCAG------------GAG................................................................................................................	20	50	0.02	0.02	0.00	0.00	0.00
........................CCCAACATCCGCAG---------CAGCA............................................................................................................................................	19	9	0.11	0.00	0.00	0.11	0.00
................................................................................................................................................................TGGCGGAGTGGGTAGT-----------A-TG.	19	1	1.00	0.00	0.00	1.00	0.00
............................................................AGCAG------------CAGCTGCGGT------AGC-AGCA...........................................................................................	22	132	0.01	0.00	0.01	0.00	0.00
................................................AGCAGC---GGCAGCAG------------CAGCAGA............................................................................................................	21	39	0.03	0.03	0.00	0.00	0.00
............................................................AGCAG------------CAGCAGCGTC------AGC-AGC............................................................................................	21	36	0.03	0.00	0.03	0.00	0.00
...............................................................AG------------CAGCAGCGGC------AGC-AGGAG..........................................................................................	20	50	0.02	0.02	0.00	0.00	0.00

droPer1

CGACAGTTG------GACACCAACGCCAACGCCCACAC---------CATCGCCAGAGGCGGCGGCAACGGCAGTAGT------------AGCGGCATTCAGACGA----TTCGTGCTGCCACTGCT---GATGCCGTTGTCTCCG-T---------TGCTC------------------------TG-GAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................CACCCACAC---------CGTCGCCAG........................................................................................................................................	18	2	15.00	0.00	0.00	0.00	0.00	15.00
.............................................................................................................................CT---GATGGCGTTGACTCCG-T---------...................................	19	2	4.00	1.00	0.50	0.00	0.00	2.50
...............................................................................................CATTCAGTCGA----TTCGCGCT..........................................................................	19	2	2.00	0.00	0.00	0.00	0.00	2.00
................................................................................................ATTCAGTCGA----TTCGCGCTGC........................................................................	20	2	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................TTCAGTCGA----TTCGCGCTG.........................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
...............................................................................................CATTCAGTCGA----TTCGCGC...........................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50

droWil1

GGACAATTG------GACGCCGTCTCCAGCAGCGGCGG---------CGGCAGC---GGCAGCAGC------AG------------CCGCACTGGCGAGCAGCAAG----TTGTTGACTCCGCCGCTGCTGCTGCCGTTGCCGCTG-A---------CGCAGACGCTACTGTTGGTCATA------TT-GTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................AGCAGCGG---------CGGCAGC---GGCAGT.................................................................................................................................	21	27	0.11	0.00	0.11	0.00	0.00
...........................AGCAACAGCGG---------CGGCAGC---GGC....................................................................................................................................	21	34	0.09	0.03	0.06	0.00	0.00
............................GCAGCAGCGG---------CGGCAGC---GGC....................................................................................................................................	20	31	0.06	0.00	0.06	0.00	0.00
...............................GCAGCGG---------CGGCAGC---GGCAGT.................................................................................................................................	20	34	0.06	0.00	0.06	0.00	0.00
..............................AGCAGCGG---------CGGCAGC---GGCA...................................................................................................................................	19	25	0.08	0.00	0.08	0.00	0.00
..................................GCGG---------CGGCTGC---GGCAGCAGC------A.......................................................................................................................	21	50	0.04	0.00	0.04	0.00	0.00
............................GCAGCGGCGG---------CGGCAGC---AGC....................................................................................................................................	20	44	0.05	0.00	0.05	0.00	0.00
..........................CAGCAGCGGCAG---------CGGCAGT---GGC....................................................................................................................................	22	26	0.04	0.04	0.00	0.00	0.00
............................GCAGTGGCGG---------CGGCAGC---GGCG...................................................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
..............................................................................................................................TGCAGCTGCCGTCGCCGCTG-.............................................	20	9	0.11	0.00	0.00	0.00	0.11
..............................AGCGGCAG---------TGGCAGC---GGCA...................................................................................................................................	19	25	0.04	0.00	0.00	0.04	0.00
...........................TGCAGCAGCGG---------CGGCAGC---GGCA...................................................................................................................................	22	32	0.03	0.00	0.03	0.00	0.00
.............................CAGCGGAGG---------TGGCAGC---GGC....................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
...........................AGCAGCGGCAG---------CGGCAGC---GGCAGC.................................................................................................................................	24	43	0.02	0.00	0.02	0.00	0.00
...............................GCGGCGA---------CGGCAAC---GGCA...................................................................................................................................	18	7	0.14	0.00	0.14	0.00	0.00
............................GCAGCAGCGG---------CGGCAGC---GGCA...................................................................................................................................	21	25	0.04	0.04	0.00	0.00	0.00
..............................AGCGGCAG---------TGGCAGC---GGCAGC.................................................................................................................................	21	15	0.07	0.07	0.00	0.00	0.00
...........................AGCAGCAGCGG---------CGGCAGC---GGCT...................................................................................................................................	22	31	0.03	0.03	0.00	0.00	0.00
....................................AG---------CGGCAGC---GGCAGCAGC------A.......................................................................................................................	19	50	0.02	0.00	0.02	0.00	0.00
..........................................................................................................................CCGCTGCTGCTCCGGTTGC...................................................	19	7	0.14	0.14	0.00	0.00	0.00
............................ACAGCGGCGG---------CGGCAGC---GGCAG..................................................................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
.......................CTTCATCAGCGGCGG---------CGG..............................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.....................................G---------CGGAAGC---GGAAGCAGC------AG------------C.........................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
...............................GCGGCGG---------CGGCAGT---GGCA...................................................................................................................................	18	29	0.03	0.00	0.03	0.00	0.00
........................ATCAGCAGCGGCGG---------CGGCAG...........................................................................................................................................	20	41	0.02	0.00	0.02	0.00	0.00
...........................TGCAGCAGCGG---------CGGCAGC---GGC....................................................................................................................................	21	37	0.03	0.00	0.03	0.00	0.00
............................GCAACGGCGA---------CGGCAGC---GGCAGC.................................................................................................................................	23	4	0.25	0.00	0.25	0.00	0.00
................................................................................................................................CTGCTGCCGTTGCCGGTG-A---------G..................................	20	2	0.50	0.00	0.00	0.00	0.50
............................GCAACAGCGG---------CGGCAGC---GGC....................................................................................................................................	20	41	0.02	0.00	0.02	0.00	0.00
......................TCATCAGCAGCGGCGG---------CGGCAG...........................................................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
.........................................................................................................................GCCGCTGCTACTGCCGTCG....................................................	19	4	0.25	0.00	0.00	0.25	0.00
.....................................G---------CGGCAGC---GGCAGCAGC------AG------------C.........................................................................................................	20	63	0.02	0.00	0.02	0.00	0.00
...............................GCGGCGG---------TGGCAGC---GGCACC.................................................................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
.............................................................GCAGC------AG------------CCGCATTGGGGA..............................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
................................CGGCGG---------CGGCAGC---AGCTGCAGC------A.......................................................................................................................	23	31	0.03	0.00	0.00	0.03	0.00
....................................GG---------CGCCAGC---GGCAGCAGC------GG------------..........................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
.................................AGCGG---------CGGCAGC---TGCAGCAGC------AG------------C.........................................................................................................	24	45	0.02	0.02	0.00	0.00	0.00
.........................................................GGCAGCAGC------AG------------CGGCATTGGC................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
............................................................................................................................GTTGCTGGTGCCGTTGCC..................................................	18	11	0.09	0.00	0.00	0.00	0.09
.........................TCATCAGCGGCGG---------CGGCAG...........................................................................................................................................	19	7	0.14	0.14	0.00	0.00	0.00
....................................AG---------CGGCAGC---GGCAGCAGC------AG------------C.........................................................................................................	21	35	0.03	0.00	0.03	0.00	0.00
...........................AGCAGCGGCGG---------CAGCAGC---GGCC...................................................................................................................................	22	11	0.09	0.00	0.09	0.00	0.00
...............................................................................................................................GCTGCTGCCGTTGCCGTG...............................................	18	14	0.07	0.00	0.07	0.00	0.00
...............................GCGGCGG---------CGGCAAC---GACA...................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...................................................AGC---AGCAGCAGC------CG------------CCGCACT...................................................................................................	21	4	0.25	0.00	0.00	0.25	0.00

droVir3

---------------------ATCGCCAGCGGCGGCGG---------CGGCGGC---GGCAGCGAC------AA------CTGC------TGCG----GCAGCATTTGCATTGTTGACCTCGCTGCT---GCTGCC--CGCCGCGA-------CAGCAGCCG-CCGTTGAGTTGGCGGCG------AC-GGC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................AGGAGGCGG---------CGGCGGC---GGC....................................................................................................................................	19	33	0.03	0.03	0.00	0.00	0.00	0.00
...........................AGCGGCGTCGC---------CGGCGGC---.......................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.00	0.11
.............................CGGCGGCAA---------CGGCGGC---GGCA...................................................................................................................................	20	22	0.05	0.00	0.05	0.00	0.00	0.00
...................................CGG---------CGGCAGC---GACAGCGAC------........................................................................................................................	19	21	0.05	0.00	0.00	0.00	0.05	0.00
................................CGGCGG---------CGAAGGC---GGCA...................................................................................................................................	17	15	0.07	0.00	0.07	0.00	0.00	0.00
..............................GGCGGCGG---------GGGCGAC---GGC....................................................................................................................................	18	29	0.03	0.00	0.03	0.00	0.00	0.00
............................GCGGCAGCGG---------CGGCGGC---GGCC...................................................................................................................................	21	38	0.03	0.00	0.00	0.03	0.00	0.00
................................CGGCGG---------CGGCGGC---GGCAGAGG...............................................................................................................................	21	31	0.03	0.03	0.00	0.00	0.00	0.00
...........................AGTGGCAGCGG---------CGGCGGC---GG.....................................................................................................................................	20	22	0.05	0.05	0.00	0.00	0.00	0.00
............................GCGGTGGCGG---------TGGCGGC---GG.....................................................................................................................................	19	31	0.03	0.03	0.00	0.00	0.00	0.00
...........................AGCAGCGGCGG---------CGGCGGA---GGC....................................................................................................................................	21	24	0.04	0.04	0.00	0.00	0.00	0.00
................................AGGTGG---------CGGCGGC---GGCA...................................................................................................................................	17	25	0.04	0.00	0.04	0.00	0.00	0.00
..........................CAACGGCGTCGG---------CGGCGGC---.......................................................................................................................................	19	11	0.09	0.00	0.00	0.00	0.09	0.00
............................GTGGTGGCGG---------CGGCGGC---GG.....................................................................................................................................	19	31	0.03	0.00	0.00	0.03	0.00	0.00
..........................CAGCGGCAGTGG---------CGGCGGC---G......................................................................................................................................	20	19	0.05	0.05	0.00	0.00	0.00	0.00

droMoj3

C----------------------CGCCAGCAGCCGGAACAGGGACAGCAGCGCTT--------GA---------------CG---------GCGGCG-ACAGCGGA----CTGGCGCCGCTGCTGCT---GCTGCCGCTGCCACCG-CTGCTAA---AGTAGTTCATTGTGTTTGCCGCC------GACGTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..........................CAGCAGCCxGAAGAGGGAC...................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................GCTT--------GA---------------CG---------GCGGCG-ACAGCGG.......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droGri2

CGTCAATTG------ACCGCAATCGTCAGGGGCAGCGA---------CAGCGGC------AGTTGC------------AACAGTCGCCGAATTGCCAAGTAGCAAG----TTATTAACGCCGCTGCTGCTGCTGCTGCTGCCGTTA-CCTCCGG---CGCCG---------------CTT------GC-AAT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:41 EDT

sblock221622

chr3R:19094949-19095044 +

Candidate

antisense_to_CDS

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