ID:

dan_165

 Coordinate:

scaffold_13248:3439730-3439786 -

 Confidence:

Candidate

 Type:

Unknown

 [View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

-38.1 -37.7 -37.5

Flybase annnotation

intergenic

Repeatable elements

NameClassFamilyStrand
(CCCA)nSimple_repeatSimple_repeat+
mature
  1. scaffold_12916:4146966-4146983 +
  2. dan_165  scaffold_13248:3439731-3439748 -
  3. scaffold_13266:8773502-8773519 +
  4. scaffold_13340:7132670-7132687 +
star

Sense Strand Reads

CCATTCCGTTGACTCATTCCGAAGAGCAAAGCGCCACGGCGCACACTCTGGCTCTCGCCATCCCGCTCGCTCTTTATCTGGTGGGTGAGTGGGTGGGTGGGTGGTAGGTTTGGGGGGGGTCGCTGGGCCCCAGAGGCGTAGGTTCGCCTATGCCGAC
***********************************.((((.....((((((.(((.((((.((((((((((((((((((...))))))).)))))))))))))))))).))))))...))))*********************************** 		Read size # Mismatch Hit Count Total Norm Total V106
head
 V105
male body		 V055
head
 M044
female body
 V039
embryo
........................................................................................GTGGGTGGGTGGGTGGTA................................................... 18 0 4 42.75 171 153 17 0 1 0
............................................................................................GTGGGTGGGTGGTAGGGTT.............................................. 19 1 4 4.50 18 16 0 2 0 0
.......................................................................................AGTGTGTGGGTGGGTGGTAG.................................................. 20 1 3 1.00 3 3 0 0 0 0
.........................................................................................TGGGAGGGTGGGTAGCAGGTTT.............................................. 22 3 1 1.00 1 0 0 1 0 0
............................................................................................GTGGGTGGGTGGTAGGTT............................................... 18 0 1 1.00 1 1 0 0 0 0
................................................................................GTGGGTGAGTGGGTGGGTG.......................................................... 19 0 8 0.75 6 6 0 0 0 0
................................................................................GTGGGTGAGTGGGTGGGT........................................................... 18 0 8 0.63 5 5 0 0 0 0
............................................................................................GTGGGTGGGTGGTAGG................................................. 16 0 8 0.50 4 0 0 4 0 0
........................................................................................GTGGGGGGGTGGGTGGTA................................................... 18 1 6 0.33 2 2 0 0 0 0
...................................................................................GGTGAGTGGGTGGGTGGGTG...................................................... 20 0 4 0.25 1 1 0 0 0 0
........................................................................................GTGGGTGGGTGAGTGGTA................................................... 18 1 13 0.23 3 3 0 0 0 0
........................................................................................GTGGGTTGGTGGGTGGTA................................................... 18 1 9 0.22 2 2 0 0 0 0
....................................................................................................GTCGTAGGTTAGGGGGGG....................................... 18 2 5 0.20 1 0 0 1 0 0
........................................................................................TTGGGTGGGTGGGTGGTA................................................... 18 1 12 0.17 2 2 0 0 0 0
............................................................................................GTGGGTGTGTGGTAGGGTT.............................................. 19 2 12 0.17 2 2 0 0 0 0
.......................................................................................AGTGTGTGGGTTGGTGGTAG.................................................. 20 2 7 0.14 1 1 0 0 0 0
...................................................................................................GGTGGGAAGTTTGGCGGGGGT..................................... 21 3 7 0.14 1 0 1 0 0 0
.................................................................................TGGGTGAGTGGGTGGGTGG......................................................... 19 0 7 0.14 1 1 0 0 0 0
............................................................................................GTGGGTGGGTGGTGGGTTT.............................................. 19 1 7 0.14 1 0 0 0 1 0
........................................................................................GTGGGTGGGTTGGTGGTA................................................... 18 1 8 0.13 1 1 0 0 0 0
.................................................................................TGGTTGAGTGGGTGGGCGGGT....................................................... 21 2 8 0.13 1 0 0 1 0 0
............................................................................................GTGGGTGGGTCGTAGGGTT.............................................. 19 2 8 0.13 1 0 1 0 0 0
.......................................................................................................GTAGGTTTGGGGGTGGTA.................................... 18 2 9 0.11 1 0 0 0 0 1
.......................................................................................................ATAGGGTTGGGGGGGGTC.................................... 18 2 9 0.11 1 0 0 0 0 1
.............................................................................CTGGTGGGTGAGTAGGCG.............................................................. 18 2 10 0.10 1 0 0 1 0 0
.........................................................................................TCGGTGGGTGGGTGGTAG.................................................. 18 1 10 0.10 1 1 0 0 0 0
.........................................................................................TGGGAGTGTGGCTGGTAGGTT............................................... 21 3 10 0.10 1 0 0 1 0 0
........................................................................................GTGGGTGGGTGGGAGGTA................................................... 18 1 10 0.10 1 0 1 0 0 0
.................................................................................................TGGGTGGAAGGTTTGGGC.......................................... 18 2 10 0.10 1 0 0 1 0 0
....................................................................................GTGAGTGGGTGGGTGGGT....................................................... 18 0 12 0.08 1 1 0 0 0 0
.................................................................................TGGCTGAGTGCGTGGGTGGGT....................................................... 21 2 12 0.08 1 0 0 1 0 0
........................................................................................GTGGTTGGGTGGGTGGTA................................................... 18 1 14 0.07 1 1 0 0 0 0
................................................................................GTTGGTGAGTGGGTGGGT........................................................... 18 1 15 0.07 1 1 0 0 0 0
............................................................................................................ATTGGGGGGGGTGGCTGGCC............................. 20 3 20 0.05 1 0 0 1 0 0
........................................................................................GTGGGTGGGTGGGGGGTAA.................................................. 19 2 20 0.05 1 1 0 0 0 0
................................................................................GTGGGTGATTGGGTGGGT........................................................... 18 1 20 0.05 1 1 0 0 0 0
...................................................................................GCTGAGAGGGTGGGTGCGTGG..................................................... 21 3 20 0.05 1 0 0 0 0 1
.........................................................................................TCGTTGGGTGGGTGGTAG.................................................. 18 2 20 0.05 1 1 0 0 0 0
.................................................................................TGGGTGAGTGGCTAGCTGGGT....................................................... 21 3 20 0.05 1 0 0 1 0 0

Anti-sense strand reads

GGTAAGGCAACTGAGTAAGGCTTCTCGTTTCGCGGTGCCGCGTGTGAGACCGAGAGCGGTAGGGCGAGCGAGAAATAGACCACCCACTCACCCACCCACCCACCATCCAAACCCCCCCCAGCGACCCGGGGTCTCCGCATCCAAGCGGATACGGCTG
***********************************.((((.....((((((.(((.((((.((((((((((((((((((...))))))).)))))))))))))))))).))))))...))))*********************************** 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 V055
head
.......................................................................................................CATGCAAACCCCCCAGAGC................................... 19 3 11 0.09 1 0 1
...............................................................................................CCACCCCACATCCAAACC............................................ 18 2 15 0.07 1 1 0
.........................................................................................ACCCACCCACATACCATTCAA............................................... 21 3 17 0.06 1 1 0
.............................................................................................ACCCACCCAACATCGAAA.............................................. 18 2 18 0.06 1 1 0
..........................................................................................ACCACCCACCCATTATCCAA............................................... 20 3 19 0.05 1 1 0
..................GCCTGCTCGTTTCTCGGTG........................................................................................................................ 19 3 20 0.05 1 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13248:3439680-3439836 - dan_165 CCATTCCGTTGACTCATTCCGAAGAGCAAAGCGCCACGGCGCACACTCTGGCTCTCGCCATCCCGCTCGCT------CTTTATCTGGTGGGTGAGTGGGTGGGTGGGTGGTAGGTTTGGGGGGGGTCGCTGGGCCCCAGA--GGCGTAGG---TTCGCCTATGCCGAC
droBip1 scf7180000396733:358615-358734 - CCATTCCGTTGACTCATTCGGAC-CGCAAAGCGCCACGGCGCACACTCTGGCTCTC--------------TCTCTTTCTTTATCCGGCG-------------------------------GGGGGGCGCTGGGCCACAGA--GGCGTATGGGTTTCGCCTATGCCGAC
droKik1 scf7180000302592:84669-84745 - CA-----------------------------------------CAGCGTTGCTCTC-CCACTCGGTTCACTCTCTCTCTGT-----GGT-------------------------------TTGGTGCTCTGGGCCCAAAAACGGCGTAGATA-------------TAC
droTak1 scf7180000415872:102280-102305 + TA------------------GAC-CCCAAAGCG--------------------------------------------------------------------------------------------------------------GCGTACATA-------------TAC

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
CCATTCCGTTGACTCATTCCGAAGAGCAAAGCGCCACGGCGCACACTCTGGCTCTCGCCATCCCGCTCGCT------CTTTATCTGGTGGGTGAGTGGGTGGGTGGGTGGTAGGTTTGGGGGGGGTCGCTGGGCCCCAGA--GGCGTAGG---TTCGCCTATGCCGACSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
..............................................................................................GTGGGTGGGTGGGTGGTA........................................................18442.75171100017153
..................................................................................................GTGGGTGGGTGGTAGGTT....................................................1811.001000001
......................................................................................GTGGGTGAGTGGGTGGGTG...............................................................1980.756000006
......................................................................................GTGGGTGAGTGGGTGGGT................................................................1880.635000005
..................................................................................................GTGGGTGGGTGGTAGG......................................................1680.504000400
.........................................................................................GGTGAGTGGGTGGGTGGGTG...........................................................2040.251000001
.......................................................................................TGGGTGAGTGGGTGGGTGG..............................................................1970.141000001
..........................................................................................GTGAGTGGGTGGGTGGGT............................................................18120.081000001
droBip1
CCATTCCGTTGACTCATTCGGAC-CGCAAAGCGCCACGGCGCACACTCTGGCTCTC--------------TCTCTTTCTTTATCCGGCG-------------------------------GGGGGGCGCTGGGCCACAGA--GGCGTATGGGTTTCGCCTATGCCGACSizeHit CountTotal NormTotal
No Reads
droKik1
CA-----------------------------------------CAGCGTTGCTCTC-CCACTCGGTTCACTCTCTCTCTGT-----GGT-------------------------------TTGGTGCTCTGGGCCCAAAAACGGCGTAGATA-------------TACSizeHit CountTotal NormTotal
No Reads
droTak1
TA------------------GAC-CCCAAAGCG--------------------------------------------------------------------------------------------------------------GCGTACATA-------------TACSizeHit CountTotal NormTotal
No Reads

Generated: 05/15/2015 at 02:53 PM