Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016262.1 Corchorus olitorius cultivar O-4 contig16295, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 334338
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:325822 original size:23 final size:23
Alignment explanation
Indices: 325792--325835 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
325782 AGGCAGGGTA
*
325792 TTTTTTGCTTTTTTGGTTTTTGG
1 TTTTTTGCTTTTTTGCTTTTTGG
325815 TTTTTTGCTTTTTTGCTTTTT
1 TTTTTTGCTTTTTTGCTTTTT
325836 TGCTTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.07, G:0.16, T:0.77
Consensus pattern (23 bp):
TTTTTTGCTTTTTTGCTTTTTGG
Found at i:327405 original size:13 final size:13
Alignment explanation
Indices: 327389--327417 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
327379 TTGCTCTACA
327389 TCAAAGATCTATG
1 TCAAAGATCTATG
327402 TC-AAGATCTATG
1 TCAAAGATCTATG
327414 TCAA
1 TCAA
327418 TTTAGACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
TCAAAGATCTATG
Found at i:327409 original size:12 final size:12
Alignment explanation
Indices: 327392--327417 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
327382 CTCTACATCA
327392 AAGATCTATGTC
1 AAGATCTATGTC
327404 AAGATCTATGTC
1 AAGATCTATGTC
327416 AA
1 AA
327418 TTTAGACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (12 bp):
AAGATCTATGTC
Found at i:331912 original size:65 final size:66
Alignment explanation
Indices: 331792--331921 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 66
331782 TACCCCAATC
*
331792 GAATGTGGTGAGAGTCCTTATTGGTTTTTTTGGTAATCCACACTTCAACTATTATTGTTTGTTAT
1 GAATGTGGTGAGAGTCCTTATTGGTTTTTTTGGAAATCCACACTTCAACTATTATTGTTTGTTAT
331857 T
66 T
331858 GAATGTGGTGAGAGTCCTTATTGG-TTTTTTGGAAATCCACACTTCAACTATTATTGTTTGTTAT
1 GAATGTGGTGAGAGTCCTTATTGGTTTTTTTGGAAATCCACACTTCAACTATTATTGTTTGTTAT
331922 ATGTATATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 39 0.62
66 24 0.38
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.45
Consensus pattern (66 bp):
GAATGTGGTGAGAGTCCTTATTGGTTTTTTTGGAAATCCACACTTCAACTATTATTGTTTGTTAT
T
Found at i:334282 original size:21 final size:20
Alignment explanation
Indices: 334256--334295 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
334246 GTTGATATCC
334256 TCTTTTCTTTTCTT-CTTTTTT
1 TCTTTT-TTTT-TTGCTTTTTT
334277 TCTTTTTTTTTTGCTTTTT
1 TCTTTTTTTTTTGCTTTTT
334296 CTTTTTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (20 bp):
TCTTTTTTTTTTGCTTTTTT
Found at i:334283 original size:8 final size:8
Alignment explanation
Indices: 334258--334301 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
334248 TGATATCCTC
334258 TTTTCTTT
1 TTTTCTTT
*
334266 TCTTCTTT
1 TTTTCTTT
334274 TTTTCTTT
1 TTTTCTTT
*
334282 TTTTTTTGCT
1 TTTTCTT--T
334292 TTTTCTTT
1 TTTTCTTT
334300 TT
1 TT
334302 AGAAATGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 23 0.77
10 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:334288 original size:11 final size:11
Alignment explanation
Indices: 334258--334301 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
334248 TGATATCCTC
*
334258 TTTTCTTTTCT
1 TTTTTTTTTCT
*
334269 TCTTTTTTTCT
1 TTTTTTTTTCT
334280 TTTTTTTTTGCT
1 TTTTTTTTT-CT
334292 TTTTCTTTTT
1 TTTT-TTTTT
334302 AGAAATGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 17 0.61
12 6 0.21
13 5 0.18
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTCT
Done.