Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009414.1 Corchorus capsularis cultivar CVL-1 contig09435, 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: 15677
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Found at i:332 original size:13 final size:13
Alignment explanation
Indices: 314--339 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
304 ATGTATAGAT
314 ATATATATATATA
1 ATATATATATATA
327 ATATATATATATA
1 ATATATATATATA
340 TATTTAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:355 original size:21 final size:20
Alignment explanation
Indices: 311--359 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
301 TATATGTATA
* *
311 GATATATATATATATAATAT
1 GATATATATATATTTAAGAT
331 -ATATATATATATTTAAGATT
1 GATATATATATATTTAAGA-T
351 GATATATAT
1 GATATATAT
360 CAATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.64
20 1 0.04
21 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
GATATATATATATTTAAGAT
Found at i:359 original size:2 final size:2
Alignment explanation
Indices: 301--342 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
291 CTCGTACTTT
* *
301 TA TA TG TA TA GA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
342 T
1 T
343 TTAAGATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:15004 original size:16 final size:16
Alignment explanation
Indices: 14985--15073 Score: 137
Period size: 16 Copynumber: 5.6 Consensus size: 16
14975 CGGGTTCGGG
14985 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
15001 CGGGTTCGGG-ATTTTT
1 CGGGTTCGGGTA-TTTT
* *
15017 CGGGTTCGGATTTTTT
1 CGGGTTCGGGTATTTT
15033 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
15048 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
15064 CGGGTTCGGG
1 CGGGTTCGGG
15074 CTCGGATTGG
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
15 16 0.24
16 50 0.76
ACGTcount: A:0.06, C:0.13, G:0.39, T:0.42
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:15040 original size:6 final size:6
Alignment explanation
Indices: 15031--15122 Score: 62
Period size: 6 Copynumber: 14.5 Consensus size: 6
15021 TTCGGATTTT
* *
15031 TTCGGG TTCGGG TATTTCGGG TTCGGG TATTTTCGGG TTCGGG CTCGGA
1 TTCGGG TTCGGG ---TTCGGG TTCGGG ---T-TCGGG TTCGGG TTCGGG
* * *
15080 TT-GGG TTCGGG TCCGGG TCCGGG -TCGGG TTCGGG TTAGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
15123 ACTTTCGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
5 8 0.12
6 48 0.70
7 1 0.01
9 7 0.10
10 5 0.07
ACGTcount: A:0.04, C:0.17, G:0.45, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:15052 original size:31 final size:32
Alignment explanation
Indices: 14985--15073 Score: 144
Period size: 31 Copynumber: 2.8 Consensus size: 32
14975 CGGGTTCGGG
*
14985 CGGGTTCGGGTATTTTCGGGTTCGGGATTTTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGATATTT
* *
15017 CGGGTTCGGATTTTTTCGGGTTCGGG-TATTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGATATTT
15048 CGGGTTCGGGTATTTTCGGGTTCGGG
1 CGGGTTCGGGTATTTTCGGGTTCGGG
15074 CTCGGATTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
31 28 0.54
32 24 0.46
ACGTcount: A:0.06, C:0.13, G:0.39, T:0.42
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGTTCGGGATATTT
Found at i:15086 original size:48 final size:48
Alignment explanation
Indices: 14985--15091 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
14975 CGGGTTCGGG
***
14985 CGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCGGGTTCGGATTTTTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCGGGTTCGGATGGATT
*
15033 CGGGTTCGGGTA-TTTCGGGTTCGGG-TATTTTCGGGTTCGGGCTCGGATT
1 CGGGTTCGGGTATTTTCGGGTTCGGGAT-TTTTCGGGTTC-GGAT-GGATT
15082 -GGGTTCGGGT
1 CGGGTTCGGGT
15092 CCGGGTCCGG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
46 1 0.02
47 24 0.46
48 25 0.48
49 2 0.04
ACGTcount: A:0.06, C:0.14, G:0.40, T:0.40
Consensus pattern (48 bp):
CGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCGGGTTCGGATGGATT
Found at i:15096 original size:23 final size:23
Alignment explanation
Indices: 15062--15114 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
15052 TTCGGGTATT
* *
15062 TTCGGGTTCGGG-CTCGGATTGGG
1 TTCGGGTCCGGGTC-CGGATCGGG
*
15085 TTCGGGTCCGGGTCCGGGTCGGG
1 TTCGGGTCCGGGTCCGGATCGGG
15108 TTCGGGT
1 TTCGGGT
15115 TAGGGTTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.02, C:0.21, G:0.49, T:0.28
Consensus pattern (23 bp):
TTCGGGTCCGGGTCCGGATCGGG
Found at i:15097 original size:12 final size:11
Alignment explanation
Indices: 15062--15114 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
15052 TTCGGGTATT
15062 TTCGGGTTCGGG
1 TTCGGG-TCGGG
* * *
15074 CTCGGATTGGG
1 TTCGGGTCGGG
15085 TTCGGGTCCGGG
1 TTCGGGT-CGGG
*
15097 TCCGGGTCGGG
1 TTCGGGTCGGG
15108 TTCGGGT
1 TTCGGGT
15115 TAGGGTTCAC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
11 19 0.59
12 13 0.41
ACGTcount: A:0.02, C:0.21, G:0.49, T:0.28
Consensus pattern (11 bp):
TTCGGGTCGGG
Done.