Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006675.1 Corchorus capsularis cultivar CVL-1 contig06696, 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: 27344
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:299 original size:2 final size:2
Alignment explanation
Indices: 292--317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
282 TTTGATCATT
292 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
318 AACTTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2007 original size:15 final size:15
Alignment explanation
Indices: 1987--2021 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1977 AAAATCAAAC
1987 CTTGTCTTCAATGCT
1 CTTGTCTTCAATGCT
2002 CTTGTCTTCAATGCT
1 CTTGTCTTCAATGCT
2017 CTTGT
1 CTTGT
2022 TTTAGCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.14, T:0.49
Consensus pattern (15 bp):
CTTGTCTTCAATGCT
Found at i:6318 original size:16 final size:16
Alignment explanation
Indices: 6297--6329 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6287 TAAGAGGTCG
6297 ATCGAGTTGAACTTCA
1 ATCGAGTTGAACTTCA
6313 ATCGAGTTGAACTTCA
1 ATCGAGTTGAACTTCA
6329 A
1 A
6330 ATGGATTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (16 bp):
ATCGAGTTGAACTTCA
Found at i:9313 original size:16 final size:17
Alignment explanation
Indices: 9282--9314 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9272 AATACTCAAA
9282 ATTTAGAAAAAAAAAAC
1 ATTTAGAAAAAAAAAAC
9299 ATTTA-AAAAACAAAAA
1 ATTTAGAAAAA-AAAAA
9315 TAATAACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
ATTTAGAAAAAAAAAAC
Found at i:15361 original size:31 final size:30
Alignment explanation
Indices: 15257--15358 Score: 134
Period size: 31 Copynumber: 3.4 Consensus size: 30
15247 CTTGTTGCTT
15257 GGGGGCAAAACATCCAAAAT-TAAAGTTTA
1 GGGGGCAAAACATCCAAAATGTAAAGTTTA
* *
15286 GGGAGCAAAACATCCAAAACGTATAAGTTTA
1 GGGGGCAAAACATCCAAAATGTA-AAGTTTA
* *
15317 GGGGGCAAAACGTCCAAAATGTACAAGTTAA
1 GGGGGCAAAACATCCAAAATGTA-AAGTTTA
*
15348 GGGGGCCAAAC
1 GGGGGCAAAAC
15359 GTCTAAAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.29
30 2 0.03
31 43 0.68
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (30 bp):
GGGGGCAAAACATCCAAAATGTAAAGTTTA
Found at i:15498 original size:29 final size:30
Alignment explanation
Indices: 15448--15511 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
15438 ACAGAGGCTC
**
15448 AAATTGAGAGTTCAGGGGATAAAATGTCCA
1 AAATTGAGAGTTCAGAAGATAAAATGTCCA
*
15478 AAATTGAGAGTTCA-AAGATAAAATGTGCA
1 AAATTGAGAGTTCAGAAGATAAAATGTCCA
15507 AAATT
1 AAATT
15512 AAAGTGTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (30 bp):
AAATTGAGAGTTCAGAAGATAAAATGTCCA
Found at i:19020 original size:8 final size:8
Alignment explanation
Indices: 19008--19042 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
18998 GAAATCAATT
19008 AATCATCA
1 AATCATCA
* *
19016 GATCATAA
1 AATCATCA
19024 AATCATCA
1 AATCATCA
19032 AATCATCA
1 AATCATCA
19040 AAT
1 AAT
19043 GATACACAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (8 bp):
AATCATCA
Found at i:19224 original size:35 final size:34
Alignment explanation
Indices: 19166--19358 Score: 311
Period size: 34 Copynumber: 5.7 Consensus size: 34
19156 TTGACTTCCA
* *
19166 ATTATCACAACCCACTGGACAGGGTCTTCCAGCT
1 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTT
19200 ATTATCACAAACCCACTGGGCAGGGTCTTCCAGTT
1 ATTATCAC-AACCCACTGGGCAGGGTCTTCCAGTT
*
19235 ATTGTCACAAACCCACTGGGCAGGGTCTTCCAGTT
1 ATTATCAC-AACCCACTGGGCAGGGTCTTCCAGTT
*
19270 ATTATCACAACCCACTGGGTAGGGTCTTCCAGTT
1 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTT
19304 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTT
1 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTT
19338 ATTAT---AACCCACTGGGCAGGG
1 ATTATCACAACCCACTGGGCAGGG
19359 CCGATAAAAC
Statistics
Matches: 152, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
31 16 0.11
34 71 0.47
35 65 0.43
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (34 bp):
ATTATCACAACCCACTGGGCAGGGTCTTCCAGTT
Found at i:19288 original size:69 final size:68
Alignment explanation
Indices: 19166--19358 Score: 311
Period size: 69 Copynumber: 2.9 Consensus size: 68
19156 TTGACTTCCA
* *
19166 ATTATCACAACCCACTGGACAGGGTCTTCCAGCTATTATCACAAACCCACTGGGCAGGGTCTTCC
1 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTTATTATCAC-AACCCACTGGGCAGGGTCTTCC
19231 AGTT
65 AGTT
* *
19235 ATTGTCACAAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGTAGGGTCTTCC
1 ATTATCAC-AACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGGTCTTCC
19300 AGTT
65 AGTT
19304 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTTATTAT---AACCCACTGGGCAGGG
1 ATTATCACAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
19359 CCGATAAAAC
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
65 15 0.13
68 31 0.26
69 39 0.33
70 32 0.27
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (68 bp):
ATTATCACAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGGTCTTCCA
GTT
Found at i:23389 original size:31 final size:32
Alignment explanation
Indices: 23354--23417 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
23344 GAACTTCAAA
* *
23354 TCACAACAACTT-ACTCTTATAA-TTTCTAAAT
1 TCACAACAA-TTAACTCCTAGAACTTTCTAAAT
23385 TCACAACAATTAACTCCTAGAACTTTCTAAAT
1 TCACAACAATTAACTCCTAGAACTTTCTAAAT
23417 T
1 T
23418 TTGAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.59
32 10 0.34
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (32 bp):
TCACAACAATTAACTCCTAGAACTTTCTAAAT
Done.