Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014389.1 Corchorus olitorius cultivar O-4 contig14422, 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: 50318
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1060 original size:6 final size:6
Alignment explanation
Indices: 1049--1074 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1039 AACAATTGTG
1049 TAGTGC TAGTGC TAGTGC TAGTGC TA
1 TAGTGC TAGTGC TAGTGC TAGTGC TA
1075 ATATAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.35
Consensus pattern (6 bp):
TAGTGC
Found at i:3685 original size:31 final size:32
Alignment explanation
Indices: 3641--3705 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
3631 CCGAACCTGC
*
3641 ATGACCCTAAATCCAGCA-GACCCGAGACCCGA
1 ATGACCCTAAATCCAG-ATGACCCGAAACCCGA
* *
3673 ATGA-CCTGAATCCAGATGAGCCGAAACCCGA
1 ATGACCCTAAATCCAGATGACCCGAAACCCGA
3704 AT
1 AT
3706 AATCTGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 24 0.83
32 4 0.14
ACGTcount: A:0.35, C:0.32, G:0.20, T:0.12
Consensus pattern (32 bp):
ATGACCCTAAATCCAGATGACCCGAAACCCGA
Found at i:5896 original size:437 final size:441
Alignment explanation
Indices: 5058--6017 Score: 1222
Period size: 437 Copynumber: 2.2 Consensus size: 441
5048 GTATTTTTTT
* *
5058 CTATTGAAAGGTAATTTCATGATCTACAA-TTTTCATGAAGAACTCAAAAGTCAATTTTAATGTT
1 CTATTAAAAGGTAATTTCATGATCTACAACTTTT-ATGAAGGACTCAAAAG-CAATTTTAATGTT
* * * * *
5122 TTGATTCTAAAAAATGCTTCCGAAATTTTGTTGTGGTTTTGATTGCCGGTCAATTTAATATCGTA
64 TTAATTCTAAAAAATGCTTCCGAAATTTTG-TGTCGTTTCGATTGCCGGTCAATTTAATACCATA
* * * * *
5187 TCATTTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGAT
128 TCATATTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGAT
* * * * *
5252 TTACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGAGTTCAAAAG
193 CTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGAGGTCAAAAA
* ** * *
5317 GGAATTTTTATACTTCAAGATCTTTATTAACAAAAATTTTCTTATTTGGATTATTTATCAAATGA
258 GGAATTTTTATACTTCAAGATATCCATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATGA
* * *
5382 CCCTCATATTTTTTTACTTTATACTACTTAGTTCTTTACAAATTCTATCTTAATCTAACTTTTAT
323 CCCTCATACTTTTCTACTTTATACTACTTAGTTCTTTACAAATTCTATCTTAATCTAAC-TTTAA
* * * * * *
5447 GATA-TATTTTTT-TATTCTTTGTTTTATTTGTCCGATTAAGTTGATTCATGTGC
387 CATATTATTTTTTGTATTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGC
*
5500 CTATTAAAAGGTAATTTCATGATCTACAACTTTTATGAAGGACTCAAAAGCAAATTTTTATGTTT
1 CTATTAAAAGGTAATTTCATGATCTACAACTTTTATGAAGGACTCAAAAGC-AATTTTAATGTTT
* * ** *
5565 TAATTCAAAAAAATGCTTCCTAAA-TTTG-GTCGTTTCGATTGTTGGTCTATTTAATACCATAT-
65 TAATTCTAAAAAATGCTTCCGAAATTTTGTGTCGTTTCGATTGCCGGTCAATTTAATACCATATC
* * *
5627 A-ATTTTCGATCCACATGTCTGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATGATC
130 ATATTTTCG-TCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATC
* *
5691 TACGACTTTCATGAAGAACCCGAAAG-TTAATTTGATCTACAAGTTTCATGAAGGGGTCAAAAAG
194 TACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGAGGTCAAAAAG
** * *
5755 GAATTTTTATGTTTCAAGATATCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGAC
259 GAATTTTTATACTTCAAGATATCCATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATGAC
* * * *
5820 CCTCATACTTTTCTATTTTATGCTACTTAG-TCATTTACAAATTCTATCTTATTC-GA-TTTAAC
324 CCTCATACTTTTCTACTTTATACTACTTAGTTC-TTTACAAATTCTATCTTAATCTAACTTTAAC
* * *
5882 ACTTCATTTTTTTTTGTTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGT
388 A--T-ATTATTTTTTGTATTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGC
* * * *
5939 CTATTAAAAGGTAATTTTATGATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTCATGTTT
1 CTATTAAAAGGTAATTTCATGATCTACAACTTTTATGAAGGACTCAAAAGC-AATTTTAATGTTT
*
6004 CAATTCTAAAAAAT
65 TAATTCTAAAAAAT
6018 ATTTTTGAAA
Statistics
Matches: 449, Mismatches: 60, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
434 5 0.01
436 4 0.01
437 141 0.31
438 81 0.18
439 133 0.30
441 5 0.01
442 76 0.17
443 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (441 bp):
CTATTAAAAGGTAATTTCATGATCTACAACTTTTATGAAGGACTCAAAAGCAATTTTAATGTTTT
AATTCTAAAAAATGCTTCCGAAATTTTGTGTCGTTTCGATTGCCGGTCAATTTAATACCATATCA
TATTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTA
CGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGAGGTCAAAAAGGA
ATTTTTATACTTCAAGATATCCATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATGACCC
TCATACTTTTCTACTTTATACTACTTAGTTCTTTACAAATTCTATCTTAATCTAACTTTAACATA
TTATTTTTTGTATTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGC
Found at i:8438 original size:2 final size:2
Alignment explanation
Indices: 8431--8459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8421 TCTTAACTTT
8431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8460 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8464 original size:2 final size:2
Alignment explanation
Indices: 8459--8497 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8449 TATATATATA
8459 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
8498 CCCCCAGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:11126 original size:21 final size:21
Alignment explanation
Indices: 11097--11136 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11087 TATAGACCTA
11097 AAACACCTATACCAACGGTGG
1 AAACACCTATACCAACGGTGG
* * *
11118 AAACCCCTATTCCGACGGT
1 AAACACCTATACCAACGGT
11137 AAATTTGGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (21 bp):
AAACACCTATACCAACGGTGG
Found at i:12276 original size:18 final size:18
Alignment explanation
Indices: 12253--12293 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
12243 AAACCAAAAA
12253 GTAAAGACCAAGAAAACT
1 GTAAAGACCAAGAAAACT
12271 GTAAAGACCAAGAAAACT
1 GTAAAGACCAAGAAAACT
12289 GTAAA
1 GTAAA
12294 CAATAAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (18 bp):
GTAAAGACCAAGAAAACT
Found at i:12301 original size:18 final size:18
Alignment explanation
Indices: 12261--12301 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12251 AAGTAAAGAC
* *
12261 CAAGAAAACTGTAAAGAC
1 CAAGAAAACTGTAAACAA
12279 CAAGAAAACTGTAAACAA
1 CAAGAAAACTGTAAACAA
*
12297 TAAGA
1 CAAGA
12302 CTGTCAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (18 bp):
CAAGAAAACTGTAAACAA
Found at i:28523 original size:15 final size:16
Alignment explanation
Indices: 28503--28532 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28493 GTTTTCTAGT
28503 TTAATTGTT-TTCTTC
1 TTAATTGTTATTCTTC
28518 TTAATTGTTATTCTT
1 TTAATTGTTATTCTT
28533 AACCCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (16 bp):
TTAATTGTTATTCTTC
Found at i:34990 original size:15 final size:15
Alignment explanation
Indices: 34967--34996 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34957 GTGACTAAAT
34967 GGGGAAAAACGTTCA
1 GGGGAAAAACGTTCA
*
34982 GGGGCAAAACGTTCA
1 GGGGAAAAACGTTCA
34997 AAATCAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.33, T:0.13
Consensus pattern (15 bp):
GGGGAAAAACGTTCA
Found at i:35493 original size:22 final size:23
Alignment explanation
Indices: 35468--35515 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
35458 ATGGATGGAG
*
35468 GTTTTGA-ATTTGGACCATTCAA
1 GTTTTGATATTTAGACCATTCAA
**
35490 G-TTTGATATTTAGATTATTCAA
1 GTTTTGATATTTAGACCATTCAA
35512 GTTT
1 GTTT
35516 ATATCATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (23 bp):
GTTTTGATATTTAGACCATTCAA
Found at i:46659 original size:99 final size:101
Alignment explanation
Indices: 46555--46756 Score: 345
Period size: 102 Copynumber: 2.0 Consensus size: 101
46545 TAATAATAGA
* * *
46555 AAAAAAATGACATCCCAAGATGAATAAATTCACTAGC-T-TCTAAGAGAGCCAAAAGTCGTCCAA
1 AAAAAAATGACATCCCAAGATCAATAAATTCACTAGCATCACTAAGAGAGCCAAAAGTCGCCCAA
*
46618 TAGGTTGAGTAAGTATAACTTTTGCAACATGCCAAC
66 TAGGCTGAGTAAGTATAACTTTTGCAACATGCCAAC
46654 AAAAAAATGACATCCCAAGATCAATAAATTCACTAGCATGCACTAAGAGAGCCAAAAGTCGCCCA
1 AAAAAAATGACATCCCAAGATCAATAAATTCACTAGCAT-CACTAAGAGAGCCAAAAGTCGCCCA
46719 ATAGGCTGAGTAAGTATAACTTTTGCAACATGCCAAC
65 ATAGGCTGAGTAAGTATAACTTTTGCAACATGCCAAC
46756 A
1 A
46757 TTAACACAAG
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
99 36 0.38
100 1 0.01
102 59 0.61
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (101 bp):
AAAAAAATGACATCCCAAGATCAATAAATTCACTAGCATCACTAAGAGAGCCAAAAGTCGCCCAA
TAGGCTGAGTAAGTATAACTTTTGCAACATGCCAAC
Found at i:48026 original size:74 final size:74
Alignment explanation
Indices: 47905--48047 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 74
47895 AAGTCTCATG
** * *
47905 CCGCACATAGCTAGCAAACATATTACAATCAAATTTTTGGTTAACTCCTGAATCTGCATAATTAA
1 CCGCACATAGCTAGCAAACATATTACAATCAAATTTTTGACTAACTCCCGAATCTCCATAATTAA
47970 ACAAACATA
66 ACAAACATA
* * *
47979 CCGCACATAGCTAGCAAACATATTACAATCAAATTTTTTACTAACTCCCGGATCTCCATAATTGA
1 CCGCACATAGCTAGCAAACATATTACAATCAAATTTTTGACTAACTCCCGAATCTCCATAATTAA
48044 ACAA
66 ACAA
48048 GCTTCTCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (74 bp):
CCGCACATAGCTAGCAAACATATTACAATCAAATTTTTGACTAACTCCCGAATCTCCATAATTAA
ACAAACATA
Done.