Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016747.1 Corchorus olitorius cultivar O-4 contig16780, 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: 45680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:680 original size:25 final size:25
Alignment explanation
Indices: 637--687 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
627 TGATAAATTT
637 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
664 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
687 T
1 T
688 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:7311 original size:18 final size:18
Alignment explanation
Indices: 7268--7302 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7258 AATTCCTGAC
7268 GTGAAAAAAAATCTTAAT
1 GTGAAAAAAAATCTTAAT
*
7286 GTGAAAAAGAATCTTAA
1 GTGAAAAAAAATCTTAA
7303 CTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (18 bp):
GTGAAAAAAAATCTTAAT
Found at i:12367 original size:17 final size:17
Alignment explanation
Indices: 12345--12377 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12335 GTTTATTTCA
*
12345 TTTTTTT-ATTTTATTT
1 TTTTTTTGATGTTATTT
12361 TTTTTTTGATGTTATTT
1 TTTTTTTGATGTTATTT
12378 GTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTGATGTTATTT
Found at i:26078 original size:14 final size:13
Alignment explanation
Indices: 26045--26127 Score: 69
Period size: 12 Copynumber: 7.2 Consensus size: 13
26035 AACCGTTTGA
26045 TAATTATATATAT
1 TAATTATATATAT
*
26058 T-ATTATATAT-G
1 TAATTATATATAT
26069 TAATTATATATAT
1 TAATTATATATAT
*
26082 T--TAATAT-TAT
1 TAATTATATATAT
26092 T--TTATATATA-
1 TAATTATATATAT
26102 TAA-TATATAT-T
1 TAATTATATATAT
*
26113 TAATTATAAATAT
1 TAATTATATATAT
26126 TA
1 TA
26128 CTAAACGGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 10 0.18
11 18 0.32
12 24 0.42
13 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:26099 original size:19 final size:20
Alignment explanation
Indices: 26044--26125 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 20
26034 AAACCGTTTG
*
26044 ATAATTATATATATTAT-TAT
1 ATAA-TATATATTTTATATAT
* *
26064 AT-ATGTA-ATTATATATAT
1 ATAATATATATTTTATATAT
*
26082 TTAATAT-TATTTTATATAT
1 ATAATATATATTTTATATAT
*
26101 ATAATATATATTTAAT-TAT
1 ATAATATATATTTTATATAT
26120 A-AATAT
1 ATAATAT
26126 TACTAAACGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 24 0.48
20 9 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATAATATATATTTTATATAT
Found at i:26118 original size:28 final size:29
Alignment explanation
Indices: 26044--26119 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
26034 AAACCGTTTG
* *
26044 ATAAT-TATATAT-ATTATTATATATGTA
1 ATAATATATATTTAATTATTATATATATA
* *
26071 ATTATATATATTTAA-TATTATTTTATATA
1 ATAATATATATTTAATTATTA-TATATATA
26100 TATAATATATATTTAATTAT
1 -ATAATATATATTTAATTAT
26120 AAATATTACT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 7 0.18
30 14 0.36
31 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
ATAATATATATTTAATTATTATATATATA
Found at i:29846 original size:53 final size:53
Alignment explanation
Indices: 29788--30063 Score: 462
Period size: 53 Copynumber: 5.1 Consensus size: 53
29778 TCTTTAAATC
29788 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
29841 CAATAGTTCATTGCATATTGCATTTTGTATTATTCGGTATGTGTGCTTATTTAATAGGTT
1 CAATAG----TT-C--ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
29901 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTACTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
29954 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTACTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
30007 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
30060 CAAT
1 CAAT
30064 TGAATAAACA
Statistics
Matches: 212, Mismatches: 4, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
53 157 0.74
55 1 0.00
56 2 0.01
57 2 0.01
58 1 0.00
60 49 0.23
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.49
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:30586 original size:105 final size:105
Alignment explanation
Indices: 30404--30614 Score: 386
Period size: 105 Copynumber: 2.0 Consensus size: 105
30394 ATCCCATGAA
*
30404 CTGGTTTTCTCCTGCAATTAATATAACCAAGAATATTTAGATTTAATGCAAAGAACACAATCTAT
1 CTGGTTTTCTCCTGCAATTAATATAACCAAGAATATTTAGATTGAATGCAAAGAACACAATCTAT
*
30469 TGACCCCAATACGTAAAAAGTAAAACTTAATCTTAGAGAG
66 TGACCCCAATACGTAAAAAGTAAAACTTAATCTTAAAGAG
*
30509 CTGGTTTTCTCCTGCAATTAATATAACCAAGAATATTTAGATTGAATGCAAAGAACGCAATCTAT
1 CTGGTTTTCTCCTGCAATTAATATAACCAAGAATATTTAGATTGAATGCAAAGAACACAATCTAT
*
30574 TGACCCCAATACGTAAAAAGTAAAACTTCATCTTAAAGAG
66 TGACCCCAATACGTAAAAAGTAAAACTTAATCTTAAAGAG
30614 C
1 C
30615 GCCTCTCAAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (105 bp):
CTGGTTTTCTCCTGCAATTAATATAACCAAGAATATTTAGATTGAATGCAAAGAACACAATCTAT
TGACCCCAATACGTAAAAAGTAAAACTTAATCTTAAAGAG
Found at i:31994 original size:15 final size:17
Alignment explanation
Indices: 31969--32010 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
31959 AGTAAGAACA
*
31969 TAATCCAAATCTC-GGCT
1 TAAT-CAAATCTCTGCCT
31986 T-ATCAAATCTCTGCCT
1 TAATCAAATCTCTGCCT
32002 TAATCAAAT
1 TAATCAAAT
32011 GAAACATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (17 bp):
TAATCAAATCTCTGCCT
Found at i:34279 original size:31 final size:31
Alignment explanation
Indices: 34244--34399 Score: 188
Period size: 31 Copynumber: 5.1 Consensus size: 31
34234 GCATGTCACA
*
34244 TGTACCAAAAAGCGACATGTGACACGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACG
*
34275 TGTACCAAAAAGCGACATGTGACACGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACG
* *
34306 TATATCAAAAAGTGACATGTGACACGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACG
** * * *
34337 TGTACC-AAAAGTGACACATGGCATGCCATG
1 TGTACCAAAAAGTGACATGTGACACGCCACG
** * *
34367 TGTTTCAAAAAGTGACACGTGACATGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACG
34398 TG
1 TG
34400 CACAAAAGGA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
30 23 0.21
31 86 0.79
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (31 bp):
TGTACCAAAAAGTGACATGTGACACGCCACG
Found at i:34389 original size:61 final size:61
Alignment explanation
Indices: 34249--34407 Score: 194
Period size: 61 Copynumber: 2.6 Consensus size: 61
34239 TCACATGTAC
* **
34249 CAAAAAGCGACATGTGACACGCCACGTGTACCAAAAAGCGACATGTGACACGCCACGTATAT
1 CAAAAAGTGACATGTGACACGCCACGTGTACC-AAAAGCGACACATGACACGCCACGTATAT
* * * * * *
34311 CAAAAAGTGACATGTGACACGCCACGTGTACCAAAAGTGACACATGGCATGCCATGTGTTT
1 CAAAAAGTGACATGTGACACGCCACGTGTACCAAAAGCGACACATGACACGCCACGTATAT
* * *
34372 CAAAAAGTGACACGTGACATGCCACGTGCA-CAAAAG
1 CAAAAAGTGACATGTGACACGCCACGTGTACCAAAAG
34408 GATACGTGCC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 6 0.07
61 48 0.56
62 31 0.36
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (61 bp):
CAAAAAGTGACATGTGACACGCCACGTGTACCAAAAGCGACACATGACACGCCACGTATAT
Found at i:36571 original size:29 final size:30
Alignment explanation
Indices: 36538--36605 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
36528 TTTTAAATTT
36538 AGGATTTTAGC-TTTTTTTTTATCAAAAAA
1 AGGATTTTAGCTTTTTTTTTTATCAAAAAA
*
36567 AGGATTTTAGCTTTTTTTTTTTTTCAAAAAA
1 AGGATTTTAGC-TTTTTTTTTTATCAAAAAA
*
36598 ATGATTTT
1 AGGATTTT
36606 GTAAATCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 11 0.31
31 24 0.69
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (30 bp):
AGGATTTTAGCTTTTTTTTTTATCAAAAAA
Found at i:38283 original size:26 final size:27
Alignment explanation
Indices: 38231--38298 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
38221 TCACCTAGGA
**
38231 GCATTTTGGTCATTTTTACACTAA-GG
1 GCATTTTGGTCATTTGCACACTAAGGG
* * *
38257 GCATTTTGGTCATTTGCATATTCAGGG
1 GCATTTTGGTCATTTGCACACTAAGGG
*
38284 GCATGTTGGTCATTT
1 GCATTTTGGTCATTT
38299 TAAGTCCACT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (27 bp):
GCATTTTGGTCATTTGCACACTAAGGG
Found at i:39474 original size:40 final size:40
Alignment explanation
Indices: 39292--39465 Score: 231
Period size: 40 Copynumber: 4.3 Consensus size: 40
39282 AAAAACACAT
* *
39292 CGGAAGGTGTTGTTTAAATACCCAGTTTGGCCTTCCCCAC
1 CGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCAC
* * *
39332 CGGAAGGTGTTGTTTAAATACCTAGTTTGCCCTTTCCCAC
1 CGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCAC
* * *
39372 TGGAAGGTGTTGTTTAAATTCCCATTTTTCCCTTCCCCAC
1 CGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCAC
* * * *
39412 CGGAAGGTATTGTCTAAATTCCCAGTTTGCCCTTCCTCAT
1 CGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCAC
*
39452 CAGAAGGTGTTGTT
1 CGGAAGGTGTTGTT
39466 CTCATTCCCT
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (40 bp):
CGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCAC
Found at i:44987 original size:14 final size:13
Alignment explanation
Indices: 44943--45007 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 13
44933 TAAAGGACAT
44943 TTTTCAAAAATGA
1 TTTTCAAAAATGA
*
44956 ATTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
*
44970 TTTTCAAGAATCGA
1 TTTTCAAAAAT-GA
44984 TTTTCAAAAATGA
1 TTTTCAAAAATGA
44997 GTTTTCAAAAA
1 -TTTTCAAAAA
45008 GGTTTTGAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.02
13 11 0.26
14 29 0.67
15 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAATGA
Done.