Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013090.1 Corchorus capsularis cultivar CVL-1 contig13111, 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: 38103
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:164 original size:42 final size:42
Alignment explanation
Indices: 68--165 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
58 GTAAGGATAG
*
68 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAATGAACAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAACAA
*
110 GCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-ACAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAACAA
*
151 GCACATACATTAATT
1 GCACAGAC-TTAATT
166 CAGGGTAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (42 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAACAA
Found at i:333 original size:37 final size:37
Alignment explanation
Indices: 292--508 Score: 362
Period size: 37 Copynumber: 5.9 Consensus size: 37
282 TAATTAAAGA
* *
292 AAAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAGC
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
329 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
366 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
403 AAGGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
440 AGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
* * * *
477 TAAGGACTTAATTTCAAGGAAGGAAATTAAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGT
509 CAAGTTAGGG
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 170 1.00
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.22
Consensus pattern (37 bp):
AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
Found at i:427 original size:19 final size:19
Alignment explanation
Indices: 332--427 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
322 GTAGAGCAAA
332 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
* * * * *
351 GGAATTAAGT--AGAGTAAA
1 GGACTTGATTCCA-AGGAAG
369 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
* * * *
388 GGAATTAAGT--AGAGTAAG
1 GGACTTGATTCCA-AGGAAG
406 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
425 GGA
1 GGA
428 ATTAAGTAGA
Statistics
Matches: 53, Mismatches: 18, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 2 0.04
18 23 0.43
19 26 0.49
20 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (19 bp):
GGACTTGATTCCAAGGAAG
Found at i:559 original size:111 final size:109
Alignment explanation
Indices: 303--542 Score: 326
Period size: 111 Copynumber: 2.2 Consensus size: 109
293 AAGGACTTGG
*
303 TTCCAAGGAAGGGAATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
1 TTCC-AGG-AGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
* * *
368 AGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAAGGGACTTGA
64 AGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTAAGGGACTTAA
* *
414 TTCCAAGGAAGGGAATTAAGTAGAGTAGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTTA
1 TTCC-AGG-AGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
* *
479 AGGACTTAATTTCAAGGAAGGAAATTAAGTCA-AGTTAGGGACTTAA
64 AGGACTTAATTCCAAGGAAGGAAATTAAGT-AGAGTAAGGGACTTAA
*
525 TT-C-GG-GGTAATTAAGTAG
1 TTCCAGGAGGGAATTAAGTAG
543 CGTCGATAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
106 12 0.10
108 2 0.02
110 1 0.01
111 103 0.87
112 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.30, T:0.23
Consensus pattern (109 bp):
TTCCAGGAGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAAAG
GACTTAATTCCAAGGAAGGAAATTAAGTAGAGTAAGGGACTTAA
Found at i:605 original size:36 final size:36
Alignment explanation
Indices: 520--670 Score: 196
Period size: 36 Copynumber: 4.2 Consensus size: 36
510 AAGTTAGGGA
* * *
520 CTTAATTCGGGGTAATTAAGTAGCGTCGATAAAGGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
*
556 ACTTAATTTAGGGTAATTAAGTAGCGTCAATAAAAGG
1 -CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* *
593 TTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* * *
629 CTTAATTCAGGATAATTAAGTGGAGTCAAT-AAAGAG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAG-G
665 CTTAAT
1 CTTAAT
671 CTAAGAAGAG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 4 0.04
36 65 0.64
37 32 0.32
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
Found at i:611 original size:73 final size:72
Alignment explanation
Indices: 521--661 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 72
511 AGTTAGGGAC
* * * * * * *
521 TTAATTCGGGGTAATTAAGTAGCGTCGATAAAGGGACTTAATTTAGGGTAATTAAGTAGCGTCAA
1 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGG-CTTAATTCAGGATAATTAAGTAGAGTCAA
586 TAAAAGGT
65 TAAAAGGT
*
594 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTGGAGTCAAT
1 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTAGAGTCAAT
659 AAA
66 AAA
662 GAGCTTAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 29 0.48
73 31 0.52
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (72 bp):
TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTAGAGTCAAT
AAAAGGT
Found at i:17433 original size:17 final size:17
Alignment explanation
Indices: 17394--17439 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
17384 AGTATTTGAC
17394 TTTG-TTGTTGTTT-GT
1 TTTGATTGTTGTTTGGT
17409 TTTGATTGTTGTTTGGT
1 TTTGATTGTTGTTTGGT
17426 TTAT-ATTG-TGTTTG
1 TT-TGATTGTTGTTTG
17440 TACTAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.14
16 15 0.54
17 8 0.29
18 1 0.04
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (17 bp):
TTTGATTGTTGTTTGGT
Found at i:26104 original size:49 final size:49
Alignment explanation
Indices: 26031--26209 Score: 261
Period size: 49 Copynumber: 3.6 Consensus size: 49
26021 CAGTGTGGCT
26031 AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAGAATA
1 AAAG-AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAGAATA
* *
26081 AAAGAAATTAAGAGAAGTAAATCTTAATTGAGCAAAATTAGGAAGAATA
1 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAGAATA
** * *
26130 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATGAAGGGA-CATA
1 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGCAAAAT-TAGGGAGAATA
* *
26179 AAGGAAATTAAGAGAAGTGAATCTTAATTCA
1 AAAGAAATTAAGAGAAGTAAATCTTAATTCA
26210 ATGAAATTAA
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 110 0.93
50 8 0.07
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.23
Consensus pattern (49 bp):
AAAGAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAGAATA
Found at i:26217 original size:98 final size:100
Alignment explanation
Indices: 26031--26239 Score: 266
Period size: 98 Copynumber: 2.1 Consensus size: 100
26021 CAGTGTGGCT
*
26031 AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAGAATAAAAGAAATTAAGAGA
1 AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATAAGGGAGAATAAAAGAAATTAAGAGA
* *
26096 AGTAAATCTTAATTGAGCAAAATT-AGGAAGAATA
66 AGTAAATCTTAATTCAACAAAATTAAGGAAGAATA
** * *
26130 AAAG-AAATTAAGAGAAGTAAATCTTAATTCAGTGAAATGAAGGGA-CATAAAGGAAATTAAGAG
1 AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGCAAAAT-AAGGGAGAATAAAAGAAATTAAGAG
* **
26193 AAGTGAATCTTAATTCAATGAAATTAAGGAA-AAT-
65 AAGTAAATCTTAATTCAACAAAATTAAGGAAGAATA
* *
26227 TAAGAAAAGTAAG
1 AAAGAAAATTAAG
26240 CATAGTTGAG
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
97 3 0.03
98 78 0.82
99 14 0.15
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (100 bp):
AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATAAGGGAGAATAAAAGAAATTAAGAGA
AGTAAATCTTAATTCAACAAAATTAAGGAAGAATA
Found at i:26296 original size:40 final size:40
Alignment explanation
Indices: 26250--26350 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
26240 CATAGTTGAG
*
26250 GACTTAATTCATAAGAATTAAGTAAAAACAGCAGTCAAAA
1 GACTTAATTCATAAGAATTAAGTAAAAACAGCAATCAAAA
* **
26290 GACTTAATTCATAAAAATTAAGTAAAAACAGCAATCTGAA
1 GACTTAATTCATAAGAATTAAGTAAAAACAGCAATCAAAA
26330 GACTTAATTCAT-AGAAATTAA
1 GACTTAATTCATAAG-AATTAA
26351 ATGGAAGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.02
40 54 0.98
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (40 bp):
GACTTAATTCATAAGAATTAAGTAAAAACAGCAATCAAAA
Found at i:26424 original size:11 final size:11
Alignment explanation
Indices: 26397--26457 Score: 81
Period size: 11 Copynumber: 5.6 Consensus size: 11
26387 TTAAGGAATT
*
26397 AGACTGAAAAAA
1 AGACTG-AAAGA
26409 AGACTGAAAGA
1 AGACTGAAAGA
26420 AGACTGAAA-A
1 AGACTGAAAGA
26430 A-ACTGAAAGA
1 AGACTGAAAGA
*
26440 AGGCTGAAAGA
1 AGACTGAAAGA
26451 AGACTGA
1 AGACTGA
26458 CTTAATTACA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
9 7 0.16
10 4 0.09
11 27 0.61
12 6 0.14
ACGTcount: A:0.56, C:0.10, G:0.25, T:0.10
Consensus pattern (11 bp):
AGACTGAAAGA
Found at i:26434 original size:20 final size:21
Alignment explanation
Indices: 26405--26457 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
26395 TTAGACTGAA
26405 AAAAAGACTGAAAGAAGACTG
1 AAAAAGACTGAAAGAAGACTG
*
26426 AAAAA-ACTGAAAGAAGGCTG
1 AAAAAGACTGAAAGAAGACTG
26446 AAAGAAGACTGA
1 AAA-AAGACTGA
26458 CTTAATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 17 0.59
21 7 0.24
22 5 0.17
ACGTcount: A:0.57, C:0.09, G:0.25, T:0.09
Consensus pattern (21 bp):
AAAAAGACTGAAAGAAGACTG
Found at i:26488 original size:35 final size:35
Alignment explanation
Indices: 26446--26523 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
26436 AAGAAGGCTG
*
26446 AAAGAAGACTGACTTAATTACAAGGAAATTAGGTA
1 AAAGAAGACTGACTTAATTACAAGAAAATTAGGTA
*
26481 AAAGAAGACTGACTTAATTTCAAGAAAATTAGGTA
1 AAAGAAGACTGACTTAATTACAAGAAAATTAGGTA
26516 AAAGAAGA
1 AAAGAAGA
26524 GAAAAACTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (35 bp):
AAAGAAGACTGACTTAATTACAAGAAAATTAGGTA
Found at i:26598 original size:36 final size:36
Alignment explanation
Indices: 26523--26602 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
26513 GTAAAAGAAG
* * *
26523 AGAAAA-ACTGGCTTAGTTTCAAGAAAACTAGGTAA
1 AGAAAAGACTGACTCAGTTTCAAGAAAACTAAGTAA
* * *
26558 AGAAAAGACTGACTCAGTTTCAAGGAAATTAAGTAC
1 AGAAAAGACTGACTCAGTTTCAAGAAAACTAAGTAA
26594 AG-AAAGACT
1 AGAAAAGACT
26603 AGCTTAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 13 0.34
36 25 0.66
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (36 bp):
AGAAAAGACTGACTCAGTTTCAAGAAAACTAAGTAA
Found at i:28667 original size:32 final size:34
Alignment explanation
Indices: 28629--28718 Score: 103
Period size: 37 Copynumber: 2.6 Consensus size: 34
28619 CAATAAAAGG
*
28629 CTTAATTCAGGGTAATTAAGT-AG-AGTAAAGAA
1 CTTAATTCAGGGTAATTAAGTCAGCAATAAAGAA
* * *
28661 CTTAATTCAGGATAATTAAAGTCGGGTCAATAAAGAG
1 CTTAATTCAGGGTAATT-AAGTC-AG-CAATAAAGAA
28698 CTTAATTCAGGGTAATTAAGT
1 CTTAATTCAGGGTAATTAAGT
28719 GGAACTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
32 16 0.33
33 4 0.08
35 1 0.02
36 4 0.08
37 23 0.48
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (34 bp):
CTTAATTCAGGGTAATTAAGTCAGCAATAAAGAA
Found at i:30040 original size:33 final size:32
Alignment explanation
Indices: 29942--30082 Score: 122
Period size: 33 Copynumber: 4.3 Consensus size: 32
29932 TTGCAAAGAG
* * * * *
29942 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTT-GGTGTTGTTTGTGATGAAACAAAATC
* * *
29975 TGATTTGAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTG-GTGTTGTTTGTGATGAAACAAAATC
30008 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTT-GGTGTTGTTTGTGATGAAACAAAATC
* * **
30041 TATTTTGGATGCTAATTGTGATGAAA-ACAAATC
1 TGTTTTGG-TGTTGTTTGTGATGAAACA-AAATC
30074 TGTTTTGGT
1 TGTTTTGGT
30083 TGATCATAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
32 5 0.05
33 85 0.93
34 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (32 bp):
TGTTTTGGTGTTGTTTGTGATGAAACAAAATC
Found at i:30529 original size:30 final size:30
Alignment explanation
Indices: 30493--30551 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
30483 TAAGGGGGAG
30493 GGAATGATGCACCCAAGG-CTTATCATGGAA
1 GGAATGATGC-CCCAAGGACTTATCATGGAA
* *
30523 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCCCCAAGGACTTATCATGGA
30552 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (30 bp):
GGAATGATGCCCCAAGGACTTATCATGGAA
Done.