Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009602.1 Corchorus capsularis cultivar CVL-1 contig09623, 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: 65336
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6700 original size:31 final size:32
Alignment explanation
Indices: 6582--6715 Score: 146
Period size: 31 Copynumber: 4.2 Consensus size: 32
6572 ACGGTGTCCG
* *
6582 ACGTGGCACACCACGTGTACC-AAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAAGTGAC
* *
6613 ATGTGGTACGCCACATGTACCAAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAAGTGAC
* * *
6645 ACATGTCACGCCACGTGTACC-AAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAAGTGAC
* ** * *
6676 ACGTGGCATGCCACATGTTTCAAAAAAATGGC
1 ACGTGGCACGCCACATGTACCAAAAAAGTGAC
6708 ACGTGGCA
1 ACGTGGCA
6716 TGTCACGTGC
Statistics
Matches: 84, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
31 42 0.50
32 42 0.50
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.17
Consensus pattern (32 bp):
ACGTGGCACGCCACATGTACCAAAAAAGTGAC
Found at i:6723 original size:63 final size:63
Alignment explanation
Indices: 6585--6724 Score: 172
Period size: 63 Copynumber: 2.2 Consensus size: 63
6575 GTGTCCGACG
* * * *
6585 TGGCACACCACGTGTACCAAAAAGTGACATGTGGTACGCCACATGTACCAAAAAAGTGACACA
1 TGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAAATGACACA
* * ** * *
6648 TGTCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTTTCAAAAAAATGGCACG
1 TGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAAATGACACA
* *
6711 TGGCATGTCACGTG
1 TGGCACGCCACGTG
6725 CACAAAAGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (63 bp):
TGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAAATGACACA
Found at i:12903 original size:12 final size:12
Alignment explanation
Indices: 12886--12911 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12876 GTTTTGCAGG
12886 ATGACTGTGACT
1 ATGACTGTGACT
12898 ATGACTGTGACT
1 ATGACTGTGACT
12910 AT
1 AT
12912 TATGGGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (12 bp):
ATGACTGTGACT
Found at i:13278 original size:31 final size:31
Alignment explanation
Indices: 13178--13279 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
13168 TACGATGAAA
* * *
13178 TCTCAAAT-AGGTATCCGAACTTCGTCATAAA-
1 TCTCAAATAAGGGA-CCCAACTTTGTCA-AAAG
*
13209 TCTCAAATAAGGGACCGAACTTTGT-AAAAG
1 TCTCAAATAAGGGACCCAACTTTGTCAAAAG
* *
13239 -GTCAAATAAGGGCCCCAA-TTTGTCAGAAAG
1 TCTCAAATAAGGGACCCAACTTTGTCA-AAAG
13269 TCTCAAATAAG
1 TCTCAAATAAG
13280 TCCATCCACT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.08
29 19 0.32
30 5 0.08
31 27 0.45
32 4 0.07
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
TCTCAAATAAGGGACCCAACTTTGTCAAAAG
Found at i:15253 original size:51 final size:51
Alignment explanation
Indices: 15177--15277 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
15167 ACTCCAATTA
*
15177 TTAGTGACACTGGTGTCAATGTTAGAAAATGTAAATTAATGATTTGTATTG
1 TTAGTGACACTGGTGTCAATGTTAGAAAATGTAAATTAATGAATTGTATTG
*
15228 TTAGTGACACTGGTGTCAATGTTAGAAAATGTAAATTCATGAATTGTATT
1 TTAGTGACACTGGTGTCAATGTTAGAAAATGTAAATTAATGAATTGTATT
15278 TTATATTAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.39
Consensus pattern (51 bp):
TTAGTGACACTGGTGTCAATGTTAGAAAATGTAAATTAATGAATTGTATTG
Found at i:20754 original size:2 final size:2
Alignment explanation
Indices: 20749--20785 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20739 TATCTAGGTA
20749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20786 CCATCAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20991 original size:34 final size:34
Alignment explanation
Indices: 20880--21011 Score: 131
Period size: 34 Copynumber: 3.8 Consensus size: 34
20870 ATCTCTGTTC
* * ** * *
20880 AAACCCTAAA-TCCAAAATACCCAAATTCTTTCA
1 AAACCCTAAATTCCCAATTACCCAAATAATATCG
* *
20913 AAACCCTAAATTCCCAATTACGCAATTAATTAATGTCG
1 AAACCCTAAATTCCCAATTAC-CCA--AA-TAATATCG
20951 AAACCCTAAATTCCCAATTACCCAAATAATATCG
1 AAACCCTAAATTCCCAATTACCCAAATAATATCG
*
20985 AAACCCTAAATTCCCAGATTCCCCAAA
1 AAACCCTAAATTCCCA-ATTACCCAAA
21012 ATCAATAACA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
33 10 0.12
34 31 0.37
35 13 0.16
37 4 0.05
38 25 0.30
ACGTcount: A:0.42, C:0.30, G:0.04, T:0.24
Consensus pattern (34 bp):
AAACCCTAAATTCCCAATTACCCAAATAATATCG
Found at i:21551 original size:31 final size:31
Alignment explanation
Indices: 21513--21618 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
21503 ACGAAATGGA
*
21513 CTTATTTGAGACTTTCTGAC-AAGTTGGGGTC
1 CTTATTTGAGA-TTTCTGACAAAGTTGGGGAC
** * *
21544 CTTATTTGACCTTT-T-ACAAAGTTCGGGCC
1 CTTATTTGAGATTTCTGACAAAGTTGGGGAC
* *
21573 CTTATTTGAGATTTATGGCAAAGTTCGGGGAC
1 CTTATTTGAGATTTCTGACAAAGTT-GGGGAC
21605 C-TATTTGAGATTTC
1 CTTATTTGAGATTTC
21619 AGCGAATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.03
29 22 0.36
30 4 0.07
31 28 0.46
32 5 0.08
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (31 bp):
CTTATTTGAGATTTCTGACAAAGTTGGGGAC
Found at i:23528 original size:244 final size:244
Alignment explanation
Indices: 23099--23583 Score: 970
Period size: 244 Copynumber: 2.0 Consensus size: 244
23089 ACATTTAAAG
23099 AAATCTTAGGATCAAAAACACAATGTTCAAGATAAGGGTTACCATAAAAAGTAGGCTCAAATGAT
1 AAATCTTAGGATCAAAAACACAATGTTCAAGATAAGGGTTACCATAAAAAGTAGGCTCAAATGAT
23164 AGTTGTAGAGAGACTGCTGCATTAACAAGATGAGTTTGAGCAGAATTTGCTTGAATCATGGATAT
66 AGTTGTAGAGAGACTGCTGCATTAACAAGATGAGTTTGAGCAGAATTTGCTTGAATCATGGATAT
23229 GAGTTGATTGTATTGGTCTTTGGTAAACTAATAAGTTGCAGAAGATGAAGATTCTTGAGTCTGAA
131 GAGTTGATTGTATTGGTCTTTGGTAAACTAATAAGTTGCAGAAGATGAAGATTCTTGAGTCTGAA
23294 TAGCCATTGCAAGAACAGAATTGATAAAAGTATTCATTACAGGAACAGA
196 TAGCCATTGCAAGAACAGAATTGATAAAAGTATTCATTACAGGAACAGA
23343 AAATCTTAGGATCAAAAACACAATGTTCAAGATAAGGGTTACCATAAAAAGTAGGCTCAAATGAT
1 AAATCTTAGGATCAAAAACACAATGTTCAAGATAAGGGTTACCATAAAAAGTAGGCTCAAATGAT
23408 AGTTGTAGAGAGACTGCTGCATTAACAAGATGAGTTTGAGCAGAATTTGCTTGAATCATGGATAT
66 AGTTGTAGAGAGACTGCTGCATTAACAAGATGAGTTTGAGCAGAATTTGCTTGAATCATGGATAT
23473 GAGTTGATTGTATTGGTCTTTGGTAAACTAATAAGTTGCAGAAGATGAAGATTCTTGAGTCTGAA
131 GAGTTGATTGTATTGGTCTTTGGTAAACTAATAAGTTGCAGAAGATGAAGATTCTTGAGTCTGAA
23538 TAGCCATTGCAAGAACAGAATTGATAAAAGTATTCATTACAGGAAC
196 TAGCCATTGCAAGAACAGAATTGATAAAAGTATTCATTACAGGAAC
23584 TAAAAATTGA
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 241 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (244 bp):
AAATCTTAGGATCAAAAACACAATGTTCAAGATAAGGGTTACCATAAAAAGTAGGCTCAAATGAT
AGTTGTAGAGAGACTGCTGCATTAACAAGATGAGTTTGAGCAGAATTTGCTTGAATCATGGATAT
GAGTTGATTGTATTGGTCTTTGGTAAACTAATAAGTTGCAGAAGATGAAGATTCTTGAGTCTGAA
TAGCCATTGCAAGAACAGAATTGATAAAAGTATTCATTACAGGAACAGA
Found at i:30399 original size:17 final size:17
Alignment explanation
Indices: 30379--30412 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30369 CCTGCTAGTT
30379 TTGAGAGAAAATTTGTA
1 TTGAGAGAAAATTTGTA
**
30396 TTGAGCTAAAATTTGTA
1 TTGAGAGAAAATTTGTA
30413 CTTGGGATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (17 bp):
TTGAGAGAAAATTTGTA
Found at i:35519 original size:32 final size:32
Alignment explanation
Indices: 35478--35543 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
35468 TGTGGCCACT
35478 AACGATGTAAGAGGAAGATCTATGGCTAGATC
1 AACGATGTAAGAGGAAGATCTATGGCTAGATC
35510 AACGATGTAAGAGGAAGATCTATGGCTAGATC
1 AACGATGTAAGAGGAAGATCTATGGCTAGATC
35542 AA
1 AA
35544 GCTTAGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (32 bp):
AACGATGTAAGAGGAAGATCTATGGCTAGATC
Found at i:36709 original size:13 final size:12
Alignment explanation
Indices: 36686--36727 Score: 75
Period size: 12 Copynumber: 3.4 Consensus size: 12
36676 TTAATACAGG
36686 TATCGACGGATA
1 TATCGACGGATA
36698 TATCGAACGGATA
1 TATCG-ACGGATA
36711 TATCGACGGATA
1 TATCGACGGATA
36723 TATCG
1 TATCG
36728 TGGTATCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:37474 original size:3 final size:3
Alignment explanation
Indices: 37466--37498 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37456 CATTTCCCCC
*
37466 CAT CAT CAT CAT CAT TAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
37499 TTCCGTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:38105 original size:10 final size:10
Alignment explanation
Indices: 38090--38115 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38080 AATTTAATAT
38090 GGATATTTAC
1 GGATATTTAC
38100 GGATATTTAC
1 GGATATTTAC
38110 GGATAT
1 GGATAT
38116 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:46412 original size:29 final size:29
Alignment explanation
Indices: 46341--46419 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
46331 GTAGCGTTTA
*
46341 GACGTTTTGTCCCCTGAACTTCAATCTTG
1 GACGTTTTGACCCCTGAACTTCAATCTTG
* * *
46370 GACATTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTGACCCCTGAACTTCAATCTT-G
*
46400 GACGTTTT-ACCCCTCAACTT
1 GACGTTTTGACCCCTGAACTT
46420 AACGGAACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 35 0.81
30 8 0.19
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (29 bp):
GACGTTTTGACCCCTGAACTTCAATCTTG
Found at i:50941 original size:18 final size:18
Alignment explanation
Indices: 50897--50942 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
50887 AAGGAAAAAC
50897 AGTAGAAACACCATTACA
1 AGTAGAAACACCATTACA
*
50915 A-TCAAAAACACCATTACA
1 AGT-AGAAACACCATTACA
50933 AGTAGAAACA
1 AGTAGAAACA
50943 GTTTTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (18 bp):
AGTAGAAACACCATTACA
Found at i:53156 original size:18 final size:18
Alignment explanation
Indices: 53133--53178 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
53123 ATTCTAAAAT
53133 TGTTTTTACTTGTAATGG
1 TGTTTTTACTTGTAATGG
53151 TGTTTTTGA-TTGTAATGG
1 TGTTTTT-ACTTGTAATGG
*
53169 TGTTTCTACT
1 TGTTTTTACT
53179 GTTTTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.57
Consensus pattern (18 bp):
TGTTTTTACTTGTAATGG
Found at i:61390 original size:30 final size:29
Alignment explanation
Indices: 61323--61394 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
61313 ACACCGAACC
****
61323 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
61352 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
61382 GTCAAATAAGCCC
1 GTCAAATAAGCCC
61395 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Done.