Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005868.1 Corchorus capsularis cultivar CVL-1 contig05886, 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: 12226
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Found at i:2211 original size:70 final size:70
Alignment explanation
Indices: 2084--2216 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 70
2074 ATAACTATGG
* * * * *
2084 TAGAAATTAGACATGCAAAAGAGGAAACAAAACAACAAAAGCTGATAGAAAACAAAATCAGAAAC
1 TAGAAATTAGACATACAAAACAGGAAACAAAACAACAAAAGATGATACAAAACAAAATAAGAAAC
2149 CATGC
66 CATGC
* * * * *
2154 TAGAAGTTAGACATACAAAACAGGAAACAAAAGAGCAAAAGATGATACAATAGAAAATAAGAA
1 TAGAAATTAGACATACAAAACAGGAAACAAAACAACAAAAGATGATACAAAACAAAATAAGAA
2217 TCCAAAATCC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.59, C:0.13, G:0.17, T:0.12
Consensus pattern (70 bp):
TAGAAATTAGACATACAAAACAGGAAACAAAACAACAAAAGATGATACAAAACAAAATAAGAAAC
CATGC
Found at i:3668 original size:20 final size:20
Alignment explanation
Indices: 3643--3680 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3633 AACATGGGAA
3643 TTATTAAATACCGCCCCCTT
1 TTATTAAATACCGCCCCCTT
**
3663 TTATTAGGTACCGCCCCC
1 TTATTAAATACCGCCCCC
3681 CCTTTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.37, G:0.11, T:0.32
Consensus pattern (20 bp):
TTATTAAATACCGCCCCCTT
Found at i:3950 original size:33 final size:33
Alignment explanation
Indices: 3900--4053 Score: 182
Period size: 33 Copynumber: 4.6 Consensus size: 33
3890 GCTGGTCGCG
* * *
3900 CGCGTGCGACCCCCACCATAGCGGGTCACGATC
1 CGCGTGCGACCCGCACCATGGCGGGTCGCGATC
* * *
3933 CGCGTGCGAGCCGCACCATGACAGGTCGCGATC
1 CGCGTGCGACCCGCACCATGGCGGGTCGCGATC
*
3966 CGCGTGCGACCCGCACCATGGCGGGTTGCGATC
1 CGCGTGCGACCCGCACCATGGCGGGTCGCGATC
* * *
3999 CACATGTGACCCGCACCATGGCGGGTCGCGATC
1 CGCGTGCGACCCGCACCATGGCGGGTCGCGATC
* * *
4032 CACATGCGACCCGTCCCCATGG
1 CGCGTGCGACCCG-CACCATGG
4054 GATGGGTCTT
Statistics
Matches: 104, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 97 0.93
34 7 0.07
ACGTcount: A:0.17, C:0.39, G:0.31, T:0.14
Consensus pattern (33 bp):
CGCGTGCGACCCGCACCATGGCGGGTCGCGATC
Found at i:4808 original size:18 final size:19
Alignment explanation
Indices: 4771--4817 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 19
4761 TTAATAAGTG
*
4771 AAAAAAAAAATCAAAAAAC
1 AAAAAAAAAAACAAAAAAC
4790 AAAAAAAAAAACAACAACAAC
1 AAAAAAAAAAACAA-AA-AAC
4811 AACAAAA
1 AA-AAAA
4818 TAGTATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 5 0.21
22 4 0.17
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAACAAAAAAC
Found at i:9114 original size:11 final size:11
Alignment explanation
Indices: 9084--9132 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
9074 CTAAACAAGA
*
9084 AATAATTTAATT
1 AATAA-TTATTT
*
9096 ATTAATTATTT
1 AATAATTATTT
9107 AATAATTATTT
1 AATAATTATTT
* *
9118 AATTATTACTT
1 AATAATTATTT
9129 AATA
1 AATA
9133 CTACTAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
11 27 0.87
12 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATTATTT
Found at i:11139 original size:58 final size:58
Alignment explanation
Indices: 10984--11257 Score: 367
Period size: 57 Copynumber: 4.7 Consensus size: 58
10974 AGCAATATCG
* * ** * * **
10984 ATCGAGCATCCATCGGCCGTACGACCAAGTGGGCATCCCCCACTTATGTAATAAGA-CG
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAA
*
11042 ATCGAGC-TCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
11099 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
* *
11157 ATCGAGCAT-CCTCGGTCACACGGCCAAGTGGACATTCCCCACTCATGTAATAAATAAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAAT-AA
* * *
11215 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGTATCCCCCAC
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCAC
11258 ACGTGCAAGA
Statistics
Matches: 196, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
56 1 0.01
57 92 0.47
58 75 0.38
59 24 0.12
60 4 0.02
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (58 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
Found at i:11186 original size:115 final size:116
Alignment explanation
Indices: 10984--11257 Score: 367
Period size: 115 Copynumber: 2.4 Consensus size: 116
10974 AGCAATATCG
* * ** * * **
10984 ATCGAGCATCCATCGGCCGTACGACCAAGTGGGCATCCCCCACTTATGTAATAAGACGATCGAGC
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAATCGAGC
* *
11049 TCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAAT-AA
66 TCCCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAATAAA
11099 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAAATCGAG
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGA-AAATCGAG
*
11163 CAT-CCTCGGTCACACGGCCAAGTGGACATTCCCCACTCATGTAATAAATAAA
65 C-TCCCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAATAAA
* * *
11215 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGTATCCCCCAC
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCAC
11258 ACGTGCAAGA
Statistics
Matches: 141, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
114 1 0.01
115 98 0.70
116 38 0.27
117 4 0.03
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (116 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAATCGAGC
TCCCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAATAAA
Found at i:11279 original size:58 final size:58
Alignment explanation
Indices: 11008--11290 Score: 324
Period size: 57 Copynumber: 4.9 Consensus size: 58
10998 GGCCGTACGA
* ** * * *
11008 CCAAGTGGGCATCCCCCACTTATGTAATAAGA-CGATCGAGC-TCCCTCGGTCGCACGG
1 CCAAGTGGGCATCCCCCACTCATGTAATAA-ATAAAACAAGCATCCCTCGGTCACACGG
* *
11065 CCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCATCCCTCGGTCACACGG
1 CCAAGTGGGCATCCCCCACTCATGTAATAAATAAAACAAGCATCCCTCGGTCACACGG
* *
11123 CCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCAT-CCTCGGTCACACGG
1 CCAAGTGGGCATCCCCCACTCATGTAATAAATAAAACAAGCATCCCTCGGTCACACGG
* * *
11180 CCAAGTGGACATTCCCCACTCATGTAATAAATAAAATCAAGCATCCCTCGGTCACATGG
1 CCAAGTGGGCATCCCCCACTCATGTAATAAATAAAA-CAAGCATCCCTCGGTCACACGG
* * * * * *
11239 CCCAA-TGGGTATCCCCCACACGTGCAAGAAGA-AAAACAAGCATCCCTTGGTC
1 -CCAAGTGGGCATCCCCCACTCATGTAATAA-ATAAAACAAGCATCCCTCGGTC
11291 GAACAACCTA
Statistics
Matches: 203, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.00
57 83 0.41
58 79 0.39
59 35 0.17
60 5 0.02
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (58 bp):
CCAAGTGGGCATCCCCCACTCATGTAATAAATAAAACAAGCATCCCTCGGTCACACGG
Found at i:11283 original size:116 final size:115
Alignment explanation
Indices: 11051--11283 Score: 317
Period size: 116 Copynumber: 2.0 Consensus size: 115
11041 GATCGAGCTC
* * *
11051 CCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCATCCCTCGGT
1 CCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGT
* * * * *
11116 CACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCAT
66 CACACGGCCAAGTGGGCATCCCCCACACATGCAAGAAATAAAACAAGCAT
*
11166 CCTCGGTCACACGGCCAAGTGGACATTCCCCACTCATGTAATAAATAAAATCAAGCATCCCTCGG
1 CCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAAT-AAATCAAGCATCCCTCGG
* * *
11231 TCACATGGCCCAA-TGGGTATCCCCCACACGTGCAAGAAGA-AAAACAAGCAT
65 TCACACGG-CCAAGTGGGCATCCCCCACACATGCAAGAA-ATAAAACAAGCAT
11282 CC
1 CC
11284 CTTGGTCGAA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
115 43 0.42
116 55 0.53
117 5 0.05
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (115 bp):
CCTCGGTCACACGGCCAAGTGGACATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGT
CACACGGCCAAGTGGGCATCCCCCACACATGCAAGAAATAAAACAAGCAT
Found at i:11347 original size:28 final size:27
Alignment explanation
Indices: 11314--11549 Score: 177
Period size: 28 Copynumber: 9.6 Consensus size: 27
11304 TGGGCACCCC
11314 CCAAAGGCATACAGCCTAAATAAAATTT
1 CCAAAGGCATACAGCCT-AATAAAATTT
* **
11342 CCAAAGGCGTACAGCC---T---A-CC
1 CCAAAGGCATACAGCCTAATAAAATTT
11362 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTA-ATAAAATTT
*
11390 CCAAAGGCATACAGCC---T---A-TC
1 CCAAAGGCATACAGCCTAATAAAATTT
11410 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTA-ATAAAATTT
*
11438 CCAAAGGCATACAGCC---T---A-TC
1 CCAAAGGCATACAGCCTAATAAAATTT
11458 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTA-ATAAAATTT
*
11486 CCAAAGGCATACAGCC---T---A-TC
1 CCAAAGGCATACAGCCTAATAAAATTT
11506 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTA-ATAAAATTT
11534 CCAAAGGCATACAGCC
1 CCAAAGGCATACAGCC
11550 AAAATAGAGC
Statistics
Matches: 164, Mismatches: 12, Indels: 64
0.68 0.05 0.27
Matches are distributed among these distances:
20 66 0.40
21 4 0.02
24 8 0.05
27 4 0.02
28 82 0.50
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.18
Consensus pattern (27 bp):
CCAAAGGCATACAGCCTAATAAAATTT
Found at i:11367 original size:20 final size:20
Alignment explanation
Indices: 11342--11379 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11332 AATAAAATTT
*
11342 CCAAAGGCGTACAGCCTACC
1 CCAAAGGCATACAGCCTACC
11362 CCAAAGGCATACAGCCTA
1 CCAAAGGCATACAGCCTA
11380 GATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.37, G:0.18, T:0.11
Consensus pattern (20 bp):
CCAAAGGCATACAGCCTACC
Found at i:11385 original size:48 final size:48
Alignment explanation
Indices: 11313--11549 Score: 447
Period size: 48 Copynumber: 4.9 Consensus size: 48
11303 ATGGGCACCC
* * *
11313 CCCAAAGGCATACAGCCTAAATAAAATTTCCAAAGGCGTACAGCCTAC
1 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
11361 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
1 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
11409 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
1 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
11457 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
1 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
11505 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCC
1 CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCC
11550 AAAATAGAGC
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 186 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.18
Consensus pattern (48 bp):
CCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTAT
Found at i:11415 original size:20 final size:20
Alignment explanation
Indices: 11390--11523 Score: 106
Period size: 20 Copynumber: 5.9 Consensus size: 20
11380 GATAAAATTT
11390 CCAAAGGCATACAGCCTATC
1 CCAAAGGCATACAGCCTATC
*
11410 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCC----T---A-TC
11438 CCAAAGGCATACAGCCTATC
1 CCAAAGGCATACAGCCTATC
*
11458 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCC----T---A-TC
11486 CCAAAGGCATACAGCCTATC
1 CCAAAGGCATACAGCCTATC
11506 CCAAAGGCATACAGCCTA
1 CCAAAGGCATACAGCCTA
11524 GATAAAATTT
Statistics
Matches: 94, Mismatches: 4, Indels: 32
0.72 0.03 0.25
Matches are distributed among these distances:
20 52 0.55
21 2 0.02
24 4 0.04
27 2 0.02
28 34 0.36
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.17
Consensus pattern (20 bp):
CCAAAGGCATACAGCCTATC
Found at i:11985 original size:29 final size:29
Alignment explanation
Indices: 11952--12207 Score: 350
Period size: 29 Copynumber: 8.8 Consensus size: 29
11942 TAAAGCTCAA
* * *
11952 GAAGTGGTAGTACTCCCTCGAAAATTCGG
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
*
11981 GAAGTGGTAGTACTCCCTCCAAAGTTCGT
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
* * * *
12010 GAAGTGATAGTACTCCCTCGAAAATTCGA
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
* *
12039 GAAGTGATAGTACTCCCTCCAAAGTTCCC
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
** *
12068 GAAGTGGTAGTACAACCTCCAAAGTTCAC
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
*
12097 GAAGTGGTAGTACTCCCTCCAAAGTTCGT
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
* **
12126 GAAGTGGTAGTACTCCCTCCAAATTTCAA
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
*
12155 GAAGTGGTAGTACTCCCTCCAAAGTTCCC
1 GAAGTGGTAGTACTCCCTCCAAAGTTCGC
12184 GAAGTGGTAGTACTCCCTCCAAAG
1 GAAGTGGTAGTACTCCCTCCAAAG
12208 GCAAAAAATA
Statistics
Matches: 202, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 202 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (29 bp):
GAAGTGGTAGTACTCCCTCCAAAGTTCGC
Done.