Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014006.1 Corchorus capsularis cultivar CVL-1 contig14027, 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: 33914
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:325 original size:32 final size:32
Alignment explanation
Indices: 289--355 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
279 TTAGTAATGG
* *
289 CAATTTAGAAATATGTTTTTAAAAA-AGGGGTA
1 CAATTTAGAAATATG-TTTAAAAAATAAGGGTA
*
321 CAA-TTGGAAATATGTTTAAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTAAAAAATAAGGGTA
352 CAAT
1 CAAT
356 CGGAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 8 0.27
31 19 0.63
32 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.31
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTAAAAAATAAGGGTA
Found at i:365 original size:32 final size:31
Alignment explanation
Indices: 296--361 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
286 TGGCAATTTA
* * *
296 GAAATATGTTTTTAAAAAAGGGGTACAATTG
1 GAAATATGTTTTAAAAAAAAGGGTACAATCG
327 GAAATATG-TTTAAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAAA-AAGGGTACAATCG
358 GAAA
1 GAAA
362 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGGGTACAATCG
Found at i:7310 original size:18 final size:18
Alignment explanation
Indices: 7287--7324 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
7277 TGTGAAGGAA
7287 TCTTGGTCAAGAGAGATG
1 TCTTGGTCAAGAGAGATG
7305 TCTTGGTCAAGAGAGATG
1 TCTTGGTCAAGAGAGATG
7323 TC
1 TC
7325 CTTTGATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (18 bp):
TCTTGGTCAAGAGAGATG
Found at i:12223 original size:36 final size:36
Alignment explanation
Indices: 12176--12249 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
12166 GGACCTGACA
12176 GGTAATCTTTCTAGGATTTCCATGCATATTTCCTCC
1 GGTAATCTTTCTAGGATTTCCATGCATATTTCCTCC
*
12212 GGTAATCTTTCTAGGATTTTCATGCATATTTCCTCC
1 GGTAATCTTTCTAGGATTTCCATGCATATTTCCTCC
12248 GG
1 GG
12250 CAATTGACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (36 bp):
GGTAATCTTTCTAGGATTTCCATGCATATTTCCTCC
Found at i:14168 original size:30 final size:30
Alignment explanation
Indices: 14132--14225 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 30
14122 TTATCTTCGT
14132 TTTGTTTGGGTCCAAACAACAGGAAGATCC
1 TTTGTTTGGGTCCAAACAACAGGAAGATCC
* * *
14162 TTTGTTTGGGTCTACACAACAGGAAGACCC
1 TTTGTTTGGGTCCAAACAACAGGAAGATCC
*
14192 TTTGTTTGGGTCCAAATTACAACACGAAGATCC
1 TTTGTTTGGGTCC-AA--ACAACAGGAAGATCC
14225 T
1 T
14226 GATCTGTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 39 0.72
31 1 0.02
33 14 0.26
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (30 bp):
TTTGTTTGGGTCCAAACAACAGGAAGATCC
Found at i:14971 original size:12 final size:12
Alignment explanation
Indices: 14956--15021 Score: 114
Period size: 12 Copynumber: 5.5 Consensus size: 12
14946 AGCGAAGAAT
14956 ATCAGAGTGAAG
1 ATCAGAGTGAAG
*
14968 ATCAGAGTGAAT
1 ATCAGAGTGAAG
14980 ATCAGAGTGAAG
1 ATCAGAGTGAAG
*
14992 ATGAGAGTGAAG
1 ATCAGAGTGAAG
15004 ATCAGAGTGAAG
1 ATCAGAGTGAAG
15016 ATCAGA
1 ATCAGA
15022 CTAAAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.18
Consensus pattern (12 bp):
ATCAGAGTGAAG
Found at i:19409 original size:13 final size:13
Alignment explanation
Indices: 19393--19417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19383 GTTCATAGTT
19393 GAGTAATTAAGTG
1 GAGTAATTAAGTG
19406 GAGTAATTAAGT
1 GAGTAATTAAGT
19418 TAAGATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (13 bp):
GAGTAATTAAGTG
Found at i:22390 original size:12 final size:12
Alignment explanation
Indices: 22373--22426 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
22363 TTTAATCCAG
**
22373 ATATCGACTCAT
1 ATATCGACGGAT
22385 ATATCGAACGGAT
1 ATATCG-ACGGAT
22398 ATATCGACGGAT
1 ATATCGACGGAT
**
22410 ATATCGGTGGAT
1 ATATCGACGGAT
22422 ATATC
1 ATATC
22427 AAGCTATCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 27 0.73
13 10 0.27
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:22719 original size:29 final size:30
Alignment explanation
Indices: 22685--22760 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
22675 CCAACTTGCT
*
22685 CAATTTGAGTCTAAACCTT-T-AAACTGAAC
1 CAATTTGAG-CTAAACCTTATGAAAATGAAC
* *
22714 CAATTTGAGCTTAAACCTTATGAAAATGCAT
1 CAATTTGAGC-TAAACCTTATGAAAATGAAC
22745 CAATTTGAGCCTAAAC
1 CAATTTGAG-CTAAAC
22761 TTGACGGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.03
29 17 0.43
30 1 0.03
31 20 0.50
32 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (30 bp):
CAATTTGAGCTAAACCTTATGAAAATGAAC
Found at i:28257 original size:67 final size:65
Alignment explanation
Indices: 28145--28289 Score: 186
Period size: 67 Copynumber: 2.2 Consensus size: 65
28135 TCAGTCAACC
* * *
28145 CAAAGAAAAAAAAGAAGCTCGTTAAGTTGAAAATCCTACAAAGGACGGCTTAGGCAAAAGC-TAG
1 CAAA-AAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACGACTTAGGCAAAA-CTTAG
28209 AG
64 AG
*
28211 CAAAAAAAAAAAAAATGGCTCGCTAAGTTGAAAATCCTGA-ATAGGACGACTTAGGCAAAACTTA
1 CAAAAAAAAAAAAAA--GCTCGCTAAGTTGAAAATCCT-ACAAAGGACGACTTAGGCAAAACTTA
28275 GAG
63 GAG
*
28278 CATAAAAAAAAA
1 CAAAAAAAAAAA
28290 TGAACTACGT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
65 10 0.14
66 5 0.07
67 54 0.77
68 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.16
Consensus pattern (65 bp):
CAAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACGACTTAGGCAAAACTTAGAG
Found at i:29058 original size:16 final size:16
Alignment explanation
Indices: 29039--29085 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
29029 AATTCAGAAA
29039 GCAGAAAAGCTCTGAT
1 GCAGAAAAGCTCTGAT
29055 GCAGAAAAGCTCTGAT
1 GCAGAAAAGCTCTGAT
29071 GCAGAAAAGCTCTGA
1 GCAGAAAAGCTCTGA
29086 AGTATTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (16 bp):
GCAGAAAAGCTCTGAT
Found at i:32172 original size:15 final size:15
Alignment explanation
Indices: 32154--32186 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32144 AGTATTAAAA
*
32154 TTTCAGTACTTAATT
1 TTTCAGCACTTAATT
32169 TTTCAGCACTTAATT
1 TTTCAGCACTTAATT
32184 TTT
1 TTT
32187 AGTTTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (15 bp):
TTTCAGCACTTAATT
Done.