Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010711.1 Corchorus capsularis cultivar CVL-1 contig10732, 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: 48476
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:55 original size:33 final size:33
Alignment explanation
Indices: 12--127 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 33
2 CTGCCGTGGC
*
12 GAAGTCGCCCCAGTGGGGCGGCCTGCCCATGGT
1 GAAGCCGCCCCAGTGGGGCGGCCTGCCCATGGT
* * * *
45 GAAGCCGCCCCA-TGAGGGTGGCTTG-CCGTGGC
1 GAAGCCGCCCCAGTG-GGGCGGCCTGCCCATGGT
* *
77 AAAGCCGCCCCAGTGGGGCGGCCTGCCCATGCT
1 GAAGCCGCCCCAGTGGGGCGGCCTGCCCATGGT
*
110 GAAGCTGCCCCAGTGGGG
1 GAAGCCGCCCCAGTGGGG
128 AGGCTCCGCG
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
32 26 0.39
33 41 0.61
ACGTcount: A:0.14, C:0.34, G:0.39, T:0.14
Consensus pattern (33 bp):
GAAGCCGCCCCAGTGGGGCGGCCTGCCCATGGT
Found at i:3613 original size:75 final size:75
Alignment explanation
Indices: 3524--3669 Score: 211
Period size: 75 Copynumber: 1.9 Consensus size: 75
3514 TCATTACGTT
** * * * * *
3524 ATTTTATTTTTGCTAAAAGAATTATATTTTACGCAACAACTCAATATTGTTGCGCAAAAATATTT
1 ATTTTATTGCTGCTAAAAGAATTATATTTAACACAACAACTCAATATTATTGCACAAAAATAGTT
3589 TAACAATGCC
66 TAACAATGCC
* *
3599 ATTTTATTGCTGCTAAAAGAATTATATTTAACATAACAACTCAATATTATTGCATAAAAATAGTT
1 ATTTTATTGCTGCTAAAAGAATTATATTTAACACAACAACTCAATATTATTGCACAAAAATAGTT
3664 TAACAA
66 TAACAA
3670 CATTGCAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (75 bp):
ATTTTATTGCTGCTAAAAGAATTATATTTAACACAACAACTCAATATTATTGCACAAAAATAGTT
TAACAATGCC
Found at i:4564 original size:2 final size:2
Alignment explanation
Indices: 4547--4580 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4537 CTATTCTATT
*
4547 TA TA TT TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4581 GTAATAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13006 original size:18 final size:17
Alignment explanation
Indices: 12977--13018 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
12967 CTCGTACTTT
12977 TATATATAATATAGATA
1 TATATATAATATAGATA
*
12994 TATATACTAATATATATA
1 TATATA-TAATATAGATA
*
13012 TGTATAT
1 TATATAT
13019 TAGTGTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (17 bp):
TATATATAATATAGATA
Found at i:13102 original size:2 final size:2
Alignment explanation
Indices: 13095--13125 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13085 GCATTTCAAA
13095 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 A
13126 CTAATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19351 original size:33 final size:33
Alignment explanation
Indices: 19314--19418 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
19304 AATAGTCCTA
19314 TTTTCAATGCTATGATCAACCAAAACAGAATTG
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
* *
19347 TTTTCAATGCTATGATCAACCAAAACAAAATAG
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
*
19380 TTTTCAATGCTATGATCAACCAAAACAGATTTG
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
19413 TTTTCA
1 TTTTCA
19419 TCACAATTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (33 bp):
TTTTCAATGCTATGATCAACCAAAACAGAATTG
Found at i:19436 original size:66 final size:66
Alignment explanation
Indices: 19314--19439 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
19304 AATAGTCCTA
* * *
19314 TTTTCAATGCTATGATCAACCAAAACAGAATTGTTTTCAATGCTATGATCAACCAAAACAAAATA
1 TTTTCAATGCTATGATCAACCAAAACAGAATTGTTTTCAATACAATGAGCAACCAAAACAAAATA
19379 G
66 G
* * *
19380 TTTTCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACA
1 TTTTCAATGCTATGATCAACCAAAACAGAATTGTTTTCAAT-ACAATGAGCAACCAAAACA
19440 GATTTAGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 2 0.04
66 51 0.96
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (66 bp):
TTTTCAATGCTATGATCAACCAAAACAGAATTGTTTTCAATACAATGAGCAACCAAAACAAAATA
G
Found at i:25392 original size:21 final size:21
Alignment explanation
Indices: 25363--25407 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25353 ATGACACTGC
* * *
25363 CCACCTGGGTGATCAGGCAAA
1 CCACATGGGTCATCAGACAAA
*
25384 CCACATGGGTCTTCAGACAAA
1 CCACATGGGTCATCAGACAAA
25405 CCA
1 CCA
25408 TGTGGGCACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCATCAGACAAA
Found at i:26628 original size:12 final size:12
Alignment explanation
Indices: 26611--26636 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26601 AGAGGAAAAC
26611 AAGTACGCTTTT
1 AAGTACGCTTTT
26623 AAGTACGCTTTT
1 AAGTACGCTTTT
26635 AA
1 AA
26637 TTAATTGTTT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (12 bp):
AAGTACGCTTTT
Found at i:26947 original size:21 final size:20
Alignment explanation
Indices: 26900--26959 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
26890 CTTACCTTTA
26900 TATTTTCTTTTTCGTTTTTTT
1 TATTTTCTTTTT-GTTTTTTT
**
26921 CCTTTTCTTTTTGTTTTATTT
1 TATTTTCTTTTTGTTTT-TTT
* *
26942 TATTTTATTTTTATTTTT
1 TATTTTCTTTTTGTTTTT
26960 CTTAGTTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (20 bp):
TATTTTCTTTTTGTTTTTTT
Found at i:40096 original size:32 final size:32
Alignment explanation
Indices: 40056--40132 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
40046 TGGGCTTGAG
*
40056 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAC
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAC
* *
40088 TCGGGTTCGAGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAC
40120 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
40133 CTGTTTGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.13, C:0.12, G:0.39, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAC
Found at i:40125 original size:15 final size:15
Alignment explanation
Indices: 40075--40125 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
40065 GGTTGGATTT
*
40075 GGGTCAGGTTAACTC
1 GGGTCAGGTTAATTC
*
40090 GGGTTC-GAGTTGAATTT
1 GGG-TCAG-GTT-AATTC
40107 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
40122 GGGT
1 GGGT
40126 TCGGGTTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
15 12 0.41
16 10 0.34
17 7 0.24
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (15 bp):
GGGTCAGGTTAATTC
Found at i:40140 original size:32 final size:31
Alignment explanation
Indices: 40056--40142 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 31
40046 TGGGCTTGAG
*
40056 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAC
1 TCGGGTTCGGGTTAG-TTTGGGTCAGGTTAAC
* * *
40088 TCGGGTTCGAGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTT-AGTTTGGGTCAGGTTAAC
*
40120 TCGGGTTCGGGTTCTGTTTGGGT
1 TCGGGTTCGGGTT-AGTTTGGGT
40143 TTTGGCCAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.38
Consensus pattern (31 bp):
TCGGGTTCGGGTTAGTTTGGGTCAGGTTAAC
Found at i:40309 original size:16 final size:16
Alignment explanation
Indices: 40288--40328 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
40278 AATTTTCGGA
*
40288 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
40304 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGCTTT
40320 TTCGGGTTC
1 TTCGGGTTC
40329 AGGTTTAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.02, C:0.15, G:0.34, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:40333 original size:16 final size:16
Alignment explanation
Indices: 40301--40334 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40291 GGGTTTGAGC
*
40301 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCAGGT
40317 TTTTTCGGGTTCAGGT
1 TTTTTCGGGTTCAGGT
40333 TT
1 TT
40335 AGACGGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.32, T:0.53
Consensus pattern (16 bp):
TTTTTCGGGTTCAGGT
Found at i:47403 original size:22 final size:22
Alignment explanation
Indices: 47371--47431 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
47361 ATGTAACTAA
* *
47371 GAAAAATAAAAATAAAACTAAAC
1 GAAAAAGAAAAATAAAAAT-AAC
*
47394 -AAAAAGAAAAAGAAAAATAAC
1 GAAAAAGAAAAATAAAAATAAC
47415 GAAAAAGAAAAGATAAA
1 GAAAAAGAAAA-ATAAA
47432 GGTAAGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 25 0.78
23 4 0.12
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (22 bp):
GAAAAAGAAAAATAAAAATAAC
Found at i:47418 original size:16 final size:17
Alignment explanation
Indices: 47399--47430 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47389 TAAACAAAAA
47399 GAAAAAGAAAA-ATAAC
1 GAAAAAGAAAAGATAAC
47415 GAAAAAGAAAAGATAA
1 GAAAAAGAAAAGATAA
47431 AGGTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (17 bp):
GAAAAAGAAAAGATAAC
Found at i:47440 original size:22 final size:21
Alignment explanation
Indices: 47368--47440 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
47358 TAAATGTAAC
*
47368 TAAGAAAAATAAAA-ATAAAA
1 TAAGAAAAAGAAAAGATAAAA
*
47388 CTAAACAAAAAGAAAAAGA-AAAA
1 -T-AAGAAAAAG-AAAAGATAAAA
*
47411 TAACGAAAAAGAAAAGATAAAGG
1 TAA-GAAAAAGAAAAGATAAA-A
47434 TAAGAAA
1 TAAGAAA
47441 TTCTTGGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
21 9 0.21
22 21 0.50
23 11 0.26
24 1 0.02
ACGTcount: A:0.74, C:0.04, G:0.12, T:0.10
Consensus pattern (21 bp):
TAAGAAAAAGAAAAGATAAAA
Found at i:48122 original size:30 final size:30
Alignment explanation
Indices: 48086--48151 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
48076 CCATCGCATG
*
48086 GGCCATCGGATGGAG-CAACCGGCCACAACC
1 GGCCATCGCATGG-GCCAACCGGCCACAACC
* *
48116 GGCCATCGCATGGGCCATCCGGGCACAACC
1 GGCCATCGCATGGGCCAACCGGCCACAACC
48146 GGCCAT
1 GGCCAT
48152 TTGACCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.09
Consensus pattern (30 bp):
GGCCATCGCATGGGCCAACCGGCCACAACC
Done.