Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015811.1 Corchorus capsularis cultivar CVL-1 contig15832, 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: 18623
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:8402 original size:16 final size:16
Alignment explanation
Indices: 8383--8457 Score: 116
Period size: 16 Copynumber: 4.7 Consensus size: 16
8373 TGGGTTCGGG
8383 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
8399 CGGGTTCGGG-ATTTTT
1 CGGGTTCGGGTA-TTTT
*
8415 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTT
*
8431 CGGGTTCTGGTATTTT
1 CGGGTTCGGGTATTTT
8447 CGGGTTCGGGT
1 CGGGTTCGGGT
8458 TCGGGTCCGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.02
16 52 0.98
ACGTcount: A:0.04, C:0.13, G:0.39, T:0.44
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:8456 original size:6 final size:6
Alignment explanation
Indices: 8445--8483 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
8435 TTCTGGTATT
*
8445 TTCGGG TTCGGG TTCGGG TCCGGG -TCGGG TTCGGG TTCG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCG
8484 CTTTCGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.00, C:0.21, G:0.49, T:0.31
Consensus pattern (6 bp):
TTCGGG
Found at i:8474 original size:17 final size:18
Alignment explanation
Indices: 8447--8480 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
8437 CTGGTATTTT
8447 CGGGTTCGGGTTCGGGTC
1 CGGGTTCGGGTTCGGGTC
8465 CGGG-TCGGGTTCGGGT
1 CGGGTTCGGGTTCGGGT
8481 TCGCTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (18 bp):
CGGGTTCGGGTTCGGGTC
Found at i:9268 original size:16 final size:16
Alignment explanation
Indices: 9247--9289 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
9237 AGGTTCGGGT
9247 TCGGGTTCGGGT-TGTC
1 TCGGGTTCGGGTAT-TC
*
9263 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTC
9279 TCGGGTTCGGG
1 TCGGGTTCGGG
9290 ACGTTGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.02, C:0.16, G:0.44, T:0.37
Consensus pattern (16 bp):
TCGGGTTCGGGTATTC
Found at i:9289 original size:6 final size:6
Alignment explanation
Indices: 9224--9259 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
9214 TATTTTGATC
*
9224 TCGGGT TCGGG- TCAGGT TCGGGT TCGGGT TCGGGT T
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT T
9260 GTCTCGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.03, C:0.17, G:0.47, T:0.33
Consensus pattern (6 bp):
TCGGGT
Found at i:14326 original size:70 final size:69
Alignment explanation
Indices: 14071--14564 Score: 597
Period size: 70 Copynumber: 7.2 Consensus size: 69
14061 AATGAACTTA
* * * * * * *
14071 GCTTATGGAAAAG-CCCT--TGCTTGGAGGGAACCAAGGC-TAAACTAACTCATATGGAAACGAA
1 GCTTGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAG
14132 TTTG
66 TTTG
* * * * * * **
14136 GCTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGC-TAAATTGACTCGGGTGGAAACGAG
1 GCTTGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAG
14200 TTTG
66 TTTG
* *
14204 GCTTGTGGAAAAGCTCCTGATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAG
1 GCTTGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAG
14269 TTTG
66 TTTG
* *
14273 GCTAGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAACTTGAACTGACTCGTATGGAAACGA
1 GCTTGTGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGA
14338 GTTTG
65 GTTTG
* * *
14343 GCTTGTGGAAAAGCCCCTAAATGTTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAATGA
1 GCTTGTGGAAAAGCCCCT-GATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGA
14408 GTTTG
65 GTTTG
* * * *
14413 GCTTGTGGAAAAGCCTCTGTTGCTTGGATGAAACCAAAGCTTGATCT-ACCTCGTATGGAAACGA
1 GCTTGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGA
14477 GTTTG
65 GTTTG
* * * *
14482 GCTTGTGGAAAAGCCCTTGAATGCTTGGGTGGAACCAAAGTTTGAGCT-ACCTCGTATGGAAACG
1 GCTTGTGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACG
*
14546 AGCTTG
64 AGTTTG
* *
14552 ACTTATGGAAAAG
1 GCTTGTGGAAAAG
14565 TCGAAGCATT
Statistics
Matches: 377, Mismatches: 44, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
65 11 0.03
66 3 0.01
68 78 0.21
69 101 0.27
70 184 0.49
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (69 bp):
GCTTGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAG
TTTG
Found at i:14352 original size:139 final size:137
Alignment explanation
Indices: 14071--14564 Score: 597
Period size: 139 Copynumber: 3.6 Consensus size: 137
14061 AATGAACTTA
* * * * * * *
14071 GCTTATGGAAAAGCCCT--TGCTTGGAGGGAACCAAGGC-TAAACTAACTCATATGGAAACGAAT
1 GCTTGTGGAAAAGCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGT
* * * * * **
14133 TTGGCTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGC-TAAATTGACTCGGGTGGAAAC
66 TTGGCTAGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
14197 GAGTTTG
131 GAGTTTG
*
14204 GCTTGTGGAAAAGCTCCTGATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAG
1 GCTTGTGGAAAAGC-CCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAG
*
14269 TTTGGCTAGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAACTTGAACTGACTCGTATGGAA
65 TTTGGCTAGTGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAA
14334 ACGAGTTTG
129 ACGAGTTTG
* * *
14343 GCTTGTGGAAAAGCCCCTAAATGTTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAATGA
1 GCTTGTGGAAAAG-CCCT-GATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGA
* * * * *
14408 GTTTGGCTTGTGGAAAAGCCTCTGTTGCTTGGATGAAACCAAAGCTTGATCT-ACCTCGTATGGA
64 GTTTGGCTAGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGA
14472 AACGAGTTTG
128 AACGAGTTTG
* * *
14482 GCTTGTGGAAAAGCCCTTGAATGCTTGGGTGGAACCAAAGTTTGAGCT-ACCTCGTATGGAAACG
1 GCTTGTGGAAAAGCCC-TG-ATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACG
* *
14546 AGCTTGACTTA-TGGAAAAG
63 AGTTTGGC-TAGTGGAAAAG
14565 TCGAAGCATT
Statistics
Matches: 315, Mismatches: 33, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
133 13 0.04
134 3 0.01
136 19 0.06
137 42 0.13
138 23 0.07
139 149 0.47
140 66 0.21
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (137 bp):
GCTTGTGGAAAAGCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGT
TTGGCTAGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
GAGTTTG
Found at i:14439 original size:209 final size:206
Alignment explanation
Indices: 14088--14564 Score: 609
Period size: 209 Copynumber: 2.3 Consensus size: 206
14078 GAAAAGCCCT
* * * * * *
14088 TGCTTGGAGGGAACCAAGGC-TAAACTAACTCATATGGAAACGAATTTGGCTAGTGGAAAAGCCC
1 TGCTTGGATGGAACCAAAGCTTGAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
*** * * *
14152 TTGCTGCTTGGATGGAACCAAGGCTAAATTGACTCGGGTGGAAACGAGTTTGGCTTGTGGAAAAG
65 TAAATGCTTGGATGGAACCAAAGCTAAACTGACTCGGATGGAAACGAGTTTGGCTTGTGGAAAAG
* *
14217 CTCCTGATGCTTGGATGGAACCAAGGCTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTAGTGG
130 CTCCTGATGCTTGGATGAAACCAAAGCTTGAACT-ACCTCGTATGGAAACGAGTTTGGCTAGTGG
14281 AAAAGCCCCTGAA
194 AAAAGCCCCTGAA
*
14294 TGCTTGGATGGAACCAAAACTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 TGCTTGGATGGAACCAAAGCTTGAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CC
* * * *
14359 CTAAATGTTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAATGAGTTTGGCTTGTGGAAA
64 CTAAATGCTTGGATGGAACCAAAGC-TAAACTGACTCGGATGGAAACGAGTTTGGCTTGTGGAAA
* * *
14424 AGC-CTCTGTTGCTTGGATGAAACCAAAGCTTGATCTACCTCGTATGGAAACGAGTTTGGCTTGT
128 AGCTC-CTGATGCTTGGATGAAACCAAAGCTTGAACTACCTCGTATGGAAACGAGTTTGGCTAGT
*
14488 GGAAAAGCCCTTGAA
192 GGAAAAGCCCCTGAA
* * * * * *
14503 TGCTTGGGTGGAACCAAAGTTTGAGCTACCTCGTATGGAAACGAGCTTGACTTATGGAAAAG
1 TGCTTGGATGGAACCAAAGCTTGAACTA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
14565 TCGAAGCATT
Statistics
Matches: 234, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
206 17 0.07
207 36 0.15
208 25 0.11
209 156 0.67
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (206 bp):
TGCTTGGATGGAACCAAAGCTTGAACTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCT
AAATGCTTGGATGGAACCAAAGCTAAACTGACTCGGATGGAAACGAGTTTGGCTTGTGGAAAAGC
TCCTGATGCTTGGATGAAACCAAAGCTTGAACTACCTCGTATGGAAACGAGTTTGGCTAGTGGAA
AAGCCCCTGAA
Found at i:15177 original size:35 final size:35
Alignment explanation
Indices: 15126--15192 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
15116 GTTCAGTTAA
* *
15126 TTGATCCAGGGCGATCTTTCTTCAGTGAATTTGGG
1 TTGATCCAGGGCGATCTCTCTACAGTGAATTTGGG
* *
15161 TTGATCTAGGGTGATCTCTCTACAGTGAATTT
1 TTGATCCAGGGCGATCTCTCTACAGTGAATTT
15193 AAACAGACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.39
Consensus pattern (35 bp):
TTGATCCAGGGCGATCTCTCTACAGTGAATTTGGG
Found at i:15486 original size:36 final size:36
Alignment explanation
Indices: 15341--15512 Score: 136
Period size: 36 Copynumber: 4.8 Consensus size: 36
15331 TCAATGCTTC
* * *
15341 AATGACCCAGGGTGGTCTTTTCTTCAGTTTAGTTCGA
1 AATGATCCAGGGTGGTC-TTTCTTCAGTTCAGTTCGG
* * * * *
15378 AATGATCGAGGGTGGTCGTTT-TTTAGTTTATTTCAG
1 AATGATCCAGGGTGGTC-TTTCTTCAGTTCAGTTCGG
* * * *
15414 -TTGACCCAGGGTGGTCTTTCTTCGGTTTGC-G-CCGG
1 AATGATCCAGGGTGGTCTTTCTTCAG-TT-CAGTTCGG
* *
15449 AATGATCGAGGGTGGTCATTCTTCAGTTCAGTTCGG
1 AATGATCCAGGGTGGTCTTTCTTCAGTTCAGTTCGG
* *
15485 AATGATCCAGGGTGGTTTTTCTCCAGTT
1 AATGATCCAGGGTGGTCTTTCTTCAGTT
15513 ATTTATTTTA
Statistics
Matches: 103, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
34 4 0.04
35 21 0.20
36 60 0.58
37 18 0.17
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.38
Consensus pattern (36 bp):
AATGATCCAGGGTGGTCTTTCTTCAGTTCAGTTCGG
Found at i:15496 original size:72 final size:72
Alignment explanation
Indices: 15341--15512 Score: 186
Period size: 71 Copynumber: 2.4 Consensus size: 72
15331 TCAATGCTTC
** * * *
15341 AATGACCCAGGGTGGTCTTTTCTTCAGTTTAGTTCGAAATGATCGAGGGTGGTCGTTTTTTAGTT
1 AATGACCCAGGGTGGTC-TTTCTTCAGTTTAGGCCGAAATGATCGAGGGTGGTCATTCTTCAGTT
* *
15406 TATTTCAG
65 CAGTTCAG
* * *
15414 -TTGACCCAGGGTGGTCTTTCTTCGGTTT-GCGCCGGAATGATCGAGGGTGGTCATTCTTCAGTT
1 AATGACCCAGGGTGGTCTTTCTTCAGTTTAG-GCCGAAATGATCGAGGGTGGTCATTCTTCAGTT
*
15477 CAGTTCGG
65 CAGTTCAG
* * *
15485 AATGATCCAGGGTGGTTTTTCTCCAGTT
1 AATGACCCAGGGTGGTCTTTCTTCAGTT
15513 ATTTATTTTA
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
70 1 0.01
71 43 0.53
72 37 0.46
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.38
Consensus pattern (72 bp):
AATGACCCAGGGTGGTCTTTCTTCAGTTTAGGCCGAAATGATCGAGGGTGGTCATTCTTCAGTTC
AGTTCAG
Found at i:18358 original size:21 final size:20
Alignment explanation
Indices: 18319--18358 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18309 ATTTATATAT
*
18319 AAAGATTGATTTTTTAAGTA
1 AAAGATTGATTTTTAAAGTA
18339 AAAGATTGAATTTTTAAAGT
1 AAAGATTG-ATTTTTAAAGT
18359 GATTTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (20 bp):
AAAGATTGATTTTTAAAGTA
Found at i:18384 original size:51 final size:49
Alignment explanation
Indices: 18300--18615 Score: 251
Period size: 51 Copynumber: 6.3 Consensus size: 49
18290 AAGTTTAAGC
* * *
18300 TTTTAAGTAATTTATATATAAAGATTGATTTTTTAAGTAAAAGATTGAAT
1 TTTTAAGTAATTTGTAAATAAAG-TTGAATTTTTAAGTAAAAGATTGAAT
* * * * *
18350 TTTTAAAGTGATTTGTAAATAAAAGTGGGATTTTTAATTAGAAGA-TGAAT
1 TTTT-AAGTAATTTGTAAAT-AAAGTTGAATTTTTAAGTAAAAGATTGAAT
** * * * *
18400 CTTGCAAGTAATTTGTAAATAGAGTTGAATTTTTAATTGAAAGATT-AAGC
1 -TTTTAAGTAATTTGTAAATAAAGTTGAATTTTTAAGTAAAAGATTGAA-T
* *
18450 TTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAAGTGAAAGATTAAAT
1 TTTTAAGTAATTTGTAAATAAAG-TTGAATTTTTAAGTAAAAGATTGAAT
* * * *
18500 CTTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAATTGAAAGATT-AAGC
1 -TTTTAAGTAATTTGTAAATAAAG-TTGAATTTTTAAGTAAAAGATTGAA-T
* ** * * * * *
18551 TTTTAAGTATGTTTGTAAATAAAAAATGTAATCTTTGATTAAAATATTGAAC
1 TTTTAAGTA-ATTTGTAAAT-AAAGTTG-AATTTTTAAGTAAAAGATTGAAT
18603 TTTTAAGTAATTT
1 TTTTAAGTAATTT
18616 TTGTAAAT
Statistics
Matches: 219, Mismatches: 34, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
49 41 0.19
50 56 0.26
51 88 0.40
52 32 0.15
53 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.42
Consensus pattern (49 bp):
TTTTAAGTAATTTGTAAATAAAGTTGAATTTTTAAGTAAAAGATTGAAT
Found at i:18484 original size:30 final size:29
Alignment explanation
Indices: 18450--18536 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 29
18440 AAGATTAAGC
18450 TTTTAAGTAATTTGTAAATAAAGATTGAAT
1 TTTTAAGTAATTTGT-AATAAAGATTGAAT
*
18480 TTTTAAG-----TG----AAAGATTAAAT
1 TTTTAAGTAATTTGTAATAAAGATTGAAT
18500 CTTTTAAGTAATTTGTGAATAAAGATTGAAT
1 -TTTTAAGTAATTTGT-AATAAAGATTGAAT
18531 TTTTAA
1 TTTTAA
18537 TTGAAAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 22
0.65 0.03 0.32
Matches are distributed among these distances:
20 10 0.23
21 7 0.16
25 2 0.05
26 2 0.05
30 13 0.30
31 10 0.23
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTTAAGTAATTTGTAATAAAGATTGAAT
Found at i:18494 original size:20 final size:21
Alignment explanation
Indices: 18469--18508 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
18459 ATTTGTAAAT
*
18469 AAAGATTGAAT-TTTTAAGTG
1 AAAGATTAAATCTTTTAAGTG
18489 AAAGATTAAATCTTTTAAGT
1 AAAGATTAAATCTTTTAAGT
18509 AATTTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (21 bp):
AAAGATTAAATCTTTTAAGTG
Done.