Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008894.1 Corchorus capsularis cultivar CVL-1 contig08915, 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: 59395
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 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 A
28 CTAGTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2279 original size:16 final size:17
Alignment explanation
Indices: 2246--2288 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
2236 TATTTTGATC
*
2246 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGGTCGGGT
2263 TCGGGTTCGGG-CGGGT
1 TCGGGTTCGGGTCGGGT
2279 TCGGGTTCGG
1 TCGGGTTCGG
2289 ATTGTCTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGTCGGGT
Found at i:2314 original size:16 final size:17
Alignment explanation
Indices: 2277--2322 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
2267 GTTCGGGCGG
2277 GTTCGGGTTC-GG-ATT
1 GTTCGGGTTCGGGTATT
2292 GTCTCGGGTTCGGGTATT
1 GT-TCGGGTTCGGGTATT
2310 -TTCGGGTTCGGGT
1 GTTCGGGTTCGGGT
2323 TCGGACGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.07
16 20 0.71
17 3 0.11
18 3 0.11
ACGTcount: A:0.04, C:0.15, G:0.41, T:0.39
Consensus pattern (17 bp):
GTTCGGGTTCGGGTATT
Found at i:2337 original size:6 final size:6
Alignment explanation
Indices: 2246--2326 Score: 60
Period size: 6 Copynumber: 12.7 Consensus size: 6
2236 TATTTTGATC
*
2246 TCGGGC TCGGG- TCGGGT TCGGGT TCGGG- -CGGGT TCGGGT TCGGATTGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGG---GT
2294 CTCGGGT TCGGGTATTT TCGGGT TCGGGT TCGG
1 -TCGGGT TCGGG----T TCGGGT TCGGGT TCGG
2327 ACGGGTTCGG
Statistics
Matches: 64, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
4 4 0.06
5 5 0.08
6 41 0.64
7 2 0.03
9 2 0.03
10 10 0.16
ACGTcount: A:0.02, C:0.19, G:0.47, T:0.32
Consensus pattern (6 bp):
TCGGGT
Found at i:13680 original size:18 final size:18
Alignment explanation
Indices: 13651--13690 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13641 TTCCAGTACT
*
13651 AGTTATTAATTTTCCTCAC
1 AGTTATTAATTTTACTC-C
13670 AGTTA-TAATTTTACTCC
1 AGTTATTAATTTTACTCC
13687 AGTT
1 AGTT
13691 TTACATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (18 bp):
AGTTATTAATTTTACTCC
Found at i:19832 original size:69 final size:70
Alignment explanation
Indices: 19752--19961 Score: 251
Period size: 69 Copynumber: 2.9 Consensus size: 70
19742 TCAGAAATTC
19752 TTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTAAAATGTTTCTTTCTGAA
1 TTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTAAAATGTTTCTTTCTGAA
19817 -ATAT
66 TATAT
* *** *
19821 TTGAAAACAACAAAAGCATTTAGCAAGACATGACAAGATTTGAGAGTACAATGTTTCTTTCCAAA
1 TTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTAAAATGTTTC--T-----
19886 ATATCTGAATATAT
59 -T-TCTGAATATAT
* * *
19900 TTGAATCCAACAAAAGCATTTAGCAAGACATGACAAGAAAATAGAGTAAAAAAGTTTCTTTC
1 TTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGT-AAAATGTTTCTTTC
19962 CAAGAAAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
69 52 0.44
71 3 0.03
72 1 0.01
77 1 0.01
78 7 0.06
79 45 0.38
80 8 0.07
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (70 bp):
TTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTAAAATGTTTCTTTCTGAA
TATAT
Found at i:22221 original size:13 final size:15
Alignment explanation
Indices: 22185--22223 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
22175 GTAGATTTTG
22185 TTTTAATTTTTGTTA
1 TTTTAATTTTTGTTA
22200 TTATTAATTTTT-TTA
1 TT-TTAATTTTTGTTA
22215 -TTTAATTTT
1 TTTTAATTTT
22224 AGCACATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 5 0.22
16 9 0.39
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTAATTTTTGTTA
Found at i:33413 original size:3 final size:3
Alignment explanation
Indices: 33405--33436 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
33395 TGTCTTGGCA
*
33405 GCC GCC GCC GCC GCC GCC GCC GCC GCC ACC GC
1 GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GC
33437 TGGCACATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.66, G:0.31, T:0.00
Consensus pattern (3 bp):
GCC
Found at i:37209 original size:62 final size:60
Alignment explanation
Indices: 37010--37209 Score: 240
Period size: 60 Copynumber: 3.3 Consensus size: 60
37000 AACGTTTGTT
* * * **
37010 AAAATGCTTAAATAAGGG-TCCGATTTTTTAATTTGCCCAAATAAGGGCCTAATATAATCA
1 AAAATGCTCAAATAAGGGCT-CGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTAATCA
* * *
37070 AAAATGCTCAAATAAGGGCTCGATCTTTTAATTTAGCCAAATAAGAGCCTAACGTGATCA
1 AAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTAATCA
** * * *
37130 AAAATGCTCAAATAAGGGCTTTATCTTTTAATCTGGCCAAATAAAAGGGCCTAACGTTATCG
1 AAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCCAAAT--AAGGGCCTAACGTAATCA
*
37192 AAAATACTCAAATAAGGG
1 AAAATGCTCAAATAAGGG
37210 TCTGACGTCA
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
60 88 0.73
61 1 0.01
62 32 0.26
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTAATCA
Found at i:37360 original size:58 final size:57
Alignment explanation
Indices: 37253--37366 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 57
37243 TTGATGTTAG
* * **
37253 GCCCTTATTTGAACATTTTGGCAAATGTTAGCCCTTATTTGGCCAAATTAAAAGATCA
1 GCCCTTATTTGAACATTTTGACAAACGTTAGCCCTTATTTGAACAAATT-AAAGATCA
**
37311 GCCCTTATTTGAGTATTTTGACAAACGTTAGACCCTTATTTGAAC-AATTAAAGATC
1 GCCCTTATTTGAACATTTTGACAAACGTTAG-CCCTTATTTGAACAAATTAAAGATC
37367 TAATAAGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
57 7 0.14
58 31 0.63
59 11 0.22
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (57 bp):
GCCCTTATTTGAACATTTTGACAAACGTTAGCCCTTATTTGAACAAATTAAAGATCA
Found at i:37584 original size:60 final size:61
Alignment explanation
Indices: 37520--37660 Score: 198
Period size: 60 Copynumber: 2.3 Consensus size: 61
37510 AACGTTTGTT
* * * *
37520 AAAATGCTTAAATAAGGGTC-CGATTTTTTAATTT-GCCCAAATAAGGGCCTAATATAATCA
1 AAAATGCTCAAATAAGGGTCTCGATCTTTTAATTTAG-CCAAATAAGAGCCTAACATAATCA
* *
37580 AAAATGCTCAAATAAGGG-CTCGATCTTTTAATTTAGCCAAATAAGAGCCTAACGTGATCA
1 AAAATGCTCAAATAAGGGTCTCGATCTTTTAATTTAGCCAAATAAGAGCCTAACATAATCA
37640 AAAATGCTCAAATAAGGGTCT
1 AAAATGCTCAAATAAGGGTCT
37661 GACGTCAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
59 1 0.01
60 68 0.94
61 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (61 bp):
AAAATGCTCAAATAAGGGTCTCGATCTTTTAATTTAGCCAAATAAGAGCCTAACATAATCA
Found at i:40068 original size:376 final size:375
Alignment explanation
Indices: 39344--40094 Score: 1369
Period size: 376 Copynumber: 2.0 Consensus size: 375
39334 TTAATTAGAC
*
39344 ACCCGAATAAGCTTAGTCGGACAAATAGAACAAAAAAAAAAAGCTTAAGCGTTAAATCGATTAAG
1 ACCCGAATAAGCTTAGTCGGACAAATAAAACAAAAAAAAAAAGCTTAAGCGTTAAATCGATTAAG
* * *
39409 ATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATT
66 ATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTAATAAATAATC
*
39474 CAAATAAGAAAATGTTTGTTGATTGAAATATAAAAATTTCCTTTTGAACCCTTAATAAAACCCGT
131 CAAATAAGAAAATGTTTGTTGATTGAAACATAAAAATTTCCTTTTGAACCCTTAATAAAACCCGT
39539 AGATCAAATCTAGTTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAAACCGA
196 AGATCAAATCTAGTTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAAACCGA
*
39604 CACTTGAATAACATTAATCGAACATGTGGTTCGAAAATTATATGATATATTAAATAGAACGGCAA
261 CACTTGAATAACATTAATCGAACATGTGGTTCGAAAATTATATGATATATTAAATAGAACGACAA
*
39669 TCAAAATCACTAATTTCGGAAGTATGTTTTTGAATTGATACATACAAATT
326 TCAAAATCACTAATTTCGGAAGTATGTTTTTGAATTGATACATAAAAATT
39719 ACCCGAATCAA-CTTAGTCGGACAAATAAAACAAAAAAAATAAAGCTTAAGCGTTAAATCGATTA
1 ACCCGAAT-AAGCTTAGTCGGACAAATAAAACAAAAAAAA-AAAGCTTAAGCGTTAAATCGATTA
*
39783 AGATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGTTCATTTAATAAATAA
64 AGATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTAATAAATAA
*
39848 TCCAAATAAGAAAATGTTTGTTGATTGAAACATAAAAATTTCCTTTTGAACCCTTAATCAAACCC
129 TCCAAATAAGAAAATGTTTGTTGATTGAAACATAAAAATTTCCTTTTGAACCCTTAATAAAACCC
*
39913 GTAGATCAAATTTAGTTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAAACC
194 GTAGATCAAATCTAGTTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAAACC
*
39978 GACACTTGAATAACATTAATCGAATATGTGGTTCGAAAATTATATGATATATTAAATAGAACGAC
259 GACACTTGAATAACATTAATCGAACATGTGGTTCGAAAATTATATGATATATTAAATAGAACGAC
*
40043 AATCAAAATCACTAATTTCGGAAGTATTTTTTTGAATTGATACATAAAAATT
324 AATCAAAATCACTAATTTCGGAAGTATGTTTTTGAATTGATACATAAAAATT
40095 GGCTTTTGAT
Statistics
Matches: 362, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
375 35 0.10
376 327 0.90
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (375 bp):
ACCCGAATAAGCTTAGTCGGACAAATAAAACAAAAAAAAAAAGCTTAAGCGTTAAATCGATTAAG
ATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTAATAAATAATC
CAAATAAGAAAATGTTTGTTGATTGAAACATAAAAATTTCCTTTTGAACCCTTAATAAAACCCGT
AGATCAAATCTAGTTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAAACCGA
CACTTGAATAACATTAATCGAACATGTGGTTCGAAAATTATATGATATATTAAATAGAACGACAA
TCAAAATCACTAATTTCGGAAGTATGTTTTTGAATTGATACATAAAAATT
Found at i:43269 original size:14 final size:15
Alignment explanation
Indices: 43252--43281 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
43242 AATGTCTTCC
43252 TTTTTTTTTC-TTTT
1 TTTTTTTTTCATTTT
43266 TTTTTTTTTCATTTT
1 TTTTTTTTTCATTTT
43281 T
1 T
43282 CATTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTCATTTT
Found at i:46360 original size:14 final size:13
Alignment explanation
Indices: 46340--46376 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
46330 TTTTTGAGGA
46340 AATATATATATGT
1 AATATATATATGT
46353 ATATATATATATGT
1 A-ATATATATATGT
46367 AATATA-ATAT
1 AATATATATAT
46377 AATTTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (13 bp):
AATATATATATGT
Found at i:59084 original size:20 final size:21
Alignment explanation
Indices: 59056--59101 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
59046 TTATTTTCCA
*
59056 TTAACAAATTACTTAAC-CCG
1 TTAATAAATTACTTAACACCG
59076 TTAATAAATTACTTAACACCG
1 TTAATAAATTACTTAACACCG
59097 TTAAT
1 TTAAT
59102 TTTACCCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (21 bp):
TTAATAAATTACTTAACACCG
Done.