Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006158.1 Corchorus capsularis cultivar CVL-1 contig06176, 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: 38495
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:6505 original size:21 final size:22
Alignment explanation
Indices: 6480--6521 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6470 TAAAATTTTC
6480 TTTTGCATTGGAGTTC-ATTAT
1 TTTTGCATTGGAGTTCTATTAT
*
6501 TTTTGTATTGGAGTTCTATTA
1 TTTTGCATTGGAGTTCTATTA
6522 GCACATTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (22 bp):
TTTTGCATTGGAGTTCTATTAT
Found at i:15475 original size:14 final size:14
Alignment explanation
Indices: 15436--15477 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
15426 TTGAATTATC
*
15436 AAGAGTTTAAAAAA
1 AAGAGTTCAAAAAA
*
15450 AA-TGTTCTAAAAAA
1 AAGAGTTC-AAAAAA
15464 AAGAGTTCAAAAAA
1 AAGAGTTCAAAAAA
15478 TTATCAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (14 bp):
AAGAGTTCAAAAAA
Found at i:19236 original size:2 final size:2
Alignment explanation
Indices: 19229--19260 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19219 GTTACATCTA
*
19229 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19261 TCATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19289 original size:14 final size:14
Alignment explanation
Indices: 19262--19299 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
19252 GATATATATT
19262 CATAAAAAAT-TAA
1 CATAAAAAATATAA
19275 CATAAAAAATATAA
1 CATAAAAAATATAA
*
19289 CTTAAAAAATA
1 CATAAAAAATA
19300 AAAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (14 bp):
CATAAAAAATATAA
Found at i:22724 original size:27 final size:27
Alignment explanation
Indices: 22666--22717 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
22656 CAGTTTAATG
** * *
22666 TAGTTTGGTGTTGTTAAGGAGTATGAA
1 TAGTTTGGTAATGTAAAGGAGTAGGAA
22693 TAGTTTGGTAATGTAAAGGAGTAGG
1 TAGTTTGGTAATGTAAAGGAGTAGG
22718 GAAAGTTGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (27 bp):
TAGTTTGGTAATGTAAAGGAGTAGGAA
Found at i:25248 original size:20 final size:20
Alignment explanation
Indices: 25223--25263 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25213 TGAAGATGTC
25223 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
25243 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
25263 T
1 T
25264 CAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:25259 original size:73 final size:73
Alignment explanation
Indices: 25170--25316 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
25160 ATGAGATGTC
25170 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCTTAAAAACCCAC
1 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCTTAAAAACCCAC
25235 TTAACATA
66 TTAACATA
25243 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCTTAAAAACCCAC
1 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCTTAAAAACCCAC
25308 TTAACATA
66 TTAACATA
25316 T
1 T
25317 CAATAATTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (73 bp):
TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCTTAAAAACCCAC
TTAACATA
Found at i:25323 original size:53 final size:53
Alignment explanation
Indices: 25243--25369 Score: 254
Period size: 53 Copynumber: 2.4 Consensus size: 53
25233 ACTTAACATA
25243 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
1 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
25296 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
1 TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
25349 TTAAAAACCCACTTAACATAT
1 TTAAAAACCCACTTAACATAT
25370 TAAAAACCCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (53 bp):
TTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
Found at i:25372 original size:126 final size:125
Alignment explanation
Indices: 25159--25408 Score: 491
Period size: 126 Copynumber: 2.0 Consensus size: 125
25149 GGGTTACCAA
25159 AATGAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCT
1 AATGAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCT
25224 TAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT
66 TAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT
25284 AATGAAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
1 AATG-AGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTC
25349 TTAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCT
65 TTAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCT
25409 CAAATTACTG
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 4 0.03
126 120 0.97
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (125 bp):
AATGAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTTAATGAAGATGTCT
TAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT
Found at i:25374 original size:20 final size:20
Alignment explanation
Indices: 25349--25389 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25339 TGAAGATGTC
25349 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
25369 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
25389 T
1 T
25390 CAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:28290 original size:87 final size:87
Alignment explanation
Indices: 28176--28365 Score: 310
Period size: 87 Copynumber: 2.2 Consensus size: 87
28166 TTTGAAATGG
*
28176 CAATTCTGGTTCTAAAGAAATTGGAACTGAACCTTAACCTTTAAGTAGAGCTTCCGGTTATGGTT
1 CAATTCTGGTTCTAAAGAAATTGGAACTGAACCTTAACCTTTAAGTAGAGCTTCCGGTTACGGTT
28241 CCAGAACC-AGCGGTTCTCAGTT
66 CCAGAACCGA-CGGTTCTCAGTT
* *
28263 CGATTCTGGTTCTAAAGAAATTTGAACTGAACCTTAACCTTTAAGTAGAGCTTCCGGTTACGGTT
1 CAATTCTGGTTCTAAAGAAATTGGAACTGAACCTTAACCTTTAAGTAGAGCTTCCGGTTACGGTT
* * *
28328 GCAGAACCGATGGTTCTCGGTT
66 CCAGAACCGACGGTTCTCAGTT
28350 CAATTCTGGTTCTAAA
1 CAATTCTGGTTCTAAA
28366 TTGGAACCTT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 94 0.99
88 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (87 bp):
CAATTCTGGTTCTAAAGAAATTGGAACTGAACCTTAACCTTTAAGTAGAGCTTCCGGTTACGGTT
CCAGAACCGACGGTTCTCAGTT
Found at i:31450 original size:107 final size:109
Alignment explanation
Indices: 31328--31530 Score: 340
Period size: 109 Copynumber: 1.9 Consensus size: 109
31318 AGAATGTAAA
* *
31328 AATTAATTAACAATAT-CTT-TATCAATTTTTTTGTTTT-TGTTTTTTCGAATATCTCAGCCTTA
1 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCT-TTTTTTCGAATATCCCAGCCTTA
*
31390 TAATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
65 AAATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
31435 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTTTCGAATATCCCAGCCTTAA
1 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTTTCGAATATCCCAGCCTTAA
*
31500 AATTTATAATGTAAAGTTGGATTATTTTGTT
66 AATTTATAATGTAAAGTCGGATTATTTTGTT
31531 GACTAATAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
107 16 0.18
108 3 0.03
109 69 0.78
110 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (109 bp):
AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTTTCGAATATCCCAGCCTTAA
AATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
Found at i:33011 original size:22 final size:22
Alignment explanation
Indices: 32993--33036 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
32983 AAATTAATTT
32993 TTAATTAATTAGTATTTAATTAC
1 TTAATTAATTAGT-TTTAATTAC
* *
33016 TTAGTTTATTAGTTTTAATTA
1 TTAATTAATTAGTTTTAATTA
33037 GTTAGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAATTAATTAGTTTTAATTAC
Found at i:33041 original size:22 final size:23
Alignment explanation
Indices: 33000--33046 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
32990 TTTTTAATTA
33000 ATTAGTATTTAATTACTTAGTTT
1 ATTAGTATTTAATTACTTAGTTT
*
33023 ATTAGT-TTTAATTAGTTAGTTT
1 ATTAGTATTTAATTACTTAGTTT
33045 AT
1 AT
33047 GATTAACTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
ATTAGTATTTAATTACTTAGTTT
Found at i:33432 original size:160 final size:161
Alignment explanation
Indices: 33255--33576 Score: 585
Period size: 160 Copynumber: 2.0 Consensus size: 161
33245 AGTGTCAAAA
*
33255 ATTATAAAACGAGGGGGGGAGGCGGTATTTAGCAAAAGGGGGATAGTGAATAACAAACCCCAG-G
1 ATTATAAAACGAGGGGGGGAGGCGGTATTTAGCAAAAGGGGGACAGTGAATAACAAA-CCCAGAG
33319 TGAATAACAAACCCCTTTTTTTT-AGATAATGTATGATATAATATCTTATCATAGATGTAGGTTT
65 TGAATAACAAACCCCTTTTTTTTGAGATAATGTATGATATAATATCTTATCATAGATGTAGGTTT
33383 GAAACCGTCATTCATCATTCACCAAATAAAGG
130 GAAACCGTCATTCATCATTCACCAAATAAAGG
**
33415 ATTATAAAACGAGGGGGGGAGGCGGTATTTAGCAAAAGGGGGACAGTGAATAACAAACCTGGAGT
1 ATTATAAAACGAGGGGGGGAGGCGGTATTTAGCAAAAGGGGGACAGTGAATAACAAACCCAGAGT
*
33480 GAATAACAAACCCCTTTTTTTTGAGATAATGTATGATATAATATCTTATCTTAGATGTAGGTTTG
66 GAATAACAAACCCCTTTTTTTTGAGATAATGTATGATATAATATCTTATCATAGATGTAGGTTTG
33545 AAACCGTCATTCATCATTCACCAAATAAAGG
131 AAACCGTCATTCATCATTCACCAAATAAAGG
33576 A
1 A
33577 ATAGGAAAAA
Statistics
Matches: 156, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
159 3 0.02
160 80 0.51
161 73 0.47
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (161 bp):
ATTATAAAACGAGGGGGGGAGGCGGTATTTAGCAAAAGGGGGACAGTGAATAACAAACCCAGAGT
GAATAACAAACCCCTTTTTTTTGAGATAATGTATGATATAATATCTTATCATAGATGTAGGTTTG
AAACCGTCATTCATCATTCACCAAATAAAGG
Found at i:33999 original size:26 final size:25
Alignment explanation
Indices: 33968--34028 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
33958 TTTAAATAAT
33968 AATTAAACAAT-ATTAAAAAAGTAAAA
1 AATTAAA-AATAATTAAAAAA-TAAAA
* *
33994 AATTAAAAATAATTTAAAAATAGAA
1 AATTAAAAATAATTAAAAAATAAAA
34019 AATTACAAAA
1 AATTA-AAAA
34029 GGGACCCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (25 bp):
AATTAAAAATAATTAAAAAATAAAA
Found at i:34865 original size:17 final size:17
Alignment explanation
Indices: 34817--34870 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
34807 TTTGTAATTT
* *
34817 TTATTTTTAAATTATTC
1 TTATTTTTTAATTATTA
34834 TTACTTTTTTATTAATTATTA
1 TTA---TTTT-TTAATTATTA
34855 TTATTTTTTAATTATT
1 TTATTTTTTAATTATT
34871 TAGATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 12 0.39
18 4 0.13
20 4 0.13
21 11 0.35
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTTTAATTATTA
Found at i:34868 original size:21 final size:21
Alignment explanation
Indices: 34826--34864 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34816 TTTATTTTTA
*
34826 AATTATTCTTACTTTTTTATT
1 AATTATTATTACTTTTTTATT
34847 AATTATTATTA-TTTTTTA
1 AATTATTATTACTTTTTTA
34865 ATTATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
AATTATTATTACTTTTTTATT
Found at i:38350 original size:2 final size:2
Alignment explanation
Indices: 38343--38376 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38333 TACTAACTTG
38343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38377 GTATTTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.