Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013161.1 Corchorus capsularis cultivar CVL-1 contig13182, 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: 25419
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3113 original size:2 final size:2
Alignment explanation
Indices: 3106--3145 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3096 CTTCTTCTTC
3106 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3146 TTCCCCCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10507 original size:15 final size:15
Alignment explanation
Indices: 10488--10526 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
10478 CTAACTCCTC
*
10488 CCCCTCCCTACCCCA
1 CCCCTCCCCACCCCA
*
10503 TCCCTCCCCACCCCA
1 CCCCTCCCCACCCCA
10518 CCCCTCCCC
1 CCCCTCCCC
10527 CATTTGAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.10, C:0.77, G:0.00, T:0.13
Consensus pattern (15 bp):
CCCCTCCCCACCCCA
Found at i:13088 original size:3 final size:3
Alignment explanation
Indices: 13080--13109 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13070 ATGTGTATGC
13080 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
13110 TTTTTGGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:13742 original size:12 final size:12
Alignment explanation
Indices: 13709--13745 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
13699 GAATTACTTC
13709 TTTGTTTTATCT
1 TTTGTTTTATCT
*
13721 TTTGACTTTATCT
1 TTTG-TTTTATCT
13734 TTTGTTTTATCT
1 TTTGTTTTATCT
13746 GCTCAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.11, C:0.11, G:0.08, T:0.70
Consensus pattern (12 bp):
TTTGTTTTATCT
Found at i:16252 original size:78 final size:78
Alignment explanation
Indices: 16160--16553 Score: 307
Period size: 78 Copynumber: 5.1 Consensus size: 78
16150 TTTTTATAGT
* * * * *
16160 TTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATTTATTATCTTTATAACTATTTTATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAACTATTATATTTT
16225 ATCATTTTACTAA
66 ATCATTTTACTAA
* * *
16238 TTTACTCAATTAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAACTATTATATTTT
*
16303 ACCATTTTACTATTTTACTGA
66 ---A---T-C-ATTTTACTAA
* *
16324 TTTACTCAACTAAAAACTCTATTTTTCTATAATTGAATCTAATAT-TCTTATAACTATTATATTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCT-TTATAACTATTATATTT
*
16388 TACCA-TTT--TAA
65 TATCATTTTACTAA
* ** * * *
16399 -TTA---AA--AAAAACT-TGATATATTAGT-TTTTTAAAAT-TTATAACTATTAT-A-TTTTAC
1 TTTACTCAACTAAAAACTCT-AT-TTTTA-TATAATT-AAATCTAATATCT-TTATAACTATTA-
* * *
16453 CATTTTACCATTTTACTGA
60 TATTTTATCATTTTACTAA
* *
16472 TTTACTCAACTAAAAACTCTATTTTTCTATAATTGAATCTAATAT-TCTTATAACTATTATATTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCT-TTATAACTATTATATTT
* *
16536 TACCATTTTACTAT
65 TATCATTTTACTAA
16550 TTTA
1 TTTA
16554 ATTAAAAAAA
Statistics
Matches: 248, Mismatches: 39, Indels: 58
0.72 0.11 0.17
Matches are distributed among these distances:
68 1 0.00
69 13 0.05
70 20 0.08
71 14 0.06
73 2 0.01
74 6 0.02
75 2 0.01
77 14 0.06
78 89 0.36
79 14 0.06
80 1 0.00
81 1 0.00
83 1 0.00
84 1 0.00
85 1 0.00
86 68 0.27
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (78 bp):
TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAACTATTATATTTT
ATCATTTTACTAA
Found at i:16365 original size:86 final size:86
Alignment explanation
Indices: 16160--16397 Score: 305
Period size: 86 Copynumber: 2.9 Consensus size: 86
16150 TTTTTATAGT
* * * * *
16160 TTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATTTATTATCTTTATAAC-----TATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
16220 ---ATTTTATCATTTTACTAA
66 ACCATTTTATCATTTTACTAA
* *
16238 TTTACTCAATTAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
*
16303 ACCATTTTA-CTATTTTACTGA
66 ACCATTTTATC-ATTTTACTAA
* * *
16324 TTTACTCAACTAAAAACTCTATTTTTCTATAATTGAATCTAATATTCTTATAACTATTATATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
16389 ACCATTTTA
66 ACCATTTTA
16398 ATTAAAAAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
78 47 0.34
83 6 0.04
85 1 0.01
86 84 0.61
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (86 bp):
TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
ACCATTTTATCATTTTACTAA
Found at i:16439 original size:148 final size:152
Alignment explanation
Indices: 16285--16587 Score: 542
Period size: 148 Copynumber: 2.0 Consensus size: 152
16275 TCTAATATCC
*
16285 TTATAACTATTATATTTTACCATTTTACTATTTTACTGATTTACTCAACTAAAAACTCTATTTTT
1 TTATAACTATTATATTTTACCATTTTACCATTTTACTGATTTACTCAACTAAAAACTCTATTTTT
16350 CTATAATTGAATCTAATATTCTTATAACTATTATATTTTACCATTTTA-A-TT-A-AAAAAAACT
66 CTATAATTGAATCTAATATTCTTATAACTATTATATTTTACCATTTTACATTTAATAAAAAAACT
16411 TGATATATTAGTTTTTTAAAAT
131 TGATATATTAGTTTTTTAAAAT
16433 TTATAACTATTATATTTTACCATTTTACCATTTTACTGATTTACTCAACTAAAAACTCTATTTTT
1 TTATAACTATTATATTTTACCATTTTACCATTTTACTGATTTACTCAACTAAAAACTCTATTTTT
16498 CTATAATTGAATCTAATATTCTTATAACTATTATATTTTACCATTTTACTATTTTAATTAAAAAA
66 CTATAATTGAATCTAATATTCTTATAACTATTATATTTTACCATTTTAC-A-TTTAA-TAAAAAA
16563 ACTTGATATATTAGTTTTTTAAAAT
128 ACTTGATATATTAGTTTTTTAAAAT
16588 ATATTTCTTG
Statistics
Matches: 147, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
148 112 0.76
150 1 0.01
152 2 0.01
153 1 0.01
155 31 0.21
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (152 bp):
TTATAACTATTATATTTTACCATTTTACCATTTTACTGATTTACTCAACTAAAAACTCTATTTTT
CTATAATTGAATCTAATATTCTTATAACTATTATATTTTACCATTTTACATTTAATAAAAAAACT
TGATATATTAGTTTTTTAAAAT
Found at i:16459 original size:31 final size:31
Alignment explanation
Indices: 16371--16459 Score: 74
Period size: 31 Copynumber: 2.9 Consensus size: 31
16361 TCTAATATTC
16371 TTATAACTATTATATTTTACCATTTTAATTAA
1 TTATAACTATTATATTTTACCATTTTAA-TAA
** * * * ***
16403 AAAAAACT-TGATATATTAGTTTTTTAA-AA
1 TTATAACTATTATATTTTACCATTTTAATAA
16432 TTTATAACTATTATATTTTACCATTTTA
1 -TTATAACTATTATATTTTACCATTTTA
16460 CCATTTTACT
Statistics
Matches: 39, Mismatches: 16, Indels: 5
0.65 0.27 0.08
Matches are distributed among these distances:
29 2 0.05
30 5 0.13
31 27 0.69
32 5 0.13
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (31 bp):
TTATAACTATTATATTTTACCATTTTAATAA
Found at i:17496 original size:20 final size:21
Alignment explanation
Indices: 17458--17496 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17448 TATATATGTG
17458 TTAATTAAGAAACTATTATAT
1 TTAATTAAGAAACTATTATAT
*
17479 TTAATTAA-AAATTATTAT
1 TTAATTAAGAAACTATTAT
17497 CTGAATATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAATTAAGAAACTATTATAT
Found at i:20294 original size:26 final size:26
Alignment explanation
Indices: 20258--20308 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20248 TTCAAGAAAT
*
20258 TGCCAGGGGCATTTTTGTCATTTTTA
1 TGCCAGGGGCATTTTCGTCATTTTTA
20284 TGCCAGGGGCATTTTCGTCATTTTT
1 TGCCAGGGGCATTTTCGTCATTTTT
20309 TTAAGCTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.45
Consensus pattern (26 bp):
TGCCAGGGGCATTTTCGTCATTTTTA
Done.