Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024056.1 Corchorus olitorius cultivar O-4 contig24089, 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: 44443
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:2232 original size:22 final size:24
Alignment explanation
Indices: 2196--2242 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2186 AAGTTCATGT
2196 CTCAACCCTGC-AAAAAGGTCAAA
1 CTCAACCCTGCAAAAAAGGTCAAA
* *
2219 CTCAA-CCTGGAAAAAAGGTGAAA
1 CTCAACCCTGCAAAAAAGGTCAAA
2242 C
1 C
2243 AACCCCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (24 bp):
CTCAACCCTGCAAAAAAGGTCAAA
Found at i:2432 original size:19 final size:18
Alignment explanation
Indices: 2408--2446 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2398 ATTTCAATCC
2408 AATTAGGGCTAATTGCACA
1 AATTAGGGC-AATTGCACA
**
2427 AATTAGTTCAATTGCACA
1 AATTAGGGCAATTGCACA
2445 AA
1 AA
2447 AACAATAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (18 bp):
AATTAGGGCAATTGCACA
Found at i:3622 original size:21 final size:21
Alignment explanation
Indices: 3598--3638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3588 TGCTCTTGTC
3598 ATTGGACC-AATAGGCATCTTT
1 ATTGGACCAAAT-GGCATCTTT
*
3619 ATTGGATCAAATGGCATCTT
1 ATTGGACCAAATGGCATCTT
3639 CTTGGTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (21 bp):
ATTGGACCAAATGGCATCTTT
Found at i:15410 original size:13 final size:13
Alignment explanation
Indices: 15392--15421 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15382 ACAAAATGTC
15392 ATGTGGTATGGGA
1 ATGTGGTATGGGA
*
15405 ATGTGGTATGGTA
1 ATGTGGTATGGGA
15418 ATGT
1 ATGT
15422 TACATTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (13 bp):
ATGTGGTATGGGA
Found at i:18069 original size:78 final size:78
Alignment explanation
Indices: 17982--18143 Score: 252
Period size: 78 Copynumber: 2.1 Consensus size: 78
17972 AACTTTTATA
* * ** *
17982 ATTTCACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATTTTTATAACTATTTTATT
1 ATTTTACTCAACTAAAAACTCTATATTTATTTAATCAAATCTAATATCCTTATAACTATTTTAGT
18047 TTACCATTTTACC
66 TTACCATTTTACC
*
18060 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTATTTTAGT
1 ATTTTACTCAACTAAAAACTCTATATTTATTTAATCAAATCTAATATCCTTATAACTATTTTAGT
* *
18125 TTACCGTTTTACT
66 TTACCATTTTACC
18138 ATTTTA
1 ATTTTA
18144 ATTAAAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.01, T:0.49
Consensus pattern (78 bp):
ATTTTACTCAACTAAAAACTCTATATTTATTTAATCAAATCTAATATCCTTATAACTATTTTAGT
TTACCATTTTACC
Found at i:18485 original size:14 final size:14
Alignment explanation
Indices: 18466--18512 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
18456 TTTTTATGAT
18466 TATTTTATTTTTAC
1 TATTTTATTTTTAC
*
18480 TATTTTA-ATTTA-
1 TATTTTATTTTTAC
*
18492 AATTTTATTTTTAC
1 TATTTTATTTTTAC
18506 TATTTTA
1 TATTTTA
18513 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 8 0.30
14 13 0.48
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATTTTTAC
Found at i:18553 original size:151 final size:150
Alignment explanation
Indices: 18345--18644 Score: 440
Period size: 151 Copynumber: 2.0 Consensus size: 150
18335 TTATAATTAC
* *
18345 TTTACTTTTACCATTTTACTATTTTTCAGTAATAACTTGGATATGTTAAAATATTTTAATATACA
1 TTTACTTTTACCATTTTACTATTTTTCAGTAAAAACTTGGATATATTAAAATATTTTAATATACA
* * * * *
18410 GTTTTATTCTACTATAAA-CTCCATTTTCATTTCATTAAATTCAATATTTTTATGATTATTTTAT
66 GTTTCATTATACTA-AAATCTCCATTTTCATTTAATTAAATTCAATATTTTTATAATTATTGTAT
*
18474 TTTTACTATTTTAATTTAAAT
130 TTTTACCATTTTAATTTAAAT
* * * * *
18495 TTTATTTTTACTATTTTACTATTTTTTTATTAAAAACTTGGATATATTAAAATTTTTTAATATAC
1 TTTACTTTTACCATTTTACTA-TTTTTCAGTAAAAACTTGGATATATTAAAATATTTTAATATAC
**
18560 AGTTTCATTATACTAAAATCTTTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTGTAT
65 AGTTTCATTATACTAAAATCTCCATTTTCATTTAATTAAATTCAATATTTTTATAATTATTGTAT
18625 TTTTACCATTTTAATTTAAA
130 TTTTACCATTTTAATTTAAA
18645 AGGTTATTGT
Statistics
Matches: 133, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
150 22 0.17
151 111 0.83
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.54
Consensus pattern (150 bp):
TTTACTTTTACCATTTTACTATTTTTCAGTAAAAACTTGGATATATTAAAATATTTTAATATACA
GTTTCATTATACTAAAATCTCCATTTTCATTTAATTAAATTCAATATTTTTATAATTATTGTATT
TTTACCATTTTAATTTAAAT
Found at i:21187 original size:12 final size:11
Alignment explanation
Indices: 21161--21203 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 11
21151 TCATGCACCC
21161 AAAACATTTATT
1 AAAACATTTA-T
21173 AAAACCATTTAT
1 AAAA-CATTTAT
21185 AAAACATATTAAT
1 AAAACAT-TT-AT
21198 AAAACA
1 AAAACA
21204 GTATCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.11
12 11 0.39
13 14 0.50
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:21212 original size:24 final size:25
Alignment explanation
Indices: 21160--21214 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
21150 TTCATGCACC
* *
21160 CAAAACATTTATTAAAACCATTTAT
1 CAAAACATTTAATAAAACCATGTAT
21185 -AAAACATATTAATAAAA-CA-GTAT
1 CAAAACAT-TTAATAAAACCATGTAT
21208 CAAAACA
1 CAAAACA
21215 GATCCTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 8 0.31
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (25 bp):
CAAAACATTTAATAAAACCATGTAT
Found at i:21331 original size:56 final size:57
Alignment explanation
Indices: 21236--21352 Score: 191
Period size: 56 Copynumber: 2.1 Consensus size: 57
21226 GAGAACCCGT
*
21236 TGAGGACAACCCACTCACAATTCAAGGGACTCGTACACCCCCAAAGTCAATCCACTG
1 TGAGGACAACCCACTCACAATTCAAGGGACTCGTACACCCCCAAAGTCAATCCACGG
* * *
21293 TGAGGACAGCCCACTCATAGTTC-AGGGACTCGTACACCCCCAAAGTCAATCCACGG
1 TGAGGACAACCCACTCACAATTCAAGGGACTCGTACACCCCCAAAGTCAATCCACGG
21349 TGAG
1 TGAG
21353 CCTAGCCGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 36 0.64
57 20 0.36
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.16
Consensus pattern (57 bp):
TGAGGACAACCCACTCACAATTCAAGGGACTCGTACACCCCCAAAGTCAATCCACGG
Found at i:21457 original size:13 final size:13
Alignment explanation
Indices: 21439--21481 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
21429 GTATCATAAT
*
21439 CAAAGTCATAAAC
1 CAAAGTAATAAAC
*
21452 CAAAGTAACAAAC
1 CAAAGTAATAAAC
21465 CTAAA-TAATAAAC
1 C-AAAGTAATAAAC
21478 CAAA
1 CAAA
21482 ATACCAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 3 0.12
13 20 0.77
14 3 0.12
ACGTcount: A:0.60, C:0.21, G:0.05, T:0.14
Consensus pattern (13 bp):
CAAAGTAATAAAC
Found at i:21490 original size:13 final size:13
Alignment explanation
Indices: 21448--21493 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
21438 TCAAAGTCAT
*
21448 AAACCAAAGTAAC
1 AAACCAAAATAAC
* *
21461 AAACCTAAATAAT
1 AAACCAAAATAAC
*
21474 AAACCAAAATACC
1 AAACCAAAATAAC
21487 AAACCAA
1 AAACCAA
21494 TCAAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.63, C:0.24, G:0.02, T:0.11
Consensus pattern (13 bp):
AAACCAAAATAAC
Found at i:28815 original size:19 final size:18
Alignment explanation
Indices: 28791--28826 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28781 TGAAGACTTA
28791 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
28810 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
28827 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:31908 original size:22 final size:23
Alignment explanation
Indices: 31867--31910 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
31857 AATCCTAATC
*
31867 CTGGTAGGAATAGTATAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
31890 CTGGTAGGAA-AGTAAAACCTT
1 CTGGTAGGAATAGTAAAACCTT
31911 CTCCTTCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:34711 original size:17 final size:17
Alignment explanation
Indices: 34681--34714 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34671 CAAAGGTAAT
*
34681 CTACTGAAACTAAATGC
1 CTACTAAAACTAAATGC
*
34698 CTACTAAAATTAAATGC
1 CTACTAAAACTAAATGC
34715 TAACATGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (17 bp):
CTACTAAAACTAAATGC
Done.