Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019617.1 Corchorus olitorius cultivar O-4 contig19650, 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: 14362
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:126 original size:40 final size:40
Alignment explanation
Indices: 54--438 Score: 375
Period size: 40 Copynumber: 9.3 Consensus size: 40
44 TTAGGTCTAT
54 TCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCA
1 TCGGAAGGTGTTGTTT-AAATTCCCAGTTTGCCCTTCCTCA
95 TCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCA
1 TCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCA
*
135 TCGGAAGGTGTCGTTTTAAATTCCCAGTTTGCCCTTCCTCA
1 TCGGAAGGTGTTG-TTTAAATTCCCAGTTTGCCCTTCCTCA
* * * *
176 TCGGAAGGTGTTG-TCAGCATTCCCCGTTTGTCCTTCCTCA
1 TCGGAAGGTGTTGTTTA-AATTCCCAGTTTGCCCTTCCTCA
* * * *
216 TCGGAAGGTATTGTTTAAGTTCACTAGTTTGTCCTTCCTCA
1 TCGGAAGGTGTTGTTTAAATTC-CCAGTTTGCCCTTCCTCA
* * *
257 CCGGAAGGTGTTGTTTAGATTTCCAGTTTGCCCTTCCTCA
1 TCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCA
*
297 TCGGAAGGTGTTGTTTAAAGCCCATTCTTTCCAGTTTGCCCTTCCCCA
1 TCGGAAGGTGTTGTTT-AA----ATTC---CCAGTTTGCCCTTCCTCA
* * * *
345 CCAGAAGGTGTTGATTT-CATTCCC-GTTATGCCCTTCCCCA
1 TCGGAAGGTGTTG-TTTAAATTCCCAGTT-TGCCCTTCCTCA
* ** * * * *
385 CCGGAATATGTTGATTT-TATTCCTATTTTGCCCTTCC-CGG
1 TCGGAAGGTGTTG-TTTAAATTCCCAGTTTGCCCTTCCTC-A
425 TCGGAAGGTGTTGT
1 TCGGAAGGTGTTGT
439 CTTCAATGAT
Statistics
Matches: 292, Mismatches: 36, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
39 7 0.02
40 154 0.53
41 93 0.32
43 4 0.01
45 3 0.01
48 28 0.10
49 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCA
Found at i:189 original size:81 final size:81
Alignment explanation
Indices: 54--438 Score: 388
Period size: 81 Copynumber: 4.7 Consensus size: 81
44 TTAGGTCTAT
* *
54 TCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
1 TCGGAAGGTGTTGTTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCC
119 AGTTTGCCCTTCCTCA
66 AGTTTGCCCTTCCTCA
* *
135 TCGGAAGGTGTCGTTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCATTCC
1 TCGGAAGGTGTTGTTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-CATTCC
* *
199 CCGTTTGTCCTTCCTCA
65 CAGTTTGCCCTTCCTCA
* * * * * * *
216 TCGGAAGGTATTG-TTTAAGTTCACTAGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAGATTTC
1 TCGGAAGGTGTTGTTTTAAATTC-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCC
280 CAGTTTGCCCTTCCTCA
65 CAGTTTGCCCTTCCTCA
* * * *
297 TCGGAAGGTGTTGTTTAAAGCCCATTCTTTCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGATTT
1 TCGGAAGGTGTTGTTTTAA----ATTC---CCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTT
*
362 -CATTCCC-GTTATGCCCTTCCCCA
58 ACATTCCCAGTT-TGCCCTTCCTCA
* ** * * *
385 CCGGAATATGTTGATTTT--ATTCCTATTTTGCCCTTCC-CGGTCGGAAGGTGTTGT
1 TCGGAAGGTGTTG-TTTTAAATTCCCAGTTTGCCCTTCCTC-ATCGGAAGGTGTTGT
439 CTTCAATGAT
Statistics
Matches: 253, Mismatches: 37, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
79 2 0.01
80 34 0.13
81 142 0.56
82 6 0.02
83 4 0.02
86 3 0.01
87 3 0.01
88 53 0.21
89 6 0.02
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.37
Consensus pattern (81 bp):
TCGGAAGGTGTTGTTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCC
AGTTTGCCCTTCCTCA
Found at i:468 original size:48 final size:48
Alignment explanation
Indices: 400--685 Score: 423
Period size: 48 Copynumber: 6.0 Consensus size: 48
390 ATATGTTGAT
**
400 TTTATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
1 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
* *
448 TTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-A
1 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
* *
495 TTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
1 -TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
* *
544 TTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAAT-A
1 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
** *
591 TTATATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
1 TT-TATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
* *
640 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGTTGTTGTTTTCAAT
1 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT
686 ATCTCGTTCC
Statistics
Matches: 213, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
47 3 0.01
48 208 0.98
49 2 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (48 bp):
TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
Found at i:562 original size:96 final size:96
Alignment explanation
Indices: 398--687 Score: 501
Period size: 96 Copynumber: 3.0 Consensus size: 96
388 GAATATGTTG
* *
398 ATTTTATTCCTA-TTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGATTTATTCTCGTTTT
1 ATTTTATTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTT
462 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
65 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
494 ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1 ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
*
559 CCCTTCCCGATCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* **
590 ATTATATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1 ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
*
655 CCCTTCCCGGTCGGAAGTTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
686 AT
1 AT
688 CTCGTTCCTG
Statistics
Matches: 185, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
95 1 0.01
96 184 0.99
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (96 bp):
ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
Found at i:615 original size:144 final size:144
Alignment explanation
Indices: 399--685 Score: 468
Period size: 144 Copynumber: 2.0 Consensus size: 144
389 AATATGTTGA
* *
399 TTTTATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGATTTATTCTCGTTTTGC
1 TTTTATTCCCATTTTGCCCTTCCCGATCGGAAGGTGTTGTCTTCAATGATTTATTCTCGTTTTGC
*
464 CCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGG
66 CCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGG
529 TGTTGTCTTCAATG
131 TGTTGTCTTCAATG
* * *
543 TTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAAT-ATTATATTCTTGTTTTG
1 TTTTATTCCCATTTTGCCCTTCCCGATCGGAAGGTGTTGTCTTCAATGATT-TATTCTCGTTTTG
* *
607 CCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAG
65 CCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAG
* *
672 TTGTTGTTTTCAAT
130 GTGTTGTCTTCAAT
686 ATCTCGTTCC
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 3 0.02
144 129 0.98
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (144 bp):
TTTTATTCCCATTTTGCCCTTCCCGATCGGAAGGTGTTGTCTTCAATGATTTATTCTCGTTTTGC
CCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGG
TGTTGTCTTCAATG
Found at i:1576 original size:38 final size:38
Alignment explanation
Indices: 1504--1605 Score: 154
Period size: 38 Copynumber: 2.7 Consensus size: 38
1494 TTATTAGTTC
*
1504 CCAAAATCTTCTTTTGG-ATT-TCTAAACTTTTATTTT
1 CCAAAATCTTCTTTTGGAATTACCTAAACTTTTATTTT
1540 CCAAAATCTTCTTTTGGAATTACCTAAACTTTTATTTT
1 CCAAAATCTTCTTTTGGAATTACCTAAACTTTTATTTT
* * *
1578 TCAAAATCTTCTTTTGTAATTACTTAAA
1 CCAAAATCTTCTTTTGGAATTACCTAAA
1606 TAAAAAGGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 17 0.28
37 3 0.05
38 40 0.67
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (38 bp):
CCAAAATCTTCTTTTGGAATTACCTAAACTTTTATTTT
Found at i:1821 original size:14 final size:14
Alignment explanation
Indices: 1791--1819 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1781 ACTTTTGATT
1791 AATGCATGAATGCA
1 AATGCATGAATGCA
1805 AATG-ATGAATGCA
1 AATGCATGAATGCA
1818 AA
1 AA
1820 ATCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Found at i:6116 original size:2 final size:2
Alignment explanation
Indices: 6109--6147 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6099 TCCCAACTTC
6109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6148 GTATCTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7470 original size:7 final size:7
Alignment explanation
Indices: 7458--7491 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
7448 CCAGTGACAG
7458 TATAAAC
1 TATAAAC
7465 TATAAAC
1 TATAAAC
7472 TATAAAC
1 TATAAAC
7479 TATAAAC
1 TATAAAC
7486 TATAAA
1 TATAAA
7492 AGCCTAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (7 bp):
TATAAAC
Found at i:10348 original size:14 final size:14
Alignment explanation
Indices: 10329--10364 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10319 CATCGGTTGT
*
10329 TGGTGTTGGTGGCG
1 TGGTGTTGATGGCG
10343 TGGTGTTGATGGCG
1 TGGTGTTGATGGCG
*
10357 TTGTGTTG
1 TGGTGTTG
10365 TGTTCGGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.03, C:0.06, G:0.50, T:0.42
Consensus pattern (14 bp):
TGGTGTTGATGGCG
Found at i:11670 original size:178 final size:177
Alignment explanation
Indices: 11316--11682 Score: 413
Period size: 177 Copynumber: 2.1 Consensus size: 177
11306 ATTATTTAAT
* *
11316 ATATTAAGTAGACCGTCTATTTTCATTAACCAAAATAACTAATTCTTTAGAAGCAATTTTTATAC
1 ATATTAAGTAGACCGTCTATTCTCATTAACCAAAACAACTAATTCTTTAGAAGCAATTTTTATAC
* *
11381 CTCTAACATTAAATTTAGTTTTTGAGTCATCATGAAAGTTGTAGATCATGGAACAACCTTTCAAG
66 CTCAAACATTAAATTTAGTTTTCGAGTCATCATGAAAGTTGTAGATCATGGAACAACCTTTCAAG
* * * * *
11446 AGACACTTGAATCATCTCAATTAGACATCTAGAGCAAAAGTTATATA
131 AGACACTTAAATCACCTCAATTAGAAACCAAGAGCAAAAGTTATATA
* * * *
11493 ATATTAAGTAGACCGTCTATTCTCGTTAATCGAAACAAC-AATT-TTTCCGGAAGC-ATTTTTGA
1 ATATTAAGTAGACCGTCTATTCTCATTAACCAAAACAACTAATTCTTT--AGAAGCAATTTTT-A
* * * * *
11555 TACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATGATGGAACAATCTTT
63 TACCTCAAACATTAAATTTAGTTTTCGAGT-CATCATGAAAGTTGTAGATCATGGAACAACCTTT
* * * *
11620 TAATAGACACTTAAATCACCT-TATTCGGATAACCGAAGAG-AAAA-TTATATA
127 CAAGAGACACTTAAATCACCTCAATT-AGA-AACC-AAGAGCAAAAGTTATATA
* *
11671 ATGTTAAATAGA
1 ATATTAAGTAGA
11683 TCGTTTAGGC
Statistics
Matches: 159, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
175 3 0.02
176 10 0.06
177 69 0.43
178 67 0.42
179 6 0.04
180 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (177 bp):
ATATTAAGTAGACCGTCTATTCTCATTAACCAAAACAACTAATTCTTTAGAAGCAATTTTTATAC
CTCAAACATTAAATTTAGTTTTCGAGTCATCATGAAAGTTGTAGATCATGGAACAACCTTTCAAG
AGACACTTAAATCACCTCAATTAGAAACCAAGAGCAAAAGTTATATA
Found at i:11901 original size:14 final size:14
Alignment explanation
Indices: 11882--11911 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11872 TATTGTTTTT
11882 TATAATTAGGTAAA
1 TATAATTAGGTAAA
11896 TATAATTAGGTAAA
1 TATAATTAGGTAAA
11910 TA
1 TA
11912 ATGAAGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (14 bp):
TATAATTAGGTAAA
Found at i:12499 original size:24 final size:25
Alignment explanation
Indices: 12470--12520 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
12460 TTATGTGAAC
*
12470 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
12494 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
12519 AA
1 AA
12521 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Done.