Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011208.1 Corchorus olitorius cultivar O-4 contig11241, 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: 17920
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2919 original size:15 final size:15
Alignment explanation
Indices: 2899--2929 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2889 TTTCTATTAT
2899 TCGTACTGTTATATA
1 TCGTACTGTTATATA
*
2914 TCGTACTTTTATATA
1 TCGTACTGTTATATA
2929 T
1 T
2930 AGTATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (15 bp):
TCGTACTGTTATATA
Found at i:2928 original size:2 final size:2
Alignment explanation
Indices: 2923--2962 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
2913 ATCGTACTTT
* *
2923 TA TA TA TA GTA TA AA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2963 TTTAATCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4064 original size:31 final size:31
Alignment explanation
Indices: 4026--4087 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4016 GAGTTTTGTA
* *
4026 AAACTTTTGAATCGCCTATTGTACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
4057 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
4088 TTTTGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:4225 original size:93 final size:93
Alignment explanation
Indices: 4123--4307 Score: 280
Period size: 93 Copynumber: 2.0 Consensus size: 93
4113 TGATTTAAAT
* *
4123 TTTTATAGTTTTAGTCAAATAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
* * *
4188 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTACTTTTACCATATTACTAATTTAC
* * * *
4216 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTTATCAAATCTAATATCTTTATACCTA
1 TTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
*
4281 TTTTACTTTTACGATATTACTAATTTA
66 TTTTACTTTTACCATATTACTAATTTA
4308 ATTAAAAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
TTTTACTTTTACCATATTACTAATTTAC
Found at i:7061 original size:22 final size:22
Alignment explanation
Indices: 7031--7176 Score: 143
Period size: 22 Copynumber: 6.6 Consensus size: 22
7021 GCCAACGTAG
*
7031 AAATATTGATAACCACACTGCGA
1 AAAT-TTGATAACCACACTGTGA
* *
7054 AAATTTGATAACCTCATTGTG-
1 AAATTTGATAACCACACTGTGA
* * *
7075 AAATTTCGATAACCTCTCTATGA
1 AAATTT-GATAACCACACTGTGA
*
7098 AAATTTGATAACCACAATGTGA
1 AAATTTGATAACCACACTGTGA
*
7120 AATTTTGATAACCACACTGTG-
1 AAATTTGATAACCACACTGTGA
**
7141 AAATTCTGATAACCACACAATGA
1 AAATT-TGATAACCACACTGTGA
**
7164 AGTTTTGATAACC
1 AAATTTGATAACC
7177 TTATTGTCTA
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
21 10 0.10
22 79 0.77
23 13 0.13
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (22 bp):
AAATTTGATAACCACACTGTGA
Found at i:7164 original size:66 final size:66
Alignment explanation
Indices: 7031--7176 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
7021 GCCAACGTAG
* * * * * *
7031 AAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTCTCTAT
1 AAAT-TTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTCGATAACCACACAAT
7096 GA
65 GA
* *
7098 AAATTTGATAACCACAATGTGAAATTTTGATAACCACACTGTGAAA-TTCTGATAACCACACAAT
1 AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTC-GATAACCACACAAT
7162 GA
65 GA
**
7164 AGTTTTGATAACC
1 AAATTTGATAACC
7177 TTATTGTCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 3 0.04
66 61 0.90
67 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (66 bp):
AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTCGATAACCACACAATG
A
Found at i:7170 original size:44 final size:43
Alignment explanation
Indices: 7030--7176 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 43
7020 CGCCAACGTA
* * * *
7030 GAAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACA-AGT
* * * *
7074 GAAATTTCGATAACCTCTCTATGAAAATTTGATAACCACAATGT
1 GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACAA-GT
*
7118 GAAATTTTGATAACCACACTGTG-AAATTCTGATAACCACACAAT
1 GAAATTTTGATAACCACACTGTGAAAATT-TGATAACCACA-AGT
*
7162 GAAGTTTTGATAACC
1 GAAATTTTGATAACC
7177 TTATTGTCTA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 5 0.06
44 80 0.93
45 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (43 bp):
GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACAAGT
Found at i:7213 original size:22 final size:22
Alignment explanation
Indices: 7184--7265 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
7174 ACCTTATTGT
7184 CTATAAAATTTTGATAATCACA
1 CTATAAAATTTTGATAATCACA
* * *
7206 TTATAAAA--TTGGTAATCGCA
1 CTATAAAATTTTGATAATCACA
*
7226 CTATGAAAATTTTGATAACCACA
1 CTAT-AAAATTTTGATAATCACA
* * *
7249 CCATGAAATTTCGATAA
1 CTATAAAATTTTGATAA
7266 CTTATGAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
20 13 0.28
21 4 0.09
22 18 0.38
23 12 0.26
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (22 bp):
CTATAAAATTTTGATAATCACA
Found at i:7558 original size:22 final size:22
Alignment explanation
Indices: 7482--7603 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 22
7472 AACCTTTTTT
* * *
7482 TATGAAATTTTGGTGACCT-CTG
1 TATGAAATTTTGATAACCTAC-A
*
7504 TATGAAATTTTGATAA-TTACA
1 TATGAAATTTTGATAACCTACA
* * *
7525 TTACGAAGTTTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTACA
*
7548 TATGAAATTTTGGTAACCATAC-
1 TATGAAATTTTGATAACC-TACA
*
7570 TATGAAATTTTAATAACCTTAC-
1 TATGAAATTTTGATAACC-TACA
*
7592 TATGTAATTTTG
1 TATGAAATTTTG
7604 GTTTGATTGT
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.01
22 73 0.92
23 5 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACA
Found at i:9359 original size:22 final size:22
Alignment explanation
Indices: 9334--9537 Score: 117
Period size: 22 Copynumber: 9.2 Consensus size: 22
9324 TTAAACCTAA
* *
9334 TATGAAATTTCGATAACCTCCC
1 TATGAAATTTCGATAACCACAC
* *
9356 TATGAAAATTCAATAACCACAC
1 TATGAAATTTCGATAACCACAC
* * *
9378 TGTGAAATTTGGGTAACCACAC
1 TATGAAATTTCGATAACCACAC
* * *
9400 TATGAAATTTCGATAATCTCAA
1 TATGAAATTTCGATAACCACAC
* * **
9422 TGTGAAATTTTGATAATCTGC-C
1 TATGAAATTTCGATAA-CCACAC
* ** *
9444 TATAAAATTTTAATAATCACAC
1 TATGAAATTTCGATAACCACAC
* * *
9466 TAAAT-AAAATT-GGTAACCGCAC
1 T--ATGAAATTTCGATAACCACAC
* *
9488 TATGAAAATTTTGGTAACCACAC
1 TATG-AAATTTCGATAACCACAC
* * *
9511 CATGAAATTTCGATAACCTCCC
1 TATGAAATTTCGATAACCACAC
9533 TATGA
1 TATGA
9538 GAATGAAACT
Statistics
Matches: 135, Mismatches: 40, Indels: 14
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.01
21 1 0.01
22 111 0.82
23 19 0.14
24 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (22 bp):
TATGAAATTTCGATAACCACAC
Found at i:9384 original size:44 final size:45
Alignment explanation
Indices: 9334--9537 Score: 148
Period size: 44 Copynumber: 4.6 Consensus size: 45
9324 TTAAACCTAA
9334 TATGAAATTTCGATAACCTCCCTATGAAAA-TTCAATAACCACAC
1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCAATAACCACAC
* * * * * * * * *
9378 TGTGAAATTTGGGTAACCACACTATG-AAATTTCGATAATCTCAA
1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCAATAACCACAC
* * * * * *
9422 TGTGAAATTTTGATAATCTGCCTAT-AAAATTTTAATAATCACAC
1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCAATAACCACAC
* * * * ***
9466 TAAAT-AAAATT-GGTAACCGCACTATGAAAATTTTGGTAACCACAC
1 T--ATGAAATTTCGATAACCTCCCTATGAAAATTTCAATAACCACAC
*
9511 CATGAAATTTCGATAACCTCCCTATGA
1 TATGAAATTTCGATAACCTCCCTATGA
9538 GAATGAAACT
Statistics
Matches: 119, Mismatches: 34, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
43 5 0.04
44 79 0.66
45 34 0.29
46 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (45 bp):
TATGAAATTTCGATAACCTCCCTATGAAAATTTCAATAACCACAC
Found at i:9497 original size:21 final size:22
Alignment explanation
Indices: 9471--9517 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
9461 CACACTAAAT
* *
9471 AAAA-TTGGTAACCGCACTATG
1 AAAATTTGGTAACCACACCATG
9492 AAAATTTTGGTAACCACACCATG
1 AAAA-TTTGGTAACCACACCATG
9515 AAA
1 AAA
9518 TTTCGATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
23 18 0.82
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (22 bp):
AAAATTTGGTAACCACACCATG
Found at i:9599 original size:21 final size:23
Alignment explanation
Indices: 9566--9614 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
9556 CTCTCTATGT
9566 ATTTTCGATAACCTCTCC-A-AAA
1 ATTTTCGATAACCTC-CCTATAAA
9588 ATTTTC-ATAACCTCCCTATAAA
1 ATTTTCGATAACCTCCCTATAAA
9610 ATTTT
1 ATTTT
9615 GTTAATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.08
21 9 0.36
22 14 0.56
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTTCGATAACCTCCCTATAAA
Found at i:10509 original size:1 final size:1
Alignment explanation
Indices: 10494--10653 Score: 140
Period size: 1 Copynumber: 160.0 Consensus size: 1
10484 AATTACGTAC
* * * * * * * * *
10494 TTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
10559 GTTTTTTGTTTTTTGTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
10624 TTTTTTTTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10654 ACGAAAGCTA
Statistics
Matches: 119, Mismatches: 40, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 119 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:10515 original size:7 final size:7
Alignment explanation
Indices: 10494--10653 Score: 178
Period size: 7 Copynumber: 23.4 Consensus size: 7
10484 AATTACGTAC
10494 TTTTG-T
1 TTTTGTT
10500 TTTTG-T
1 TTTTGTT
10506 TTTTG-T
1 TTTTGTT
10512 TTTTG-T
1 TTTTGTT
10518 TTTTGTT
1 TTTTGTT
10525 TTTTGTT
1 TTTTGTT
10532 TTTTGTT
1 TTTTGTT
10539 TTTTGTTT
1 TTTTG-TT
10547 TTTTGTTT
1 TTTTG-TT
10555 TTTTGTT
1 TTTTGTT
10562 TTTTGTT
1 TTTTGTT
10569 TTTTGTT
1 TTTTGTT
10576 TTTTG-T
1 TTTTGTT
10582 TTTT-TT
1 TTTTGTT
*
10588 TGTT-TT
1 TTTTGTT
10594 TTTTGTTT
1 TTTTG-TT
10602 TTTTGTTT
1 TTTTG-TT
10610 TTTTGTT
1 TTTTGTT
10617 TTTT-TT
1 TTTTGTT
10623 GTTTT-TT
1 -TTTTGTT
*
10630 TTGTTTTT
1 TT-TTGTT
10638 TTTTGTT
1 TTTTGTT
10645 TTTT-TT
1 TTTTGTT
10651 TTT
1 TTT
10654 ACGAAAGCTA
Statistics
Matches: 143, Mismatches: 3, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
6 46 0.32
7 63 0.44
8 34 0.24
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:10534 original size:8 final size:8
Alignment explanation
Indices: 10499--10653 Score: 182
Period size: 8 Copynumber: 19.5 Consensus size: 8
10489 CGTACTTTTG
10499 TTTTTGTT
1 TTTTTGTT
*
10507 TTTGTTTTT
1 TTT-TTGTT
10516 GTTTTTG-T
1 -TTTTTGTT
10524 TTTTTG-T
1 TTTTTGTT
10531 TTTTTG-T
1 TTTTTGTT
10538 TTTTTGTT
1 TTTTTGTT
10546 TTTTTGTT
1 TTTTTGTT
10554 TTTTTG-T
1 TTTTTGTT
10561 TTTTTG-T
1 TTTTTGTT
10568 TTTTTG-T
1 TTTTTGTT
10575 TTTTTGTTT
1 TTTTTG-TT
10584 TTTTTGTTT
1 TTTTTG-TT
10593 TTTTTGTT
1 TTTTTGTT
10601 TTTTTGTT
1 TTTTTGTT
10609 TTTTTGTTT
1 TTTTTG-TT
10618 TTTTTGTTT
1 TTTTTG-TT
10627 TTTTTGTT
1 TTTTTGTT
10635 TTTTT-TT
1 TTTTTGTT
10642 GTTTTT-TT
1 -TTTTTGTT
10650 TTTT
1 TTTT
10654 ACGAAAGCTA
Statistics
Matches: 138, Mismatches: 2, Indels: 15
0.89 0.01 0.10
Matches are distributed among these distances:
7 47 0.34
8 49 0.36
9 39 0.28
10 3 0.02
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:10576 original size:44 final size:44
Alignment explanation
Indices: 10494--10653 Score: 204
Period size: 44 Copynumber: 3.6 Consensus size: 44
10484 AATTACGTAC
*
10494 TTTTGTTTTTGTTTTTGTTTTTG-TTTTTGTTTTTTGTTTTTTGTT
1 TTTTGTTTTT-TTGTT-TTTTTGTTTTTTGTTTTTTGTTTTTTGTT
10539 TTTTGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTT
1 TTTTGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTG--TT
10585 TTTTGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTT-TTGTTTT-TT
1 TTTTG-TTTTTTTGTTTTTTTG-TTTTTTGTTTTTTGTT-TTTTGTT
10630 TTGTT-TTTTTTTGTTTTTTT-TTTT
1 TT-TTGTTTTTTTGTTTTTTTGTTTT
10654 ACGAAAGCTA
Statistics
Matches: 107, Mismatches: 1, Indels: 17
0.86 0.01 0.14
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 39 0.36
45 14 0.13
46 9 0.08
47 18 0.17
48 17 0.16
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (44 bp):
TTTTGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTGTT
Found at i:11697 original size:15 final size:15
Alignment explanation
Indices: 11677--11709 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11667 TAGTAGTAAG
11677 ATAAGATATATATAT
1 ATAAGATATATATAT
11692 ATAAGATATATATAT
1 ATAAGATATATATAT
11707 ATA
1 ATA
11710 TACACGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATAAGATATATATAT
Done.