Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024070.1 Corchorus olitorius cultivar O-4 contig24103, 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: 28285
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1105 original size:29 final size:29
Alignment explanation
Indices: 1046--1125 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
1036 AAGTGGGCTT
* * *
1046 AAAATGACCACAATGCCCCTTGAGTGTGCA
1 AAAATGACCAAAATGCCCC-TGAATATGCA
*
1076 AAAATGACCAAAATACCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
1105 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
1126 GATGACCTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.62
30 17 0.38
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.17
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATATGCA
Found at i:4587 original size:19 final size:18
Alignment explanation
Indices: 4563--4598 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4553 TGAAGACTTA
4563 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
4582 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
4599 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:5355 original size:12 final size:12
Alignment explanation
Indices: 5338--5362 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5328 TTTTCCCGAA
5338 TCCATGAGTAGC
1 TCCATGAGTAGC
5350 TCCATGAGTAGC
1 TCCATGAGTAGC
5362 T
1 T
5363 AAATTCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TCCATGAGTAGC
Found at i:7992 original size:14 final size:15
Alignment explanation
Indices: 7964--7992 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7954 TTCCATTTAC
7964 TTTTTCTTTGCATTG
1 TTTTTCTTTGCATTG
7979 TTTTTCTTTG-ATTG
1 TTTTTCTTTGCATTG
7993 ATTGCCTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.07, C:0.10, G:0.14, T:0.69
Consensus pattern (15 bp):
TTTTTCTTTGCATTG
Found at i:9757 original size:19 final size:18
Alignment explanation
Indices: 9733--9768 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9723 TGAAGACTTA
9733 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
9752 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
9769 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:10383 original size:11 final size:11
Alignment explanation
Indices: 10367--10392 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10357 AGATAATTTC
10367 TTTTCTTCTAG
1 TTTTCTTCTAG
10378 TTTTCTTCTAG
1 TTTTCTTCTAG
10389 TTTT
1 TTTT
10393 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:15902 original size:19 final size:18
Alignment explanation
Indices: 15869--15904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15859 TGGAAATAAT
15869 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
15887 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
15905 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:17520 original size:22 final size:21
Alignment explanation
Indices: 17494--17534 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17484 CTAAGATGCA
*
17494 TAAAAAAAATAAATCTTAAATC
1 TAAAAAAAAGAAA-CTTAAATC
*
17516 TAAAAACAAGAAACTTAAA
1 TAAAAAAAAGAAACTTAAA
17535 ATTGAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAAAAGAAACTTAAATC
Found at i:17536 original size:22 final size:21
Alignment explanation
Indices: 17494--17544 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
17484 CTAAGATGCA
* *
17494 TAAAAAAAATAAATCTTAAAT
1 TAAAAACAAGAAATCTTAAAT
17515 CTAAAAACAAGAAA-CTTAAAAT
1 -TAAAAACAAGAAATCTT-AAAT
17537 TGAAAAAC
1 T-AAAAAC
17545 TAAACCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAACAAGAAATCTTAAAT
Found at i:19065 original size:9 final size:9
Alignment explanation
Indices: 19051--19077 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19041 ATAACAAATT
19051 TCAATGGCA
1 TCAATGGCA
19060 TCAATGGCA
1 TCAATGGCA
19069 TCAATGGCA
1 TCAATGGCA
19078 CAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (9 bp):
TCAATGGCA
Found at i:19147 original size:21 final size:22
Alignment explanation
Indices: 19122--19169 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
19112 CTTCATAAAT
19122 ATCAAATTCAAT-GAGTTTCCC
1 ATCAAATTCAATCGAGTTTCCC
*
19143 ATCAAATTCCATGCCGAGTTTCCC
1 ATCAAATTCAAT--CGAGTTTCCC
19167 ATC
1 ATC
19170 TTGGACTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
24 12 0.52
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (22 bp):
ATCAAATTCAATCGAGTTTCCC
Found at i:22496 original size:19 final size:18
Alignment explanation
Indices: 22463--22498 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22453 TGGAAATAAT
22463 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
22481 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
22499 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:23680 original size:17 final size:17
Alignment explanation
Indices: 23658--23692 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23648 CTCCTCTATC
23658 ATGAAAACACTTTTTTT
1 ATGAAAACACTTTTTTT
* *
23675 ATGAAAAGATTTTTTTT
1 ATGAAAACACTTTTTTT
23692 A
1 A
23693 AAAAACTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (17 bp):
ATGAAAACACTTTTTTT
Found at i:24695 original size:21 final size:21
Alignment explanation
Indices: 24671--24742 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
24661 ATGGGCTAGA
* *
24671 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCTTGGCC
*
24692 GGTGGTGGCACGGGCTTGGCT
1 GGTGGTGGCACGGGCTTGGCC
* *
24713 GGTGGTAGCACGGGCTTGGTC
1 GGTGGTGGCACGGGCTTGGCC
24734 GGTGGTGGC
1 GGTGGTGGC
24743 TCTTCTGTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.08, C:0.19, G:0.51, T:0.21
Consensus pattern (21 bp):
GGTGGTGGCACGGGCTTGGCC
Found at i:25511 original size:12 final size:12
Alignment explanation
Indices: 25496--25523 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25486 CTTGGTCTAC
25496 AAGTTGGCTTAA
1 AAGTTGGCTTAA
25508 AAGTTGGCTTAA
1 AAGTTGGCTTAA
25520 AAGT
1 AAGT
25524 CTTCCTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (12 bp):
AAGTTGGCTTAA
Done.