Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024769.1 Corchorus olitorius cultivar O-4 contig24802, 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: 39316
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2551 original size:15 final size:14
Alignment explanation
Indices: 2518--2556 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2508 TATCCACCAT
2518 GAAATAAAATAAAA
1 GAAATAAAATAAAA
*
2532 CAAATAAAATTAAAA
1 GAAATAAAA-TAAAA
2547 GAAATTAAAA
1 GAAA-TAAAA
2557 GTAGCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 8 0.38
16 5 0.24
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAA
Found at i:3799 original size:14 final size:15
Alignment explanation
Indices: 3752--3805 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 15
3742 CTGCAAAGTT
*
3752 ACAAAAAA-AAGAAC
1 ACAAAAAATAAAAAC
*
3766 ACAAAATA-AAAAAC
1 ACAAAAAATAAAAAC
3780 ACAAAAAATAAAAA-
1 ACAAAAAATAAAAAC
*
3794 ATAAAAAATAAA
1 ACAAAAAATAAA
3806 GTAGCAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 30 0.86
15 5 0.14
ACGTcount: A:0.81, C:0.09, G:0.02, T:0.07
Consensus pattern (15 bp):
ACAAAAAATAAAAAC
Found at i:3801 original size:16 final size:16
Alignment explanation
Indices: 3768--3801 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3758 AAAAGAACAC
*
3768 AAAATAAAAAACACAA
1 AAAATAAAAAACAAAA
*
3784 AAAATAAAAAATAAAA
1 AAAATAAAAAACAAAA
3800 AA
1 AA
3802 TAAAGTAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAACAAAA
Found at i:4027 original size:24 final size:25
Alignment explanation
Indices: 3998--4048 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
3988 TTATGTGAAC
*
3998 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
4022 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
4047 AA
1 AA
4049 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:8672 original size:16 final size:17
Alignment explanation
Indices: 8653--8685 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
8643 ATTTATAAAA
*
8653 TATATCTTAT-AATTTT
1 TATATATTATAAATTTT
8669 TATATATTATAAATTTT
1 TATATATTATAAATTTT
8686 GATTATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTATAAATTTT
Found at i:10789 original size:22 final size:22
Alignment explanation
Indices: 10747--10789 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10737 TTTCTGATTA
**
10747 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
10769 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
10790 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:20147 original size:22 final size:21
Alignment explanation
Indices: 20095--20148 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
20085 GCTTCTTGGA
20095 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
20116 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
20135 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
20149 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:23935 original size:21 final size:21
Alignment explanation
Indices: 23894--23937 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23884 ATTACATTCC
*
23894 CATCTGTACAGTACCTCATCT
1 CATCTGTACAGTACCTAATCT
23915 CATCTGTACAGTAACC-AATCT
1 CATCTGTACAGT-ACCTAATCT
23936 CA
1 CA
23938 CCATTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (21 bp):
CATCTGTACAGTACCTAATCT
Found at i:34557 original size:66 final size:66
Alignment explanation
Indices: 34456--34579 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
34446 CCGACAGGAT
* * * * *
34456 TATATGTGTCACGTTGGTGGGCCTCGTAACGACGAGACCG-GATTACTCTCTCTTCTACGACAAG
1 TATATGAGCCACGTTGGTGGACCTCGTAACAACGAGAACGAG-TTACTCTCTCTTCTACGACAAG
34520 TA
65 TA
34522 TATATGAGCCACGTTGGTGGACCTCGTAACAACGAGAACGAGTTACTCTCTCTTCTAC
1 TATATGAGCCACGTTGGTGGACCTCGTAACAACGAGAACGAGTTACTCTCTCTTCTAC
34580 AGCTAGCCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (66 bp):
TATATGAGCCACGTTGGTGGACCTCGTAACAACGAGAACGAGTTACTCTCTCTTCTACGACAAGT
A
Found at i:35826 original size:14 final size:14
Alignment explanation
Indices: 35807--35833 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35797 TTATGAATTT
35807 TCTTCCAAGACTGC
1 TCTTCCAAGACTGC
35821 TCTTCCAAGACTG
1 TCTTCCAAGACTG
35834 AATCATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (14 bp):
TCTTCCAAGACTGC
Found at i:36988 original size:21 final size:21
Alignment explanation
Indices: 36964--37048 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 21
36954 TCTCACAGAG
**
36964 AGGTTATAAAAAATCATAGGA
1 AGGTTATAAAATTTCATAGGA
*
36985 AGGTTACAAAATTTCATAGGA
1 AGGTTATAAAATTTCATAGGA
37006 AGGTTTATTAAAATTTCATAGGA
1 AGG-TTA-TAAAATTTCATAGGA
*
37029 ATGTTTATTAAAATTTCATA
1 A-GGTTA-TAAAATTTCATA
37049 ATTAGGTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 21 0.38
22 3 0.05
23 31 0.55
24 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATAAAATTTCATAGGA
Found at i:37010 original size:42 final size:44
Alignment explanation
Indices: 36928--37048 Score: 104
Period size: 43 Copynumber: 2.7 Consensus size: 44
36918 CTACAGTAAC
* * * *
36928 AAAAAATTATAGGGAGATTAACAAAATCTCACAGAGAGG-TTA-T
1 AAAAAATCATAGGAAGATT-ACAAAATTTCATAGAGAGGTTTATT
*
36971 AAAAAATCATAGGAAGGTTACAAAATTTCATAG-GAAGGTTTATT
1 AAAAAATCATAGGAAGATTACAAAATTTCATAGAG-AGGTTTATT
** * *
37015 AAAATTTCATAGGAATGTTTATTAAAATTTCATA
1 AAAAAATCATAGGAA-GATTA-CAAAATTTCATA
37049 ATTAGGTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 15 0.23
43 19 0.30
44 14 0.22
45 4 0.06
46 11 0.17
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (44 bp):
AAAAAATCATAGGAAGATTACAAAATTTCATAGAGAGGTTTATT
Found at i:37022 original size:23 final size:23
Alignment explanation
Indices: 36977--37048 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
36967 TTATAAAAAA
*
36977 TCATAGGAAGG-TTA-CAAAATT
1 TCATAGGAAGGTTTATTAAAATT
36998 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
*
37021 TCATAGGAATGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
37044 TCATA
1 TCATA
37049 ATTAGGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.23
22 3 0.06
23 33 0.70
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (23 bp):
TCATAGGAAGGTTTATTAAAATT
Found at i:37112 original size:22 final size:22
Alignment explanation
Indices: 37084--37144 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
37074 CATAGGTAAA
*
37084 TTATCAAAATTCT-ATAACATGG
1 TTATCAAAATT-TAATAACATAG
*
37106 TTATCAAAATTTAATAAGATAG
1 TTATCAAAATTTAATAACATAG
*
37128 TTATCAAAATTTCATAA
1 TTATCAAAATTTAATAA
37145 AAACATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTAATAACATAG
Found at i:37333 original size:15 final size:16
Alignment explanation
Indices: 37313--37342 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37303 ATTGATTGGC
37313 ATTTGGG-TTTTGGGT
1 ATTTGGGATTTTGGGT
37328 ATTTGGGATTTTGGG
1 ATTTGGGATTTTGGG
37343 CATTACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (16 bp):
ATTTGGGATTTTGGGT
Found at i:37992 original size:11 final size:11
Alignment explanation
Indices: 37949--37986 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
37939 TTCCTATATA
*
37949 AAATAAATTAT
1 AAATTAATTAT
37960 CAAA-TAATTAT
1 -AAATTAATTAT
37971 AAATTAATTAT
1 AAATTAATTAT
37982 AAATT
1 AAATT
37987 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:39128 original size:11 final size:11
Alignment explanation
Indices: 39085--39122 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39075 TTCCTATATA
*
39085 AAATAAATTAT
1 AAATTAATTAT
39096 CAAA-TAATTAT
1 -AAATTAATTAT
39107 AAATTAATTAT
1 AAATTAATTAT
39118 AAATT
1 AAATT
39123 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.