Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017215.1 Corchorus olitorius cultivar O-4 contig17248, 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: 20888
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Found at i:6939 original size:41 final size:40
Alignment explanation
Indices: 6842--6945 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 40
6832 AATCAAAAAT
* * *
6842 AAAATCCTAAATCAGGGGCGAAATTGAATCAATTAACAAAT
1 AAAATCCT-AATCAGGGACCAAATTGAATCAATTAACAAAC
* *
6883 AAACATTCC-AATCAGGGACCAAATTGTATCAATTAATAAAC
1 AAA-A-TCCTAATCAGGGACCAAATTGAATCAATTAACAAAC
*
6924 AAAAACCTAATTCAGGGACCAA
1 AAAATCCTAA-TCAGGGACCAA
6946 GGGGAAAACA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.04
40 3 0.06
41 44 0.83
42 1 0.02
43 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (40 bp):
AAAATCCTAATCAGGGACCAAATTGAATCAATTAACAAAC
Found at i:7042 original size:22 final size:23
Alignment explanation
Indices: 6998--7042 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6988 ACAATTTGTA
* * *
6998 GGATTTAATTGAATTAAATTTAG
1 GGATTAAATTGAATGAAAGTTAG
7021 GGATTAAATTGAA-GAAAGTTAG
1 GGATTAAATTGAATGAAAGTTAG
7043 AAACTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (23 bp):
GGATTAAATTGAATGAAAGTTAG
Found at i:8914 original size:58 final size:57
Alignment explanation
Indices: 8834--8961 Score: 211
Period size: 58 Copynumber: 2.2 Consensus size: 57
8824 GCTAACTTAC
8834 CAATGATAGCATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTTTCCAAATG
1 CAAT-ATAG-ATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTTT-CAAATG
* *
8894 CAATATAGATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTTTTAATTG
1 CAATATAGATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTTTCAAATG
8951 CAATATAGATG
1 CAATATAGATG
8962 ATTAAGAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
57 15 0.23
58 43 0.65
59 4 0.06
60 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (57 bp):
CAATATAGATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTTTCAAATG
Found at i:9070 original size:27 final size:27
Alignment explanation
Indices: 8998--9069 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
8988 AAGTGAATCT
*
8998 AAAATGACCAAAATGCCCCTGGATGTG
1 AAAATGACCAAAATGCCCCTGGATGTA
* *
9025 CAAATGACCAAAATGCCCCTTG-TGTA
1 AAAATGACCAAAATGCCCCTGGATGTA
9051 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
9070 CTAGGTGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGATGTA
Found at i:9611 original size:69 final size:69
Alignment explanation
Indices: 9527--9947 Score: 646
Period size: 69 Copynumber: 6.1 Consensus size: 69
9517 CTCATTAAAC
* * * * * * * * *
9527 TTGGCTTATGGAAAAGCCTCTGTTG-TATGGATGGAACCAATGTTTAAACTGACTCGCATGGAAA
1 TTGGCTTGTGGAAAAGCCTATATGGCT-TGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAA
*
9591 CAAGT
65 CGAGT
* * * * *
9596 TTGACTTATGGAAAAGTCTATATGGCTTGGATGAAACCAAGACTTGAACTGACTTGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
9661 GAGT
66 GAGT
*
9665 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
9730 GAGT
66 GAGT
9734 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
9799 GAGT
66 GAGT
*
9803 TCGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
9868 GAGT
66 GAGT
* * *
9872 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAAACAAGGCTTGAACTGACTCGTACGAAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
9937 GAGT
66 GAGT
9941 TTGGCTT
1 TTGGCTT
9948 TGCCTATGTT
Statistics
Matches: 326, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
69 325 1.00
70 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:10024 original size:50 final size:50
Alignment explanation
Indices: 9949--10136 Score: 349
Period size: 50 Copynumber: 3.8 Consensus size: 50
9939 GTTTGGCTTT
*
9949 GCCTATGTTGATAATTAACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
1 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
*
9999 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAA
1 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
10049 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
1 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
*
10099 ACCTATGTTGATAATTGACTCGTATGGAAACGAGTTTG
1 GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTG
10137 ACTTATGTAA
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (50 bp):
GCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
Found at i:10339 original size:91 final size:91
Alignment explanation
Indices: 10236--10528 Score: 459
Period size: 91 Copynumber: 3.3 Consensus size: 91
10226 ATACCTTTGG
* * ** *
10236 AAAATAACTCTGAATCTGATGTTGTAACTGGAACCTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAAGGACCAATT
*
10301 TGCAGTCAACTTGAAAAACAACTTGA
66 TGCGGTCAACTTGAAAAACAACTTGA
10327 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAAGGACCAATT
10392 TGCGGTCAACTTGAAAAACAACTTGA
66 TGCGGTCAACTTGAAAAACAACTTGA
*
10418 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAATGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAAGGACCAATT
* *
10483 TGCGGTCAATTTTG----ATAACTTGA
66 TGCGGTCAA-CTTGAAAAACAACTTGA
*
10506 AGAATAACTCTGAGTCTGATGTT
1 AAAATAACTCTGAGTCTGATGTT
10529 ATGATTAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
88 30 0.16
91 158 0.83
92 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (91 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAAAAGGACCAATT
TGCGGTCAACTTGAAAAACAACTTGA
Found at i:11024 original size:49 final size:49
Alignment explanation
Indices: 10938--11051 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 49
10928 CCCTTCGAAG
*
10938 AGCGAGTTTTGATCTTAGACTCACAAATGAAATGCAATCCTACTTTGAAA
1 AGCGAATTTTGATC-TAGACTCACAAATGAAATGCAATCCTACTTTGAAA
* * * **
10988 AGCGAATTTTGATCTGGGCTCACAAATGGAAA-GCAATCTTGTTTTGAAA
1 AGCGAATTTTGATCTAGACTCACAAAT-GAAATGCAATCCTACTTTGAAA
* *
11037 ACCAAATTTTGATCT
1 AGCGAATTTTGATCT
11052 TGCAACCTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 38 0.69
50 17 0.31
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (49 bp):
AGCGAATTTTGATCTAGACTCACAAATGAAATGCAATCCTACTTTGAAA
Found at i:11063 original size:33 final size:33
Alignment explanation
Indices: 11020--11086 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
11010 CAAATGGAAA
*
11020 GCAATCTTGTTTTGAAAACCAAATTTTGATCTT
1 GCAACCTTGTTTTGAAAACCAAATTTTGATCTT
*
11053 GCAACCTTGTTTTGAAAAGCAAATTTTGATCTT
1 GCAACCTTGTTTTGAAAACCAAATTTTGATCTT
11086 G
1 G
11087 AACTCACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
GCAACCTTGTTTTGAAAACCAAATTTTGATCTT
Found at i:11755 original size:20 final size:20
Alignment explanation
Indices: 11726--11775 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11716 CCCTTTTTGG
11726 TTTTGATTTTGAT-TTGATTTT
1 TTTTG-TTTTGATATTGA-TTT
**
11747 TTTTGTTTTTTTATTGATTT
1 TTTTGTTTTGATATTGATTT
11767 TTTTGTTTT
1 TTTTGTTTT
11776 TTTTTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTGATATTGATTT
Found at i:11763 original size:26 final size:28
Alignment explanation
Indices: 11734--11797 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
11724 GGTTTTGATT
11734 TTGATTTGATTTT-TTTTGTTTT-TTTA
1 TTGATTTGATTTTGTTTTGTTTTCTTTA
*
11760 TTGATTT--TTTTGTTTTTTTTTCTTTA
1 TTGATTTGATTTTGTTTTGTTTTCTTTA
11786 TTGATTTTGATT
1 TTGA-TTTGATT
11798 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 4 0.12
25 8 0.25
26 15 0.47
27 3 0.09
29 2 0.06
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.77
Consensus pattern (28 bp):
TTGATTTGATTTTGTTTTGTTTTCTTTA
Found at i:11776 original size:21 final size:21
Alignment explanation
Indices: 11739--11847 Score: 78
Period size: 23 Copynumber: 5.0 Consensus size: 21
11729 TGATTTTGAT
11739 TTGATTTTTTTTGTTTTTTTA
1 TTGATTTTTTTTGTTTTTTTA
*
11760 TTGATTTTTTTGTTTTTTTTTCTTTA
1 TTGA---TTTT-TTTTGTTTT-TTTA
**
11786 TTGATTTTGATTGATTTTTTTA
1 TTGATTTTTTTTG-TTTTTTTA
**
11808 TTTGATTTTTTTTG-AATTTT-
1 -TTGATTTTTTTTGTTTTTTTA
* *
11828 TTGAATTTTTGTGTTTTTTT
1 TTGATTTTTTTTGTTTTTTT
11848 TTAATTTCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
19 11 0.16
20 4 0.06
21 8 0.12
22 6 0.09
23 19 0.28
24 4 0.06
25 8 0.12
26 8 0.12
ACGTcount: A:0.12, C:0.01, G:0.11, T:0.76
Consensus pattern (21 bp):
TTGATTTTTTTTGTTTTTTTA
Found at i:11803 original size:26 final size:26
Alignment explanation
Indices: 11734--11806 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
11724 GGTTTTGATT
* *
11734 TTGA-TTTGATTTTTTTTGTTTTTTTA
1 TTGATTTTGATTGTTTTT-TTTCTTTA
*
11760 TTGATTTT-TTTGTTTTTTTTTCTTTA
1 TTGATTTTGATTG-TTTTTTTTCTTTA
*
11786 TTGATTTTGATTGATTTTTTT
1 TTGATTTTGATTGTTTTTTTT
11807 ATTTGATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 28 0.72
27 11 0.28
ACGTcount: A:0.11, C:0.01, G:0.11, T:0.77
Consensus pattern (26 bp):
TTGATTTTGATTGTTTTTTTTCTTTA
Found at i:11819 original size:26 final size:24
Alignment explanation
Indices: 11732--11819 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 24
11722 TTGGTTTTGA
*
11732 TTTTGATTTGA-TTTTTT-TTGTT
1 TTTTTATTTGATTTTTTTGTTGTT
11754 TTTTTA-TTGATTTTTTTGTT-TT
1 TTTTTATTTGATTTTTTTGTTGTT
* *
11776 TTTTTCTTT-ATTGATTTTGATTGATT
1 TTTTTATTTGATT-TTTTTG-TTG-TT
11802 TTTTTATTTGATTTTTTT
1 TTTTTATTTGATTTTTTT
11820 TGAATTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.08
22 21 0.40
23 9 0.17
24 2 0.04
26 14 0.26
27 3 0.06
ACGTcount: A:0.11, C:0.01, G:0.10, T:0.77
Consensus pattern (24 bp):
TTTTTATTTGATTTTTTTGTTGTT
Found at i:15067 original size:13 final size:13
Alignment explanation
Indices: 15049--15078 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15039 GACAAGCTGG
15049 AGGGTATAAAGGT
1 AGGGTATAAAGGT
15062 AGGGTATAAAGGT
1 AGGGTATAAAGGT
15075 -GGGT
1 AGGGT
15079 CACTCAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (13 bp):
AGGGTATAAAGGT
Found at i:18515 original size:41 final size:40
Alignment explanation
Indices: 18470--18555 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
18460 TTGAATGAAG
*
18470 CAGGGA-TCAAATTGCATTCAATCAAGAAAT-AAATCATAAAT
1 CAGGGACTCAAA-TGCA-TAAATCAA-AAATAAAATCATAAAT
* * *
18511 CAGGGACTGAGATGCATAAATCAAAAATAAAATCCTAAAT
1 CAGGGACTCAAATGCATAAATCAAAAATAAAATCATAAAT
18551 CAGGG
1 CAGGG
18556 GCGGAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 4 0.10
40 22 0.56
41 10 0.26
42 3 0.08
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.21
Consensus pattern (40 bp):
CAGGGACTCAAATGCATAAATCAAAAATAAAATCATAAAT
Found at i:18739 original size:22 final size:23
Alignment explanation
Indices: 18695--18739 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18685 ACAATTTGTA
* * *
18695 GGATTTAATTGAATTAAATTTAG
1 GGATTAAATTGAATGAAAGTTAG
18718 GGATTAAATTGAA-GAAAGTTAG
1 GGATTAAATTGAATGAAAGTTAG
18740 AAACTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (23 bp):
GGATTAAATTGAATGAAAGTTAG
Done.