Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024394.1 Corchorus olitorius cultivar O-4 contig24427, 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: 10395
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Found at i:783 original size:21 final size:20
Alignment explanation
Indices: 749--819 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
739 AAAGTGCTAA
* * *
749 GACCAATTTATTAAAACAATT
1 GACCAAGTT-TTAAGACAAGT
770 GACCCAAGTTTTAAGACAAGT
1 GA-CCAAGTTTTAAGACAAGT
*
791 GAACAAAGTTTTAAGACAAGT
1 G-ACCAAGTTTTAAGACAAGT
812 GACCAAGT
1 GACCAAGT
820 GCAAATATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.14
21 30 0.70
22 7 0.16
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
GACCAAGTTTTAAGACAAGT
Found at i:1034 original size:27 final size:27
Alignment explanation
Indices: 975--1044 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
965 AATCTAACTT
*
975 AAAATGACCAAAATGCTTCTGAATGTG
1 AAAATGACCAAAATGCTTCTGAATGTA
** *
1002 CGAATGACCAAAATGCTTCT-AGTGTAA
1 AAAATGACCAAAATGCTTCTGAATGT-A
1029 AAAATGACCAAAATGC
1 AAAATGACCAAAATGC
1045 CCCCTAGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (27 bp):
AAAATGACCAAAATGCTTCTGAATGTA
Found at i:1852 original size:69 final size:69
Alignment explanation
Indices: 1741--2005 Score: 377
Period size: 69 Copynumber: 3.8 Consensus size: 69
1731 CTCTGCAGGA
* * * * * * *
1741 TGGATGGAACCAATGTTTGAATTGACTCGCATGGAAACGAGTTTGACTTACGGACAAGTCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCTATAT
1806 GGCT
66 GGCT
* * * *
1810 TGGATGGGACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCTATAT
1875 GGCT
66 GGCT
* * * *
1879 TGGATGGAACCAAGACTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCTATAT
1944 GGCT
66 GGCT
* *
1948 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGACTTATGTAAAAG
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAG
2006 TCAAAGCATT
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 176 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (69 bp):
TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCTATAT
GGCT
Found at i:2195 original size:91 final size:91
Alignment explanation
Indices: 2092--2270 Score: 270
Period size: 92 Copynumber: 2.0 Consensus size: 91
2082 ATACCTTTGG
*** * *
2092 AAAATAACTCTGAATCTGATGTTGTGGTTG-AAACTTCTTGATTGATGATGAGAAAGGACCCATG
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
2156 TGCGGTCAACTTTGAAAAACAACTTGA
66 TGCGGTCAAC-TTGAAAAACAACTTGA
*
2183 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
* *
2248 TGTGGTCAACTTGAAAAATAACT
66 TGCGGTCAACTTGAAAAACAACT
2271 CTGGTCTGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 38 0.48
92 41 0.52
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (91 bp):
AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
TGCGGTCAACTTGAAAAACAACTTGA
Found at i:2762 original size:48 final size:50
Alignment explanation
Indices: 2697--2819 Score: 160
Period size: 48 Copynumber: 2.5 Consensus size: 50
2687 TAGTCTTTGT
* * * *
2697 CTCATAAATGGAGTGCAATCTTATTTTTAAAAGCGAA-TTTGAT-TTGGA
1 CTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAATTTTGATCTTGAA
* *
2745 CTCACAAATGGAATGCAATCTTGTTTTGAAAAGTGAATTTTGATCTTGAA
1 CTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAATTTTGATCTTGAA
* *
2795 CTCGCAAATGGGATGCAATCTTATT
1 CTCACAAATGGAATGCAATCTTATT
2820 ATAAAAATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 32 0.50
49 6 0.09
50 26 0.41
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (50 bp):
CTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAATTTTGATCTTGAA
Found at i:3424 original size:6 final size:6
Alignment explanation
Indices: 3413--3440 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3403 CAATTCTCTT
3413 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
3441 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:3465 original size:12 final size:12
Alignment explanation
Indices: 3450--3495 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
3440 TTTTTAAAAA
3450 TTTTTTGTTGTT
1 TTTTTTGTTGTT
3462 TTTTTTGTTGTT
1 TTTTTTGTTGTT
* *
3474 GTTTTTTTTTGAT
1 -TTTTTTGTTGTT
3487 TTTTTTGTT
1 TTTTTTGTT
3496 TTTGAATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (12 bp):
TTTTTTGTTGTT
Found at i:3472 original size:15 final size:14
Alignment explanation
Indices: 3450--3483 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
3440 TTTTTAAAAA
3450 TTTTTTGTTGTTTT
1 TTTTTTGTTGTTTT
3464 TTTTGTTGTTGTTTT
1 TTTT-TTGTTGTTTT
3479 TTTTT
1 TTTTT
3484 GATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (14 bp):
TTTTTTGTTGTTTT
Found at i:3504 original size:16 final size:14
Alignment explanation
Indices: 3450--3500 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3440 TTTTTAAAAA
3450 TTTTTTG-TTGTTTT
1 TTTTTTGATT-TTTT
*
3464 TTTTGTTG-TTGTTT
1 TTTT-TTGATTTTTT
3478 TTTTTTGATTTTTT
1 TTTTTTGATTTTTT
3492 TGTTTTTGA
1 T-TTTTTGA
3501 ATTTCTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 3 0.09
14 17 0.53
15 12 0.38
ACGTcount: A:0.04, C:0.00, G:0.16, T:0.80
Consensus pattern (14 bp):
TTTTTTGATTTTTT
Found at i:3790 original size:13 final size:13
Alignment explanation
Indices: 3774--3798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3764 AACGAGTTTC
3774 GAAATCAATTTTG
1 GAAATCAATTTTG
3787 GAAATCAATTTT
1 GAAATCAATTTT
3799 ATCAAAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
GAAATCAATTTTG
Found at i:8085 original size:78 final size:78
Alignment explanation
Indices: 7988--8149 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 78
7978 CTTTGAATTA
7988 TCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACCGTCTTCCAATTCAATC
1 TCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACCGTCTTCCAATTCAATC
8053 TTAAAAAGGACCG
66 TTAAAAAGGACCG
* * ** *
8066 TCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAATTGTCTTCCAATTCATTC
1 TCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACCGTCTTCCAATTCAATC
8131 TTAAAAAGGACCG
66 TTAAAAAGGACCG
8144 TCTTCC
1 TCTTCC
8150 GCTTATCCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (78 bp):
TCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACCGTCTTCCAATTCAATC
TTAAAAAGGACCG
Found at i:8094 original size:27 final size:28
Alignment explanation
Indices: 8034--8098 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
8024 TATCCTTTGA
8034 ACCGTCTTCCAATTCAATCTTAAAAAGG
1 ACCGTCTTCCAATTCAATCTTAAAAAGG
8062 ACCGTCTTCCAATTCAATCTT-AAAAGG
1 ACCGTCTTCCAATTCAATCTTAAAAAGG
8089 ACCGTCTTCC
1 ACCGTCTTCC
8099 GCTTATCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (28 bp):
ACCGTCTTCCAATTCAATCTTAAAAAGG
Found at i:8154 original size:51 final size:51
Alignment explanation
Indices: 8065--8599 Score: 814
Period size: 51 Copynumber: 10.5 Consensus size: 51
8055 AAAAAGGACC
* *
8065 GTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAATT
1 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
8115 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
* *
8166 GTATTCCAATTCATTCTTAAAAAGGACCGTCTTTCGCTTATCCTTTGAACT
1 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
*
8217 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTATGAACT
1 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
*
8268 GTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
8319 GTCTTCCAATTCCATTC-TAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATT-CATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
*
8370 GTCTACCAATTCAATTC-T-AAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATTC-ATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
*
8420 GTCTACCAATTCAATTC-TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATTC-ATTCTTA-AAAAGGACCGTCTTCCGCTTATCCTTTGAACT
*
8472 GTCTACCAATTCAATTC-TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCAATTC-ATTCTTA-AAAAGGACCGTCTTCCGCTTATCCTTTGAACT
* **
8524 GTCTACCAATTCAATTC-TATAAAAGGACCGTCTTCCATTTATCCTTTGAACT
1 GTCTTCCAATTC-ATTCTTA-AAAAGGACCGTCTTCCGCTTATCCTTTGAACT
* *
8576 GTCTACCAATTCAATCTTGAAAAA
1 GTCTTCCAATTCATTCTT-AAAAA
8600 AGGTAATGCA
Statistics
Matches: 464, Mismatches: 14, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
50 68 0.15
51 240 0.52
52 155 0.33
53 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (51 bp):
GTCTTCCAATTCATTCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
Found at i:8713 original size:50 final size:50
Alignment explanation
Indices: 8654--8989 Score: 548
Period size: 50 Copynumber: 6.7 Consensus size: 50
8644 AGGTTTGAAA
* * * *
8654 TGACTCGTATGGAAATGAGTTCGACTTGTGGAAAAACCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
8704 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
8754 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
8804 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
8854 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
8904 TGACTCGTATGGGAAA-GAGTGTGGCTTGTGGAAAAGCCTCTGTTGATAAT
1 TGACTCGTAT-GGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
8954 TGACTCGTATGGAAACGAGTGTGGCTTATGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
8990 TCCACACATT
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 5 0.02
50 260 0.96
51 5 0.02
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Done.