Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017375.1 Corchorus olitorius cultivar O-4 contig17408, 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: 44493
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:3003 original size:141 final size:140
Alignment explanation
Indices: 2749--3034 Score: 502
Period size: 141 Copynumber: 2.0 Consensus size: 140
2739 CCTAGACATC
* * *
2749 ATTATTCTTAATTCAGATGACAAAGTCCATCATAAAATCCTTTTACAGGATCAACTAACTACAGT
1 ATTATTCTTAATTCAGATGACAAAGTCCATAATAAAATCCTTTTACAAGATCAACTAACTACAAT
2814 CTCAAGCTTTCATCCTTCAAAATGATACAAGCAAACACGAGAATGGGCTCAATTTTTGAAGTTGA
66 CTCAAGCTTTCATCCTTCAAAATGATACAAGCAAACACGAGAATGGGCTCAA-TTTTGAAGTTGA
2879 GACTTGTAGAT
130 GACTTGTAGAT
*
2890 ATTATTCTTAATTCAGATGACAAAGTCTATAAT-AAATCCTTATTACAAGATCAACTAACTACAA
1 ATTATTCTTAATTCAGATGACAAAGTCCATAATAAAATCCTT-TTACAAGATCAACTAACTACAA
*
2954 TCTCAAGCTTTCATCCTTCAAAATGTTACAAGCAAACACGAGAATGGGCTCAATTTTGAAGTTGA
65 TCTCAAGCTTTCATCCTTCAAAATGATACAAGCAAACACGAGAATGGGCTCAATTTTGAAGTTGA
3019 GACTTGTAGAT
130 GACTTGTAGAT
3030 ATTAT
1 ATTAT
3035 GGCCGGAGGT
Statistics
Matches: 139, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
140 36 0.26
141 103 0.74
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (140 bp):
ATTATTCTTAATTCAGATGACAAAGTCCATAATAAAATCCTTTTACAAGATCAACTAACTACAAT
CTCAAGCTTTCATCCTTCAAAATGATACAAGCAAACACGAGAATGGGCTCAATTTTGAAGTTGAG
ACTTGTAGAT
Found at i:6441 original size:20 final size:20
Alignment explanation
Indices: 6412--6449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6402 TTATAGAAAG
*
6412 TAAAAGGAAAAGGAAAAGAA
1 TAAAAGGAAAAAGAAAAGAA
*
6432 TAAAATGAAAAAGAAAAG
1 TAAAAGGAAAAAGAAAAG
6450 TGTCAATGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (20 bp):
TAAAAGGAAAAAGAAAAGAA
Found at i:11990 original size:2 final size:2
Alignment explanation
Indices: 11983--12021 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11973 TGGAAAGAAA
*
11983 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12022 ATAATCCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15413 original size:34 final size:34
Alignment explanation
Indices: 15372--15456 Score: 170
Period size: 34 Copynumber: 2.5 Consensus size: 34
15362 TTTAACTGCA
15372 TGCTTCTTTTGTATTGAAACCCTTTAGCAATGAC
1 TGCTTCTTTTGTATTGAAACCCTTTAGCAATGAC
15406 TGCTTCTTTTGTATTGAAACCCTTTAGCAATGAC
1 TGCTTCTTTTGTATTGAAACCCTTTAGCAATGAC
15440 TGCTTCTTTTGTATTGA
1 TGCTTCTTTTGTATTGA
15457 CTATTGAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (34 bp):
TGCTTCTTTTGTATTGAAACCCTTTAGCAATGAC
Found at i:18138 original size:39 final size:39
Alignment explanation
Indices: 18083--18504 Score: 349
Period size: 39 Copynumber: 10.8 Consensus size: 39
18073 CCAAGCTGAA
* *
18083 TTTTGTTGAGAACCCCAACCTTGTGAAGGTTCAGGTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
18122 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
18161 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
18200 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
* * * * *
18239 TTTTCTTGTA-AGCCCCCACCTTGTGAATGGTCCA-TTGAC
1 TTTTGTTG-AGAGCCCCAACCTGGTGAA-GGTTCAGGTGAC
* * * * *
18278 TTCTT-TTGAGACCCCCAACCTTGTGTATGTTCTGGTGAC
1 TT-TTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
* * * * ** * *
18317 TTTTGGTGTGAGTCCCAGCCTTCTGAATGGTCCA-CTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAA-GGTTCAGGTGAC
* * * * * ***
18356 TTTTTTTGGGACCCCCAACCCGGCGAAGAG-TCTTCTGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAAG-GTTCAGGTGAC
* * * * **
18395 TTCTGTTGGGAGTCCCAACCTCGTGAATGG-TCAGCAGAC
1 TTTTGTTGAGAGCCCCAACCTGGTGAA-GGTTCAGGTGAC
* * *
18434 TTTTGTTGGGAGCCCCAACCTGGTGAATGG-TCCGCTGA-
1 TTTTGTTGAGAGCCCCAACCTGGTGAA-GGTTCAGGTGAC
* *
18472 TTTCTGTTGGGAGCCCCATA-CTGGTGAATGTTC
1 TTT-TGTTGAGAGCCCCA-ACCTGGTGAAGGTTC
18505 CACCAACTTT
Statistics
Matches: 317, Mismatches: 53, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
38 12 0.04
39 292 0.92
40 13 0.04
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (39 bp):
TTTTGTTGAGAGCCCCAACCTGGTGAAGGTTCAGGTGAC
Found at i:31710 original size:21 final size:22
Alignment explanation
Indices: 31679--31722 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
31669 TTTGGCGCGC
31679 GAAATTTCAAAATTCGAATTTT
1 GAAATTTCAAAATTCGAATTTT
*
31701 GAAA-TTCAAAATTTGAATTTT
1 GAAATTTCAAAATTCGAATTTT
31722 G
1 G
31723 GAAGTTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
GAAATTTCAAAATTCGAATTTT
Found at i:31957 original size:42 final size:41
Alignment explanation
Indices: 31874--31957 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
31864 TTTCCTGAAA
* * *
31874 TTTCCTAAACTTTATCCTCGTTGTTCGTCAAGTTCTCCAGC
1 TTTCCTAAACTTTATCCTCGTCGCTCGTCAAATTCTCCAGC
* * *
31915 TTTCCTAAGCTTTATTCTCGTACGCTCGTCAAATTTTCCAGC
1 TTTCCTAAACTTTATCCTCGT-CGCTCGTCAAATTCTCCAGC
31957 T
1 T
31958 CTTGTCTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 19 0.53
42 17 0.47
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.42
Consensus pattern (41 bp):
TTTCCTAAACTTTATCCTCGTCGCTCGTCAAATTCTCCAGC
Found at i:35603 original size:77 final size:76
Alignment explanation
Indices: 35467--35691 Score: 333
Period size: 77 Copynumber: 2.9 Consensus size: 76
35457 AACATGGGTG
* *
35467 GACGAACGGGGGTGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTTTGCGTGGACGCTCTG
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
35532 TCTCACTAAATA
66 TCTCACT-AATA
* * *
35544 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTAAGCGGCGTCTGCGGGGACGCTCCG
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
**
35609 TCTCACTGGTA
66 TCTCACTAATA
* * * * *
35620 GACGAACGGGGGCGCCAGTCTAGGCACTGAGCCGTTTAGTGAGCGGCGTCTACGTGGACGCTCTA
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
35685 TCTCACT
66 TCTCACT
35692 GGTGGGCGAA
Statistics
Matches: 133, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 66 0.50
77 67 0.50
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (76 bp):
GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
TCTCACTAATA
Found at i:35665 original size:76 final size:76
Alignment explanation
Indices: 35467--35708 Score: 349
Period size: 76 Copynumber: 3.2 Consensus size: 76
35457 AACATGGGTG
* *
35467 GACGAACGGGGGTGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTTTGCGTGGACGCTCTG
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
**
35532 TCTCACTAAATA
66 TCTCACT-GGTA
* * *
35544 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTAAGCGGCGTCTGCGGGGACGCTCCG
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
35609 TCTCACTGGTA
66 TCTCACTGGTA
* * * * *
35620 GACGAACGGGGGCGCCAGTCTAGGCACTGAGCCGTTTAGTGAGCGGCGTCTACGTGGACGCTCTA
1 GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
*
35685 TCTCACTGGTG
66 TCTCACTGGTA
*
35696 GGCGAACGGGGGC
1 GACGAACGGGGGC
35709 ACCATTCTGG
Statistics
Matches: 148, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 81 0.55
77 67 0.45
ACGTcount: A:0.18, C:0.26, G:0.37, T:0.20
Consensus pattern (76 bp):
GACGAACGGGGGCGCCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
TCTCACTGGTA
Found at i:42949 original size:26 final size:28
Alignment explanation
Indices: 42897--42950 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
42887 ACCATCTAAC
**
42897 TATATTAATAAACTTTTTTTGAGATAAAT
1 TATATTAATAAAC-TTTTTACAGATAAAT
42926 TATATTAATAAAC-TTTTACA-ATAAA
1 TATATTAATAAACTTTTTACAGATAAA
42951 AAACTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 5 0.22
29 13 0.57
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATTAATAAACTTTTTACAGATAAAT
Found at i:43625 original size:145 final size:145
Alignment explanation
Indices: 43362--43650 Score: 551
Period size: 145 Copynumber: 2.0 Consensus size: 145
43352 TACACTGATG
43362 TTGTATTGTATAATCATCCTTTAAGAATTATATTAAAAATTTCTAATATATCTTAGTTTTTTAAT
1 TTGTATTGTATAATCATCCTTTAAGAATTATATTAAAAATTTCTAATATATCTTAGTTTTTTAAT
*
43427 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTAAATTAAATTAAATTAAAAATT
66 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTAAATTAAATTAAATTAAAAAAT
43492 TCTAATATAACTCAA
131 TCTAATATAACTCAA
43507 TTGTATTGTATAATCATCCTTTAAGAATTATATTAAAAATTTCTAATATATCTTAGTTTTTTAAT
1 TTGTATTGTATAATCATCCTTTAAGAATTATATTAAAAATTTCTAATATATCTTAGTTTTTTAAT
* *
43572 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATTAAAAAAT
66 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTAAATTAAATTAAATTAAAAAAT
43637 TCTAATATAACTCA
131 TCTAATATAACTCA
43651 GTTCTTAATA
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 141 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (145 bp):
TTGTATTGTATAATCATCCTTTAAGAATTATATTAAAAATTTCTAATATATCTTAGTTTTTTAAT
TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTAAATTAAATTAAATTAAAAAAT
TCTAATATAACTCAA
Done.