Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015798.1 Corchorus olitorius cultivar O-4 contig15831, 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: 59445
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2228 original size:31 final size:31
Alignment explanation
Indices: 2190--2256 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2180 TTGATTATAT
*
2190 ATATTTTTTCTATAATTAAAGGTCAAAGGTA
1 ATATTTTTTCTATAAATAAAGGTCAAAGGTA
* * *
2221 ATATTTTTTTTTTAAATGAAGGTCAAAGGTA
1 ATATTTTTTCTATAAATAAAGGTCAAAGGTA
2252 ATATT
1 ATATT
2257 AGTTTGACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (31 bp):
ATATTTTTTCTATAAATAAAGGTCAAAGGTA
Found at i:2783 original size:15 final size:15
Alignment explanation
Indices: 2763--2792 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2753 AATTAGAAAA
2763 GGGTGTAAAACAACT
1 GGGTGTAAAACAACT
2778 GGGTGTAAAACAACT
1 GGGTGTAAAACAACT
2793 TAATCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
GGGTGTAAAACAACT
Found at i:3597 original size:3 final size:3
Alignment explanation
Indices: 3589--3629 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
3579 TTAAGGTAAA
*
3589 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3630 TTCAAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:10382 original size:17 final size:16
Alignment explanation
Indices: 10357--10388 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
10347 CTTCTTCTTC
10357 TTTTTTTTTTTTTAAT
1 TTTTTTTTTTTTTAAT
10373 TTTTTATTTTTTTTAA
1 TTTTT-TTTTTTTTAA
10389 CCTTAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTTTTAAT
Found at i:19184 original size:21 final size:21
Alignment explanation
Indices: 19159--19223 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
19149 ATTATGTTGA
*
19159 GAGTAGCTAGATTGCCTAACT
1 GAGTAGCTAAATTGCCTAACT
*
19180 GAGTAGCTACATTGCCTAACT
1 GAGTAGCTAAATTGCCTAACT
* *
19201 AAGTAGTTAAATTGCCTAACT
1 GAGTAGCTAAATTGCCTAACT
19222 GA
1 GA
19224 CGGTGTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (21 bp):
GAGTAGCTAAATTGCCTAACT
Found at i:21841 original size:16 final size:16
Alignment explanation
Indices: 21792--21845 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
21782 AGCAGTTATC
*
21792 TCGGGTCATTTGGGTT
1 TCGGGTCATTCGGGTT
*
21808 TCGAGTCA-TCTGGG-T
1 TCGGGTCATTC-GGGTT
*
21823 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
21839 TCGGGTC
1 TCGGGTC
21846 TCGAGTCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.07, C:0.17, G:0.37, T:0.39
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:21873 original size:39 final size:38
Alignment explanation
Indices: 21803--21885 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 38
21793 CGGGTCATTT
* * * * *
21803 GGGTTTCGAGTCATCTGGGTTCGGGTTATTCGGGTTTC
1 GGGTCTCGAGTCATCAGGGTTCGGGTCATTCGAGTCTC
*
21841 GGGTCTCGAGTCATACAGGTTTCGGGTCATTCGAGTCTC
1 GGGTCTCGAGTCAT-CAGGGTTCGGGTCATTCGAGTCTC
21880 GGGTCT
1 GGGTCT
21886 ACCGGGTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.35
Consensus pattern (38 bp):
GGGTCTCGAGTCATCAGGGTTCGGGTCATTCGAGTCTC
Found at i:22757 original size:32 final size:32
Alignment explanation
Indices: 22716--22795 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
22706 GTCGACACAG
22716 GTCATTCGGGTCTC-GAGTCA-CTCGAGTTACGA
1 GTCATTCGGGTCTCGGA-TCATCT-GAGTTACGA
* * * *
22748 GTCATTCGGGTTTCGGATCATCTGGGTTGCGG
1 GTCATTCGGGTCTCGGATCATCTGAGTTACGA
22780 GTCATTCGGGTCTCGG
1 GTCATTCGGGTCTCGG
22796 GTTGGGCGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 37 0.90
33 4 0.10
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (32 bp):
GTCATTCGGGTCTCGGATCATCTGAGTTACGA
Found at i:22796 original size:16 final size:15
Alignment explanation
Indices: 22715--22797 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 15
22705 GGTCGACACA
22715 GGTCATTCGGGTCTCG
1 GGTCATTCGGGT-TCG
* * *
22731 AGTCACTCGAGTTACG
1 GGTCATTCGGGTT-CG
*
22747 AGTCATTCGGGTTTCG
1 GGTCATTCGGG-TTCG
*
22763 GATCA-TCTGGGTTGCG
1 GGTCATTC-GGGTT-CG
22779 GGTCATTCGGGTCTCG
1 GGTCATTCGGGT-TCG
22795 GGT
1 GGT
22798 TGGGCGGGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.09
16 43 0.81
17 5 0.09
ACGTcount: A:0.12, C:0.22, G:0.35, T:0.31
Consensus pattern (15 bp):
GGTCATTCGGGTTCG
Found at i:23314 original size:22 final size:22
Alignment explanation
Indices: 23286--23340 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
23276 TACATTAAAA
*
23286 ATGGGTCGTGCTGCGTCGGCAC
1 ATGGGTCGTGCTGCGCCGGCAC
*
23308 ATGGGTCGTGCTGTGCCGGCAC
1 ATGGGTCGTGCTGCGCCGGCAC
*
23330 GTGGGTCGTGC
1 ATGGGTCGTGC
23341 CATGCCATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.07, C:0.25, G:0.44, T:0.24
Consensus pattern (22 bp):
ATGGGTCGTGCTGCGCCGGCAC
Found at i:26337 original size:57 final size:57
Alignment explanation
Indices: 26249--26413 Score: 278
Period size: 57 Copynumber: 2.9 Consensus size: 57
26239 TCGAATATCT
*
26249 AAACTTTGCCCGAAATCACGAATAATTAACAACTTGTTTGGGATTAAAATGTATTCG
1 AAACTTTGCCCGAAATTACGAATAATTAACAACTTGTTTGGGATTAAAATGTATTCG
* * *
26306 AAACTTTGCCCGAAATTACAAATAATTAACAACTTATTTGGGGTTAAAATGTATTCG
1 AAACTTTGCCCGAAATTACGAATAATTAACAACTTGTTTGGGATTAAAATGTATTCG
26363 AAACTTTGCCCGAAATTACGAATAATTAACAACTTGTTT-GGAGTTAAAATG
1 AAACTTTGCCCGAAATTACGAATAATTAACAACTTGTTTGGGA-TTAAAATG
26414 GTGGATGAGG
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
56 2 0.02
57 98 0.98
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (57 bp):
AAACTTTGCCCGAAATTACGAATAATTAACAACTTGTTTGGGATTAAAATGTATTCG
Found at i:29744 original size:23 final size:23
Alignment explanation
Indices: 29717--29760 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29707 TTTTATTTCT
29717 TCCATTTGAAATGAGAAGAAACA
1 TCCATTTGAAATGAGAAGAAACA
*
29740 TCCATTTGAAATGATAAGAAA
1 TCCATTTGAAATGAGAAGAAA
29761 AAGGTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (23 bp):
TCCATTTGAAATGAGAAGAAACA
Found at i:30922 original size:16 final size:16
Alignment explanation
Indices: 30901--30936 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
30891 ATGAGGTAAT
30901 TTTTAACAACTTTCTG
1 TTTTAACAACTTTCTG
*
30917 TTTTAACAACTTTTTG
1 TTTTAACAACTTTCTG
30933 TTTT
1 TTTT
30937 GGTAATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTAACAACTTTCTG
Found at i:35884 original size:31 final size:33
Alignment explanation
Indices: 35836--35896 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
35826 CCATTTTGTA
35836 AACGGGCCTTAAAA-TTTTGTCCAAACCCGTCC
1 AACGGGCCTTAAAATTTTTGTCCAAACCCGTCC
* *
35868 AACGGG-CTTCAAATTTTTGTCCAAGCCCG
1 AACGGGCCTTAAAATTTTTGTCCAAACCCG
35897 CCCCCGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (33 bp):
AACGGGCCTTAAAATTTTTGTCCAAACCCGTCC
Found at i:38170 original size:2 final size:2
Alignment explanation
Indices: 38163--38222 Score: 102
Period size: 2 Copynumber: 29.0 Consensus size: 2
38153 TAATATTTAG
38163 TA TA TA TA TA TA TA TA GTA TA GTA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA
38207 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
38223 AGGATTAGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 52 0.93
3 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40564 original size:20 final size:20
Alignment explanation
Indices: 40539--40577 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40529 TGTACGTAGT
40539 AATAGAGGTCCTACCTCTGG
1 AATAGAGGTCCTACCTCTGG
40559 AATAGAGGTCCTACCTCTG
1 AATAGAGGTCCTACCTCTG
40578 ATTGGTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (20 bp):
AATAGAGGTCCTACCTCTGG
Found at i:50793 original size:13 final size:13
Alignment explanation
Indices: 50775--50799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50765 CTTATTTCGA
50775 TCTGAGTTTTAGC
1 TCTGAGTTTTAGC
50788 TCTGAGTTTTAG
1 TCTGAGTTTTAG
50800 TTGTAAAACT
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:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
TCTGAGTTTTAGC
Done.