Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017070.1 Corchorus olitorius cultivar O-4 contig17103, 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: 8394
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Found at i:737 original size:18 final size:18
Alignment explanation
Indices: 677--737 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
667 TAAAGCTGCT
677 ATGT-ATAAGCATGATTA
1 ATGTCATAAGCATGATTA
*
694 ATGTCATAAG-A-AATCTA
1 ATGTCATAAGCATGAT-TA
*
711 TTG-CATAAGCATGATTA
1 ATGTCATAAGCATGATTA
728 ATGTCATAAG
1 ATGTCATAAG
738 AAATCTACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
16 8 0.23
17 14 0.40
18 13 0.37
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (18 bp):
ATGTCATAAGCATGATTA
Found at i:6224 original size:93 final size:93
Alignment explanation
Indices: 6119--6306 Score: 279
Period size: 93 Copynumber: 2.0 Consensus size: 93
6109 TAAACTTTTT
* ** *
6119 AATTAAATTAGTAATATGGTAAAAATAAAATAGGCATAAGGATATTAGATTTAATTAAATAAAAA
1 AATTAAATTAGTAAAATGGTAAAAATAAAATAAACAAAAGGATATTAGATTTAATTAAATAAAAA
*
6184 TAGAGTTTTTAGTTGAATAGAACTATAA
66 TAGAGTTTTTAGTTGAATAAAACTATAA
* * *
6212 AATTGAAA-TAGTAAAATGGTAAAAGTAAAATAAATAAAAGGATATTAGATTTAATTAAATAAAG
1 AATT-AAATTAGTAAAATGGTAAAAATAAAATAAACAAAAGGATATTAGATTTAATTAAATAAAA
*
6276 ATAGAGTTTTTAGTTGACTAAAACTATAA
65 ATAGAGTTTTTAGTTGAATAAAACTATAA
6305 AA
1 AA
6307 ATTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 82 0.96
94 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (93 bp):
AATTAAATTAGTAAAATGGTAAAAATAAAATAAACAAAAGGATATTAGATTTAATTAAATAAAAA
TAGAGTTTTTAGTTGAATAAAACTATAA
Found at i:6380 original size:31 final size:31
Alignment explanation
Indices: 6342--6403 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6332 ATATTTGAAA
* * *
6342 AATAAGGGTATGATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGACAATTCAAAAGTTT
6373 AATAAGGGTATAATAGACAATTCAAAAGTTT
1 AATAAGGGTATAATAGACAATTCAAAAGTTT
6404 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATAATAGACAATTCAAAAGTTT
Found at i:6605 original size:31 final size:31
Alignment explanation
Indices: 6564--6625 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6554 ATATTCAAAA
*
6564 AATAAGGATATAATAAGCGATTCAAAAGTTT
1 AATAAAGATATAATAAGCGATTCAAAAGTTT
*
6595 AATAAAGATATAATAGGCGATTCAAAAGTTT
1 AATAAAGATATAATAAGCGATTCAAAAGTTT
6626 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (31 bp):
AATAAAGATATAATAAGCGATTCAAAAGTTT
Found at i:6623 original size:222 final size:222
Alignment explanation
Indices: 6230--6655 Score: 699
Period size: 222 Copynumber: 1.9 Consensus size: 222
6220 TAGTAAAATG
* * *
6230 GTAAAAGTAAAATAAATAAAAGGATATTAGATTTAATTAAATAAAGATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAAATAAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGCTGACT
** * * *
6295 AAAACTATAAAAATTTAAACAATGACATTTAAGAAATATATTTGAAAAATAAGGGTATGATAGGC
66 AAAACTATAAAAATTTAAACAATGACATTTAAGAAATATATTCAAAAAATAAGGATATAATAAGC
* * *
6360 GATTCAAAAGTTTAATAAGGGTATAATAGACAATTCAAAAGTTTTACAAAACTCGTACTTTTATA
131 GATTCAAAAGTTTAATAAAGATATAATAGACAATTCAAAAGTTTTACAAAACTCATACTTTTATA
6425 TATAGTATAGATAGATTAGTTAATATC
196 TATAGTATAGATAGATTAGTTAATATC
** *
6452 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGCTGACT
1 GTAAAAATAAAATAAATAAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGCTGACT
*
6517 AAAACTATAAAAATTTAAACAATGATATTTAAGAAATATATTCAAAAAATAAGGATATAATAAGC
66 AAAACTATAAAAATTTAAACAATGACATTTAAGAAATATATTCAAAAAATAAGGATATAATAAGC
* *
6582 GATTCAAAAGTTTAATAAAGATATAATAGGCGATTCAAAAGTTTTACAAAACTCATACTTTTATA
131 GATTCAAAAGTTTAATAAAGATATAATAGACAATTCAAAAGTTTTACAAAACTCATACTTTTATA
6647 TATAGTATA
196 TATAGTATA
6656 AATTTAAATC
Statistics
Matches: 187, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
222 187 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.33
Consensus pattern (222 bp):
GTAAAAATAAAATAAATAAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGCTGACT
AAAACTATAAAAATTTAAACAATGACATTTAAGAAATATATTCAAAAAATAAGGATATAATAAGC
GATTCAAAAGTTTAATAAAGATATAATAGACAATTCAAAAGTTTTACAAAACTCATACTTTTATA
TATAGTATAGATAGATTAGTTAATATC
Found at i:7725 original size:2 final size:2
Alignment explanation
Indices: 7709--7772 Score: 51
Period size: 2 Copynumber: 32.0 Consensus size: 2
7699 TAGTAATTAT
* * *
7709 TA TA CTA TA -A TA TA TA TA TA TA TA TA TC TA TA TT TA TA TC TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
7751 -A TC TA TA TC TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA
7773 AGTCTAAACT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
1 2 0.04
2 42 0.88
3 4 0.08
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7778 original size:23 final size:22
Alignment explanation
Indices: 7709--7778 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
7699 TAGTAATTAT
* *
7709 TATA-CTATAATATATATATATA
1 TATATCTATATTATATATA-ATC
*
7731 TATATCTATATTTATATCTAATC
1 TATATCTATA-TTATATATAATC
7754 TATATCTATA-TACTATATAAGTC
1 TATATCTATATTA-TATATAA-TC
7777 TA
1 TA
7779 AACTTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.05
22 10 0.25
23 21 0.52
24 7 0.17
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (22 bp):
TATATCTATATTATATATAATC
Found at i:8044 original size:39 final size:40
Alignment explanation
Indices: 7988--8068 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
7978 TTTAATTCCT
7988 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
8028 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
8067 AT
1 AT
8069 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:8094 original size:24 final size:23
Alignment explanation
Indices: 8059--8104 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
8049 AATACTTACA
8059 TTAATTAAATTCTTAGGTATTTT
1 TTAATTAAATTCTTAGGTATTTT
8082 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
8105 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGGTATTTT
Done.