Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009998.1 Corchorus olitorius cultivar O-4 contig10030, 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: 8868
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:513 original size:18 final size:18
Alignment explanation
Indices: 474--529 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
464 ATCGACAGCT
*
474 TCATCCTCCACCTCAACT
1 TCATCCTCCACCTCAACA
*
492 TCATCCT-CACTCTGAACA
1 TCATCCTCCAC-CTCAACA
** *
510 TCATTTTCAACCTCAACA
1 TCATCCTCCACCTCAACA
528 TC
1 TC
530 TTGCAAATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 3 0.10
18 25 0.83
19 2 0.07
ACGTcount: A:0.27, C:0.41, G:0.02, T:0.30
Consensus pattern (18 bp):
TCATCCTCCACCTCAACA
Found at i:1281 original size:15 final size:15
Alignment explanation
Indices: 1263--1292 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1253 TATATATAGA
1263 ACAAACCCAGAAAAC
1 ACAAACCCAGAAAAC
1278 ACAAACCCAGAAAAC
1 ACAAACCCAGAAAAC
1293 CCATAAAAAA
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:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (15 bp):
ACAAACCCAGAAAAC
Found at i:1672 original size:11 final size:11
Alignment explanation
Indices: 1656--1697 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1646 ATCGAGTTCG
1656 AAGAGAGAGAA
1 AAGAGAGAGAA
1667 AAGAGAGAG--
1 AAGAGAGAGAA
*
1676 AACAGAGAGAA
1 AAGAGAGAGAA
*
1687 AAGGGAGAGAA
1 AAGAGAGAGAA
1698 TTATCGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (11 bp):
AAGAGAGAGAA
Found at i:1684 original size:20 final size:20
Alignment explanation
Indices: 1659--1697 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1649 GAGTTCGAAG
1659 AGAGAGAAAAGAGAGAGAAC
1 AGAGAGAAAAGAGAGAGAAC
*
1679 AGAGAGAAAAGGGAGAGAA
1 AGAGAGAAAAGAGAGAGAA
1698 TTATCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (20 bp):
AGAGAGAAAAGAGAGAGAAC
Found at i:2558 original size:5 final size:5
Alignment explanation
Indices: 2548--2584 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
2538 GAAATAGCTC
2548 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
2585 CCTTAATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:3874 original size:15 final size:15
Alignment explanation
Indices: 3856--3885 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3846 ATATAATTTT
3856 CCTTTATAAATTAAA
1 CCTTTATAAATTAAA
3871 CCTTTATAAATTAAA
1 CCTTTATAAATTAAA
3886 TTAATTAGCC
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:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
CCTTTATAAATTAAA
Found at i:4385 original size:2 final size:2
Alignment explanation
Indices: 4380--4431 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
4370 TAAAAAACCC
* * * *
4380 TA TA TA TA TA TA TA TA TA CA CA TA TA TC TA TA CTA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
4423 CTA TA TA TA
1 -TA TA TA TA
4432 AAAGTACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5390 original size:20 final size:21
Alignment explanation
Indices: 5353--5415 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
5343 AGGGAGATTA
* *
5353 ACAAAATTTCATAGGAAGG-T
1 ACAAAATATCATAAGAAGGTT
5373 ATCAAAA-ATCATAAGAAGGTT
1 A-CAAAATATCATAAGAAGGTT
*
5394 ACAAAATTTCATAAGGAAGGTT
1 ACAAAATATCATAA-GAAGGTT
5416 TATTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 16 0.44
21 13 0.36
22 7 0.19
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
ACAAAATATCATAAGAAGGTT
Found at i:5426 original size:24 final size:23
Alignment explanation
Indices: 5354--5474 Score: 94
Period size: 22 Copynumber: 5.5 Consensus size: 23
5344 GGGAGATTAA
5354 CAAAATTTCAT-AGGAAGG-TAT
1 CAAAATTTCATAAGGAAGGTTAT
*
5375 CAAAA-ATCATAA-GAAGGTTA-
1 CAAAATTTCATAAGGAAGGTTAT
5395 CAAAATTTCATAAGGAAGGTTTAT
1 CAAAATTTCATAAGGAAGG-TTAT
* ***
5419 TAAAATTTCAT-ATTTAGGTTAT
1 CAAAATTTCATAAGGAAGGTTAT
* * *
5441 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATAAGGAAGGTTAT
**
5463 CACGATTTCATA
1 CAAAATTTCATA
5475 GGTAATTATC
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
20 14 0.18
21 14 0.18
22 33 0.42
23 7 0.09
24 10 0.13
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
CAAAATTTCATAAGGAAGGTTAT
Found at i:5621 original size:2 final size:2
Alignment explanation
Indices: 5582--5607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5572 GCTAAAACTA
5582 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5608 CTTACTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7717 original size:439 final size:437
Alignment explanation
Indices: 6979--7966 Score: 1288
Period size: 439 Copynumber: 2.3 Consensus size: 437
6969 ACAAAAGTCA
*
6979 AAGCGTTAAATCGTCCAACCTATAATTGTAAAGGATTCAAA-AGCATGAAA-CATAAAAGTATGA
1 AAGCGTTAAATCGTCCAACCTATAATTGTAAAGGATT-AAATAGCAT-AAAGCATAAAAGTATAA
* * * * *
7042 GGGTCATTAGATAAATAATCCAGCAAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTC
64 GGATCATTTGATAAATAATCCAGC-AAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTC
* * * * * *
7107 CCTCTTGAATCCTCCATGAAACTCATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTCGCA
128 CCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTTAACGAAAGTCACA
* *
7172 GATCACACCAATAACCTTTTAACCGACACTTGAGCAACTTCAACCAGACAAGTGGACCGAAAATT
193 GATCACACCAATAACCTTTTAACCGACACTTGAACAACCTCAACCAGACAAGTGGACCGAAAATT
* * * **
7237 ATGCGATATTAAATAGATCGGGAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAA
258 ATACAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAA
* ** * *
7302 CATTAAAATTGGATTCTG-AGTTTTTTATGAAAGTTGTAGATCATGAGATTACCTTTTAATAGAC
323 CATGAAAATTGG-TT-TGTAGTCCTTCATGAAAGTTGT--ATCATGAAATTACCTTTTAATAGAC
* * *
7366 ACTTGAATCACCTTGATCAGACAAATAGAACAGAAAATACAAA-AATAAAAGCTG
384 ACTTGAATCACCTTGATCAGACAAATAAAACAAAAAATA-AAAGAATAAAAGCCG
* * *
7420 AAGCGTTAAATCGTTCAACCCATAATTGTAAAGGATTAAATAACATAAAGCATAAAAGTATAAGG
1 AAGCGTTAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGG
*
7485 ATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACCAAACATAAAAATTCCCT
66 ATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTCCCT
* * * * *
7550 CTCGAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAAGTCCTTGACGGAAGTCATAGAT
131 CTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTTAACGAAAGTCACAGAT
* *
7615 CACA-CAATAACCTTTTAACCGACACTTGAACAACCTCAATCAGACAAGTGGATCGAAAATTATA
196 CACACCAATAACCTTTTAACCGACACTTGAACAACCTCAACCAGACAAGTGGACCGAAAATTATA
* * * * * *
7679 CAATATTATATAGACCGACATTC-AAGACCACAAAATTTAATAAGCGTTTTTTAGAATCGAAACA
261 CAATATTAAATAGACCGACAATCGAA-ACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACA
* *
7743 TGAAAATTGGTTTGTAGTCCTTCATGAAAGTTGTATCATGAAATTACCTTTTAATATACACTTGT
325 TGAAAATTGGTTTGTAGTCCTTCATGAAAGTTGTATCATGAAATTACCTTTTAATAGACACTTGA
* * * *
7808 ATCACCTTGATCGGACAAGTAAAATAAAAAATAAAAGAATTAAAGCCG
390 ATCACCTTGATCAGACAAATAAAACAAAAAATAAAAGAATAAAAGCCG
* * * * * * *
7856 AAACATTCAATCGTCCAACCTAGAATTTGTGAGGGATTAAATAGCATAAAGCATAAAAGTATAGG
1 AAGCGTTAAATCGTCCAACCTATAA-TTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAG
* * * *
7921 GATCATTTGATAAATATTCCAGTAAAAAAT-GATTTGTTTATTGAGA
65 GATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGA
7967 GGCCCACCAA
Statistics
Matches: 477, Mismatches: 64, Indels: 17
0.85 0.11 0.03
Matches are distributed among these distances:
435 3 0.01
436 98 0.21
437 65 0.14
438 20 0.04
439 115 0.24
440 103 0.22
441 73 0.15
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (437 bp):
AAGCGTTAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGG
ATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTCCCT
CTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTTAACGAAAGTCACAGAT
CACACCAATAACCTTTTAACCGACACTTGAACAACCTCAACCAGACAAGTGGACCGAAAATTATA
CAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACAT
GAAAATTGGTTTGTAGTCCTTCATGAAAGTTGTATCATGAAATTACCTTTTAATAGACACTTGAA
TCACCTTGATCAGACAAATAAAACAAAAAATAAAAGAATAAAAGCCG
Done.