Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017335.1 Corchorus olitorius cultivar O-4 contig17368, 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: 75125
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5043 original size:21 final size:21
Alignment explanation
Indices: 5017--5058 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5007 AATGGAAAAG
* * *
5017 CTTGTTGATGGACAATTGTTA
1 CTTGTTAAAGGACAATCGTTA
5038 CTTGTTAAAGGACAATCGTTA
1 CTTGTTAAAGGACAATCGTTA
5059 ATTAAACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (21 bp):
CTTGTTAAAGGACAATCGTTA
Found at i:9523 original size:13 final size:13
Alignment explanation
Indices: 9502--9538 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
9492 GATAATTCTT
9502 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
9515 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
9528 CTTGACCCTCC
1 TTTGACCCTCC
9539 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:14885 original size:19 final size:20
Alignment explanation
Indices: 14847--14885 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14837 CCAAAAACTA
*
14847 ATATTAAATCAGGTTTAAAT
1 ATATGAAATCAGGTTTAAAT
*
14867 ATATGAAATTAGG-TTAAAT
1 ATATGAAATCAGGTTTAAAT
14886 TTCATAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (20 bp):
ATATGAAATCAGGTTTAAAT
Found at i:27957 original size:18 final size:19
Alignment explanation
Indices: 27934--27971 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
27924 GTGCATGGGT
*
27934 TGCATGGAGGC-ATGGAGA
1 TGCATGGAGACGATGGAGA
27952 TGCATGGAGACGATGGAGA
1 TGCATGGAGACGATGGAGA
27971 T
1 T
27972 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.29, C:0.11, G:0.42, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACGATGGAGA
Found at i:29546 original size:25 final size:25
Alignment explanation
Indices: 29495--29546 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
29485 ATGCAATCCC
*
29495 TCATAGAAAGACACATTTTCTTATT
1 TCATAGAAAGACACATTTTCATATT
* *
29520 TCATAGAAATACACATTTTCATGTT
1 TCATAGAAAGACACATTTTCATATT
29545 TC
1 TC
29547 TGCAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (25 bp):
TCATAGAAAGACACATTTTCATATT
Found at i:43698 original size:53 final size:53
Alignment explanation
Indices: 43618--43720 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
43608 TATGTAATAT
* * * *
43618 ATGGAAAGACTTTTCATGGATTGGTTAAATCAAAATATGTGGGTAAGTAAATG
1 ATGGAAAGACTTTCCATGGATTGGTTAAATCAAAAAATATGGGAAAGTAAATG
* * *
43671 ATGGAAATACTTTCCATGGTTTGGTTAAATTAAAAAATATGGGAAAGTAA
1 ATGGAAAGACTTTCCATGGATTGGTTAAATCAAAAAATATGGGAAAGTAA
43721 TTTAAAGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (53 bp):
ATGGAAAGACTTTCCATGGATTGGTTAAATCAAAAAATATGGGAAAGTAAATG
Found at i:49727 original size:41 final size:41
Alignment explanation
Indices: 49670--49752 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
49660 TAAAAGCGGC
*
49670 AGAGGTTTGTTCAAGTTGTTAAATGCGGAATTCAGGATCTA
1 AGAGGTTTGTTCAAGTTGTTAAATGCGCAATTCAGGATCTA
*
49711 AGAGGTTTGTTCAAGTTGTTAAATGCGCAATTCGGGATCTA
1 AGAGGTTTGTTCAAGTTGTTAAATGCGCAATTCAGGATCTA
49752 A
1 A
49753 TTTCTGCCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (41 bp):
AGAGGTTTGTTCAAGTTGTTAAATGCGCAATTCAGGATCTA
Found at i:62548 original size:143 final size:144
Alignment explanation
Indices: 62162--62551 Score: 579
Period size: 143 Copynumber: 2.7 Consensus size: 144
62152 TTCCCACATT
* * *
62162 CAAGTTTTCTTCGTTTATTCC-AAAATGCCCTTCCCGGTTGGAAGGCGCAAGTTTTCTTCATTTA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGCACAAGTTTTCTTCATTTA
* *
62226 TTCCAAAAATGCCCTTCCCGGTCGGAAGGTACAAGTTTTCTTCACTTATTCCCAAAATGCCCTTC
66 TTCCAAAAATGCCCTTCCCGGTCGGAAGGTACCAGTTTTCTTCACCTATTCCCAAAATGCCCTTC
*
62291 CCGGTCGGAAGGCG
131 CCGGTCGAAAGGCG
62305 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTC-GAATGGCACAAGTTTTCTTCATTT
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAA-GGCACAAGTTTTCTTCATTT
* ** *
62369 ATTCCAAAAATACCCTTCCCGGTCAAAAGGTACCAGTTTTCTTCACCTATTCCC-AAATTCCCTT
65 ATTCCAAAAATGCCCTTCCCGGTCGGAAGGTACCAGTTTTCTTCACCTATTCCCAAAATGCCCTT
*
62433 CCCGGTCGAAAGGTG
130 CCCGGTCGAAAGGCG
* * **
62448 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGAACTAGTTTTCTTCGCTTA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGCACAAGTTTTCTTCATTTA
* * * *
62513 TTCCCAAAGTGCCCTTCCCGGTCGGAGGGTGCCAGTTTT
66 TTCCAAAAATGCCCTTCCCGGTCGGAAGGTACCAGTTTT
62552 GTCTTTACAT
Statistics
Matches: 222, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
143 134 0.60
144 88 0.40
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (144 bp):
CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGCACAAGTTTTCTTCATTTA
TTCCAAAAATGCCCTTCCCGGTCGGAAGGTACCAGTTTTCTTCACCTATTCCCAAAATGCCCTTC
CCGGTCGAAAGGCG
Found at i:62551 original size:48 final size:48
Alignment explanation
Indices: 62162--62538 Score: 499
Period size: 48 Copynumber: 7.9 Consensus size: 48
62152 TTCCCACATT
* * **
62162 CAAGTTTTCTTCGTTTATTCC-AAAATGCCCTTCCCGGTTGGAAGGCG
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
62209 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
* * **
62257 CAAGTTTTCTTCACTTATTCCCAAAATGCCCTTCCCGGTCGGAAGGCG
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
*
62305 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTC-GAATGGCA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAA-GGTA
* **
62353 CAAGTTTTCTTCATTTATTCCAAAAATACCCTTCCCGGTCAAAAGGTA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
* ** * * * *
62401 CCAGTTTTCTTCACCTATTCC-CAAATTCCCTTCCCGGTCGAAAGGTG
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
*
62448 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGAA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
* ** * *
62496 CTAGTTTTCTTCGCTTATTCCCAAAGTGCCCTTCCCGGTCGGA
1 CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGA
62539 GGGTGCCAGT
Statistics
Matches: 292, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
47 63 0.22
48 227 0.78
49 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (48 bp):
CAAGTTTTCTTCATTTATTCCAAAAATGCCCTTCCCGGTCGGAAGGTA
Found at i:73086 original size:445 final size:439
Alignment explanation
Indices: 72266--73439 Score: 1533
Period size: 445 Copynumber: 2.7 Consensus size: 439
72256 ATTGGATATT
* * *
72266 TGGATAAAAAATTATAT-GATATTAAATAGACTGTCAATTGAAACCACAAAATGTCGGAAGC-TT
1 TGGATAAAAAATTATATAG-TATTAAATAGACCGACAATCGAAACCACAAAAT-TCGGAAGCATT
* *
72329 TTTTTAGAATTAAAACA-ATAAAATTGGTTTTTGAGTCCTTCATGAAATTTGTAAATCATGAAAT
64 TTTTT-GAATTGAAACATA-AAAATTGGTTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAAT
* * * **
72393 TACCTTTTAATAGACACATGAATTACCTTAATTGGACAAATAG-AACAAA-GGAA-AA-AAA--T
127 TACCTTTTAATAGACACCTGAATCACCTTAATTGGACAAATAGAAAAAAATAAAATAATAAAGCT
* * * *
72452 GAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAAGACTAAGTAGTATAAAGTAGAAAACTATGA
192 GAAGCGTTAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAAAAAAATATGA
72517 GGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAAT
257 GGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAAT
* * *
72582 TCCTTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTCATGAAAGTCG
322 TCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTCGGGCCCTTCATGAAAGTCG
* ** * *
72647 TAGATTATGCAATCATCTTTTAACCGACACTTGAATAACTTTAATTAGACATG
387 TAGATCATGCAAAAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATG
* * * * *
72700 TTGATAAAAAATTATATAGTATTAAATAGACCGGCAATCGAAACCACCAAATTAAGGAAACATTT
1 TGGATAAAAAATTATATAGTATTAAATAGACCGACAATCGAAACCACAAAATT-CGGAAGCATTT
* *
72765 TTTTGAATTGAAAGATAAAAATTGGCTTTTGAGTCCTTTCATGAAAGTTGTAAATCATGAAATTA
65 TTTTGAATTGAAACATAAAAATTGGTTTTTGAGTCC-TTCATGAAAGTTGTAAATCATGAAATTA
* * *
72830 CCTTTTAATAGACACCTGAATCACCTTTATAGGACAAATAGAAAAAAATAAAATAATAAAGCTTA
129 CCTTTTAATAGACACCTGAATCACCTTAATTGGACAAATAGAAAAAAATAAAATAATAAAGCTGA
* * * *
72895 AGAGTTAAATCAATTAAGATAGAATTAT-TAAAGGACTAGGTAGTATAAATTAAAAAAAATATAT
194 AGCGTTAAATCGATTAAGATAGAATT-TGTAAAGGACTAAGTAGTATAAAGT--AAAAAA-ATAT
* * * *
72959 GAGGGTCATTTGATGAATAATCCAAATAAGAAAATTTTTTTTTGATGGAGATCTTGTAACATAAA
255 GAGGGTCATTTGATAAATAATCCAAATAAGAAAA-TGTTTGTTGATGGAGATCTTGAAACATAAA
*
73024 AATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTACCTTTCGGGCCCTTCATGAAAG
319 AATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTCGGGCCCTTCATGAAAG
*
73089 TCGTAGATCATGCAAAAACCTTTTAAGCGACACTTGAATAACTTTAATCAGACATG
384 TCGTAGATCATGCAAAAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATG
** * * * *
73145 TGGATCGAAAATCATATAATAATAAGTAGACCGACAATCGAAACCACAAAATTTCGGAAGCATTT
1 TGGATAAAAAATTATATAGTATTAAATAGACCGACAATCGAAACCACAAAA-TTCGGAAGCATTT
* * *
73210 TTTTGAATTGAAACATAAAAATTGGTTTTTAAGTCCTTCATGAAAGTTGTAGATCATGAAATCAC
65 TTTTGAATTGAAACATAAAAATTGGTTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTAC
* *
73275 CTTTTAATAGACACCGGAATCACCTGAATTGGACAAATAGAACAAAAAATAAAAAATAAATAAAG
130 CTTTTAATAGACACCTGAATCACCTTAATTGGACAAATAG-A-AAAAAAT--AAAAT-AATAAAG
* * ** ** *
73340 CTGAAGCGTCAAATTGATTAAGATAGAATTTGTAAAGGACTCAA-TAACATAAAGTGGAAAAGTA
190 CTGAAGCGTTAAATCGATTAAGATAGAATTTGTAAAGGACT-AAGTAGTATAAAGTAAAAAAATA
* *
73404 TGGGGGGGTCATTTGATAAATAATCCAACTAAGAAA
254 T--GAGGGTCATTTGATAAATAATCCAAATAAGAAA
73440 GTGGTTTTTC
Statistics
Matches: 638, Mismatches: 76, Indels: 38
0.85 0.10 0.05
Matches are distributed among these distances:
433 1 0.00
434 77 0.12
435 73 0.11
436 5 0.01
437 2 0.00
438 2 0.00
439 3 0.00
441 45 0.07
442 1 0.00
443 5 0.01
444 99 0.16
445 223 0.35
446 12 0.02
447 4 0.01
448 36 0.06
449 49 0.08
450 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (439 bp):
TGGATAAAAAATTATATAGTATTAAATAGACCGACAATCGAAACCACAAAATTCGGAAGCATTTT
TTTGAATTGAAACATAAAAATTGGTTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTACC
TTTTAATAGACACCTGAATCACCTTAATTGGACAAATAGAAAAAAATAAAATAATAAAGCTGAAG
CGTTAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAAAAAAATATGAGGGT
CATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCC
TTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTCGGGCCCTTCATGAAAGTCGTAGA
TCATGCAAAAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATG
Found at i:74949 original size:27 final size:24
Alignment explanation
Indices: 74919--74973 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 24
74909 AATAATTTAG
* *
74919 AATATCATATATTACTTTATAATAAA
1 AATATAATATA-TAATTTA-AATAAA
74945 TAATATAATATATAATTTAAATAAA
1 -AATATAATATATAATTTAAATAAA
74970 AATA
1 AATA
74974 AAAATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 6 0.23
26 6 0.23
27 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAATATATAATTTAAATAAA
Done.