Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012066.1 Corchorus olitorius cultivar O-4 contig12099, 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: 25732
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:9857 original size:2 final size:2
Alignment explanation
Indices: 9850--9881 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9840 TTTGTATCTT
9850 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9882 ACATGAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13082 original size:16 final size:16
Alignment explanation
Indices: 13063--13139 Score: 68
Period size: 16 Copynumber: 4.9 Consensus size: 16
13053 GTGCTTTCTA
13063 GGGAGAGTGATTCCAT
1 GGGAGAGTGATTCCAT
* *
13079 GGGAGAATCATTCCA-
1 GGGAGAGTGATTCCAT
* *
13094 AGGAGAGTGATTACAT
1 GGGAGAGTGATTCCAT
* * * *
13110 GGTAGATTCATTCCGT
1 GGGAGAGTGATTCCAT
13126 -GGAGAGTGATTCCA
1 GGGAGAGTGATTCCA
13140 AGGAAAGTGC
Statistics
Matches: 44, Mismatches: 16, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
15 21 0.48
16 23 0.52
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (16 bp):
GGGAGAGTGATTCCAT
Found at i:13099 original size:31 final size:31
Alignment explanation
Indices: 13064--13139 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
13054 TGCTTTCTAG
13064 GGAGAGTGATTCCATGGGAGAATCATTCCAA
1 GGAGAGTGATTCCATGGGAGAATCATTCCAA
* * * **
13095 GGAGAGTGATTACATGGTAGATTCATTCCGT
1 GGAGAGTGATTCCATGGGAGAATCATTCCAA
13126 GGAGAGTGATTCCA
1 GGAGAGTGATTCCA
13140 AGGAAAGTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.26
Consensus pattern (31 bp):
GGAGAGTGATTCCATGGGAGAATCATTCCAA
Found at i:13361 original size:53 final size:53
Alignment explanation
Indices: 13253--13405 Score: 191
Period size: 53 Copynumber: 2.9 Consensus size: 53
13243 CCCACCTTTT
* * * *
13253 TTTTAGTTTAACCAAACCATAGAAAGTG-TTCCATCTTTTACTTTCCTACATG
1 TTTTAATTTAACCAAACTATAGAAAGTGTTTCCATCATTTACTTTCCCACATG
* *
13305 TTTTATTTTAACCAAACTATAGAAAGTGTTTCCATCATTTACTTTCCCGCATG
1 TTTTAATTTAACCAAACTATAGAAAGTGTTTCCATCATTTACTTTCCCACATG
* * * * *
13358 TTTTAATTCAACCAAACTATGGAAAGTCTTTCCACCCTATTACTTTCC
1 TTTTAATTTAACCAAACTATAGAAAGTGTTTCCATCAT-TTACTTTCC
13406 ATGTAAAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 26 0.30
53 53 0.60
54 9 0.10
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (53 bp):
TTTTAATTTAACCAAACTATAGAAAGTGTTTCCATCATTTACTTTCCCACATG
Found at i:13861 original size:221 final size:221
Alignment explanation
Indices: 13478--13919 Score: 821
Period size: 221 Copynumber: 2.0 Consensus size: 221
13468 CAAAGTACAG
13478 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAATATTACTATTTTTACAA
1 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAATATTACTATTTTTACAA
13543 AAAATAAATAAAGCCTTACTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCTG
66 AAAATAAATAAAGCCTTACTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCTG
* *
13608 AAATTCTGTCATAAGAATCCATATGTGCAACGGAGGTTCTCAACAAGGAACAGAAAATGAGATAT
131 AAATTCTGTCATAAGAATCCATATGCGCAACGGAGGTTCTCAACAAGGAACAGAAAATCAGATAT
*
13673 AAACAATGGTGTAGTTTTTACATTCT
196 AAACAATGATGTAGTTTTTACATTCT
*
13699 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAATATTACTATTTTTACAG
1 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAATATTACTATTTTTACAA
*
13764 AAAATAAATAAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCTG
66 AAAATAAATAAAGCCTTACTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCTG
*
13829 AAATTCTGTCATAAGAATCCATGTGCGCAACGGAGGTTCTCAACAAGGAACAGAAAATCAGATAT
131 AAATTCTGTCATAAGAATCCATATGCGCAACGGAGGTTCTCAACAAGGAACAGAAAATCAGATAT
*
13894 AAACAATGATGTATTTTTTACATTCT
196 AAACAATGATGTAGTTTTTACATTCT
13920 CAATCATATA
Statistics
Matches: 214, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
221 214 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (221 bp):
AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAATATTACTATTTTTACAA
AAAATAAATAAAGCCTTACTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCTG
AAATTCTGTCATAAGAATCCATATGCGCAACGGAGGTTCTCAACAAGGAACAGAAAATCAGATAT
AAACAATGATGTAGTTTTTACATTCT
Found at i:15435 original size:32 final size:32
Alignment explanation
Indices: 15379--15456 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
15369 AATATATGCA
15379 AATATTTAATCTCAG----TTTTTTTTGGCAC
1 AATATTTAATCTCAGTTTTTTTTTTTTGGCAC
*
15407 AATATTTAATCTCGGTTTTTTTTTTTTGGCAC
1 AATATTTAATCTCAGTTTTTTTTTTTTGGCAC
15439 AATATTTAATCTCAGTTT
1 AATATTTAATCTCAGTTT
15457 AACTAACCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 14 0.32
32 30 0.68
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (32 bp):
AATATTTAATCTCAGTTTTTTTTTTTTGGCAC
Found at i:17143 original size:22 final size:22
Alignment explanation
Indices: 17118--17161 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17108 TGTCCTCTTA
*
17118 ATGAAGCGTTTAATTTCCTGCT
1 ATGAAGCATTTAATTTCCTGCT
17140 ATGAAGCATTTAATTTCCTGCT
1 ATGAAGCATTTAATTTCCTGCT
17162 TACTTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (22 bp):
ATGAAGCATTTAATTTCCTGCT
Found at i:20894 original size:13 final size:13
Alignment explanation
Indices: 20876--20900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20866 TTAAATGTTT
20876 TAAATATTATTTA
1 TAAATATTATTTA
20889 TAAATATTATTT
1 TAAATATTATTT
20901 GGAATTTCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:21477 original size:34 final size:38
Alignment explanation
Indices: 21407--21483 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
21397 GACATCCACA
*
21407 ACATACATGTATATTCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
21445 ACATACATGTATATGCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
21483 A
1 A
21484 TAATTATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (38 bp):
ACATACATGTATATGCATAACAAATTTATAATTAATTT
Found at i:21481 original size:11 final size:11
Alignment explanation
Indices: 21467--21504 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21457 ATGCATAACA
21467 AATTTATAATT
1 AATTTATAATT
21478 AATTTATAATT
1 AATTTATAATT
21489 -ATTTGATAATT
1 AATTT-ATAATT
*
21500 TATTT
1 AATTT
21505 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22055 original size:77 final size:77
Alignment explanation
Indices: 21934--22094 Score: 304
Period size: 77 Copynumber: 2.1 Consensus size: 77
21924 GGATAATAAG
*
21934 AAATAAGAAACAATAATAAGAGAAAGTGAAATTACCTAAAAACCAATCCAACCTTAACTTCTCAT
1 AAATAAGAAACAATAATAAGAGAAAGTGAAATTACCTAAAAACCAATCCAACATTAACTTCTCAT
21999 GACTTGAAGAAC
66 GACTTGAAGAAC
*
22011 AAATAAGAAACAATAATAGGAGAAAGTGAAATTACCTAAAAACCAATCCAACATTAACTTCTCAT
1 AAATAAGAAACAATAATAAGAGAAAGTGAAATTACCTAAAAACCAATCCAACATTAACTTCTCAT
22076 GACTTGAAGAAC
66 GACTTGAAGAAC
22088 AAATAAG
1 AAATAAG
22095 GAGGGGTATT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (77 bp):
AAATAAGAAACAATAATAAGAGAAAGTGAAATTACCTAAAAACCAATCCAACATTAACTTCTCAT
GACTTGAAGAAC
Found at i:23364 original size:156 final size:156
Alignment explanation
Indices: 22868--23714 Score: 1173
Period size: 156 Copynumber: 5.4 Consensus size: 156
22858 AAAATGCTTC
* * * *
22868 CTAAAAACTTAACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAA
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
* * *
22933 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAACAAATGGGCCCCGAATTGC
66 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
*
22998 CCAAAATAACAAGTGTTTAAAATGAG
131 CCAAAATAACAAGTGTTCAAAATGAG
* * * * * *
23024 TTAAAAACTTCATAGTTGACTAATCTTACTAAAAAGATAATAGTTAGGCCATAAACAATTGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
* * * * *
23089 AAAAGGATTGTGGATTGCCAAATCGAAGACGA-TTCT-AAATCGAACTAATGGGCCCTCGAAGGG
66 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCC-CGAATGG
* *
23152 CACAAAATAACAAGTATTCAAAATGAG
130 CCCAAAATAACAAGTGTTCAAAATGAG
* * *
23179 TTAAAAACTTCACAGTGAACTAATCTTACCAAAATGATTATA-TATAGGCCATAAACAATGGAAA
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGT-TAGGCCATAAACAATGGAAA
* * * * **
23243 CAAAAGCTTTGTGGATAGATAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGG
65 GAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGG
*
23308 CCCAAAATAACAAGTGTTCAAAATTAG
130 CCCAAAATAACAAGTGTTCAAAATGAG
* * * **
23335 CTAAAAACTTCATAGTGGACTAAACTTACCAAAATAATTGTAGTTAGGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
*
23400 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAACTAATGGGCCCCGAATGGC
66 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
*
23465 CCAAAATAACAAGTGTTTAAAATGAG
131 CCAAAATAACAAGTGTTCAAAATGAG
* * **
23491 CTAAAAACTTCACAGTGGACTAATCTTACTAAAATGATAATAGTTAGGCCAAAAACAATAAAAAG
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
* * * * *
23556 AAAAGCATTCTGGTTTGCCAAATCGAAAAC-A-GTTCAAAATCGAACTAATGGGCCCCGAATGGC
66 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
*
23619 ACAAAATAACAAGTGTTCAAAATGAG
131 CCAAAATAACAAGTGTTCAAAATGAG
* * * *
23645 CTAAAAACTTCACAATGAACTAATCTTACCAAAATGATAATAGATAGGCCATAAATAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
23710 AAAAG
66 AAAAG
23715 TCTTGTGAAA
Statistics
Matches: 606, Mismatches: 80, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
154 131 0.22
155 115 0.19
156 341 0.56
157 19 0.03
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (156 bp):
CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAG
AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
CCAAAATAACAAGTGTTCAAAATGAG
Found at i:23432 original size:311 final size:312
Alignment explanation
Indices: 22868--23714 Score: 1195
Period size: 311 Copynumber: 2.7 Consensus size: 312
22858 AAAATGCTTC
* *
22868 CTAAAAACTTAACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAA
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAA
* * *
22933 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAACAAATGGGCCCCGAATTGC
66 AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
* * * *
22998 CCAAAATAACAAGTGTTTAAAATGAGTTAAAAACTTCATAGTTGACTAATCTTACTAAAA-AGAT
131 CCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATA-AT
* *
23062 AATAGTTAGGCCATAAACAATTGAAAGAAAAGGATTGTGGATTGCCAAATCGAAGACGA-TTCTA
195 AATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGATTGCCAAATCGAAGACGATTTCTA
*
23126 AATC-GAACTAATGGGCCCTCGAAGGGCACAAAATAACAAGTATTCAAAATGAG
260 AAACGGAACTAATGGGCCC-CGAAGGGCACAAAATAACAAGTATTCAAAATGAG
* *
23179 TTAAAAACTTCACAGTGAACTAATCTTACCAAAATGATTATA-TATAGGCCATAAACAATGGAAA
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGT-TAGGCCATAAACAATGGAAA
* * * * **
23243 CAAAAGCTTTGTGGATAGATAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGG
65 AAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGG
* *
23308 CCCAAAATAACAAGTGTTCAAAATTAGCTAAAAACTTCATAGTGGACTAAACTTACCAAAATAAT
130 CCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATAAT
** * *
23373 TGTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTA
195 AATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGATTGCCAAATCGAAGACGATTTCTA
* * * *
23438 AAACGGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTTAAAATGAG
260 AAACGGAACTAATGGGCCCCGAAGGGCACAAAATAACAAGTATTCAAAATGAG
* * * *
23491 CTAAAAACTTCACAGTGGACTAATCTTACTAAAATGATAATAGTTAGGCCAAAAACAAT-AAAAA
1 CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAA
* * * * *
23555 GAAAAGCATTCTGGTTTGCCAAATCGAAAAC-A-GTTCAAAATCGAACTAATGGGCCCCGAATGG
66 -AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGG
* * * * *
23618 CACAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGAACTAATCTTACCAAAATGAT
130 CCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATAAT
* *
23683 AATAGATAGGCCATAAATAATGGAAAGAAAAG
195 AATAGTTAGGCCATAAACAATGGAAAGAAAAG
23715 TCTTGTGAAA
Statistics
Matches: 472, Mismatches: 58, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
310 115 0.24
311 229 0.49
312 113 0.24
313 15 0.03
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (312 bp):
CTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAA
AAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGC
CCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATAATA
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGATTGCCAAATCGAAGACGATTTCTAA
AACGGAACTAATGGGCCCCGAAGGGCACAAAATAACAAGTATTCAAAATGAG
Done.