Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015608.1 Corchorus olitorius cultivar O-4 contig15641, 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: 28278
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:14407 original size:14 final size:13
Alignment explanation
Indices: 14382--14406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14372 TACTTGGGAT
14382 TTTTGGTATTTTC
1 TTTTGGTATTTTC
14395 TTTTGGTATTTT
1 TTTTGGTATTTT
14407 TTTGGATTTT
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:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (13 bp):
TTTTGGTATTTTC
Found at i:14494 original size:10 final size:11
Alignment explanation
Indices: 14479--14507 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
14469 TTCTTGCATC
14479 TTTTTTTTCT-
1 TTTTTTTTCTA
14489 TTTTTTTTCTA
1 TTTTTTTTCTA
14500 TTTTTTTT
1 TTTTTTTT
14508 GTTTCTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTA
Found at i:16623 original size:10 final size:10
Alignment explanation
Indices: 16579--16623 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
16569 TAAAAGAAGA
* *
16579 TTTTCTTTTC
1 TTTTATTTTT
16589 TTTTATTTTT
1 TTTTATTTTT
*
16599 ATTTATTTATT
1 TTTTATTT-TT
16610 TTTTATTTTT
1 TTTTATTTTT
16620 TTTT
1 TTTT
16624 TGCTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:17117 original size:40 final size:38
Alignment explanation
Indices: 17043--17251 Score: 127
Period size: 40 Copynumber: 5.3 Consensus size: 38
17033 ATCCTAAATC
* * **
17043 AGGATCCT-AAGTTGGATGCTGAAATCAACTGATAAGCCA
1 AGGATCCTGAA-TAGGATTCTGAAATTGACTGATAAG-CA
* * *
17082 CTGG-TCCTGAATATGATTTTTGAAATTGACTGATAAAGCA
1 -AGGATCCTGAATAGGA-TTCTGAAATTGACTGAT-AAGCA
*
17122 AGGATCCTGAATAGGATTCTGAAATTGATTGATAA-CAAAA
1 AGGATCCTGAATAGGATTCTGAAATTGACTGATAAGC---A
* * * *
17162 ATGATCCTGAACAAGATTCTGAAATTCACTTGATAAAGCA
1 AGGATCCTGAATAGGATTCTGAAATTGAC-TGAT-AAGCA
* * * * *
17202 ATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAGCA
1 AGGATCCTGAATAGGATTCTGAAATTGA-CTGAT-AAGCA
*
17242 ATGATCCTGA
1 AGGATCCTGA
17252 GCAGGGTTTT
Statistics
Matches: 136, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
37 1 0.01
38 2 0.01
39 24 0.18
40 99 0.73
41 7 0.05
42 2 0.01
43 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (38 bp):
AGGATCCTGAATAGGATTCTGAAATTGACTGATAAGCA
Found at i:17252 original size:40 final size:40
Alignment explanation
Indices: 17099--17776 Score: 909
Period size: 40 Copynumber: 17.0 Consensus size: 40
17089 TGAATATGAT
* * * ** *
17099 TTTTGAAATTGA-CTGATAAAGCAAGGATCCTGAATAGGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
* * ** * * *
17138 TTCTGAAATTGA-TTGATAACAAAAATGATCCTGAACAAGA
1 TTTTGAAATTAATTTGATAA-AGCAATGATCCTGAGCAGGG
* * * * *
17178 TTCTGAAATTCACTTGATAAAGCAATGATCCTGAGTAGGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
17218 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
17258 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
* * *
17298 TTTTGAAATTAATTTGATAAA-AAGATTATCCTGAGCAGGA
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGG
* *
17338 TTCTGAAATTAATTTGATAAAACAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
*
17378 TTTTGAAATTAATTTGATAAAGCAATGATGCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
* * *
17418 TTTTGAAATTAATTTGATAAA-AAGATTATCCTGAGCAGGA
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGG
*
17458 TTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
17498 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
* * * *
17538 TTTTGAAATTAATTTGATAAA-AAGATAATCATGAGCAGGA
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGG
** *
17578 TTCAGAAATTAATTTGATAAAACAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
17618 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
* * * *
17658 TTTTGAAATTAATTTGATAAA-AAGATAATCGTGAGCAGGA
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGG
*
17698 TTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
17738 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
17777 ATTAAAATCG
Statistics
Matches: 569, Mismatches: 60, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
39 21 0.04
40 537 0.94
41 11 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGG
Found at i:17265 original size:120 final size:120
Alignment explanation
Indices: 17112--17776 Score: 1064
Period size: 120 Copynumber: 5.5 Consensus size: 120
17102 TGAAATTGAC
* ** * * * ** * *
17112 TGATAAAGCAAGGATCCTGAATAGGATTCTGAAATTGA-TTGATAACAAAAATGATCCTGAACAA
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAA-AGCAATGATCCTGAGCAG
* * * * * * * *
17176 GATTCTGAAATTCACTTGATAAAGCA-ATGATCCTGAGTAGGATTTTGAAATTAATT
65 GGTTTTGAAATTAATTTGATAAA-AAGATAATCCTGAGCAGGATTCTGAAATTAATT
17232 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
17297 GTTTTGAAATTAATTTGATAAAAAGATTATCCTGAGCAGGATTCTGAAATTAATT
66 GTTTTGAAATTAATTTGATAAAAAGATAATCCTGAGCAGGATTCTGAAATTAATT
* *
17352 TGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATGCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
17417 GTTTTGAAATTAATTTGATAAAAAGATTATCCTGAGCAGGATTCTGAAATTAATT
66 GTTTTGAAATTAATTTGATAAAAAGATAATCCTGAGCAGGATTCTGAAATTAATT
17472 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
* *
17537 GTTTTGAAATTAATTTGATAAAAAGATAATCATGAGCAGGATTCAGAAATTAATT
66 GTTTTGAAATTAATTTGATAAAAAGATAATCCTGAGCAGGATTCTGAAATTAATT
*
17592 TGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
17657 GTTTTGAAATTAATTTGATAAAAAGATAATCGTGAGCAGGATTCTGAAATTAATT
66 GTTTTGAAATTAATTTGATAAAAAGATAATCCTGAGCAGGATTCTGAAATTAATT
17712 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
17777 ATTAAAATCG
Statistics
Matches: 514, Mismatches: 29, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
119 1 0.00
120 506 0.98
121 7 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (120 bp):
TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
GTTTTGAAATTAATTTGATAAAAAGATAATCCTGAGCAGGATTCTGAAATTAATT
Found at i:18182 original size:139 final size:139
Alignment explanation
Indices: 17880--18958 Score: 1280
Period size: 139 Copynumber: 7.9 Consensus size: 139
17870 ATATGGAATG
* * *** * * * * *
17880 CCCGGAGGACTTGTCAGAATTAATACCTAAAGGTTTCTAAAATTGTGCCCAGAGGTCTTACCAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* *
17945 GCAAACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACAGCTTTGATTAAAAACTTTA
66 GCAAACTCAACCTTGAGCAA-G----G-TTTTGAAACTTAAACACAACTTTGATTAAAAACTTAA
*
18010 TGAAAAGAAATGATA
125 TAAAAAGAAATGATA
* *
18025 CCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGAAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* * * *
18090 GCGAACTCGACCTCGAGCAAGGTTTTGAAACTTAAACACAACTTTAATTAAAAACTTAATAAAAA
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
18155 GAAATGATA
131 GAAATGATA
* ** *
18164 CCCAGAGGATTTATCAGAATTAATACCCAAAGATTTCTGAAATGGTGCCCGGAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* * *
18229 GCAAACTCAACCTTGAGCACGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTGATGAAAA
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
18294 GAAATGATA
131 GAAATGATA
* * *
18303 CCCGGAGGATTAATCAGAAATAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* ** ** * * *
18368 GTAAACTTGACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGATTAAAAACTTGATGAAAT
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
18433 GAAATGATA
131 GAAATGATA
* ** *
18442 CCCGGAGGATTTATCAGAATTAATACCCGGAGGACTTAC--AAATGCGAACTC--A--ACCTTGA
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGG--TTTCTGAAATG-GTGCCCGGAGGA-CTT-A
**** * * * * *
18501 GC-AA-G-GTTTTGAAACTTAAACACA-GTTTTG--A-TT-AA-A-AAC-TTGA-T--GAA---A
61 -CAAATGCAAACTCAACCTTGAGCA-AGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTA
* *
18549 AG----A-ACATGATA
124 ATAAAAAGAAATGATA
18560 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* * *
18625 GCAAACTCAACCTTGAGAAAAGTTTTGAAACTTAAACACAGCTTTGATTAAAAACTTAATAAAAA
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
18690 GAAATGATA
131 GAAATGATA
*
18699 CCCAGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* *
18764 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTT-AATAAAAACTTAATAAAAA
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
18828 GAAATGATA
131 GAAATGATA
*
18837 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGACTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
* **
18902 GTAAACTTGACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTT
66 GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTT
18959 GCCAAAATGG
Statistics
Matches: 801, Mismatches: 97, Indels: 78
0.82 0.10 0.08
Matches are distributed among these distances:
116 3 0.00
117 3 0.00
118 46 0.06
119 4 0.00
120 5 0.01
121 15 0.02
123 2 0.00
124 2 0.00
125 2 0.00
126 3 0.00
127 2 0.00
128 5 0.01
129 5 0.01
130 1 0.00
131 3 0.00
132 2 0.00
133 2 0.00
134 3 0.00
136 15 0.02
137 5 0.01
138 136 0.17
139 459 0.57
140 4 0.00
141 3 0.00
144 1 0.00
145 70 0.09
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (139 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGATTAAAAACTTAATAAAAA
GAAATGATA
Found at i:18522 original size:117 final size:118
Alignment explanation
Indices: 18350--18592 Score: 434
Period size: 117 Copynumber: 2.1 Consensus size: 118
18340 TGAAATTGTG
* **
18350 CCCGGAGGACTTACAAATGTAAACTTGACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
*
18415 TTAAAAACTTGATGAAATGAA-ATGATACCCGGAGGATTTATCAGAATTAATA
66 TTAAAAACTTGATGAAAAGAACATGATACCCGGAGGATTTATCAGAATTAATA
*
18467 CCCGGAGGACTTACAAATGCGAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
18532 TTAAAAACTTGATGAAAAGAACATGATACCCGGAGGATTTATCAGAATTAATA
66 TTAAAAACTTGATGAAAAGAACATGATACCCGGAGGATTTATCAGAATTAATA
18585 CCCGGAGG
1 CCCGGAGG
18593 TTTCTGAAAT
Statistics
Matches: 120, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 81 0.68
118 39 0.32
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (118 bp):
CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
TTAAAAACTTGATGAAAAGAACATGATACCCGGAGGATTTATCAGAATTAATA
Found at i:18921 original size:138 final size:139
Alignment explanation
Indices: 18467--18958 Score: 851
Period size: 138 Copynumber: 3.5 Consensus size: 139
18457 AGAATTAATA
* *
18467 CCCGGAGGACTTACAAATGCGAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGTTTTGA
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTTGA
* *
18532 TTAAAAACTTGATGAAAAGAACATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTC
66 TTAAAAACTTAATAAAAAGAA-ATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTC
18597 TGAAATGGTG
130 TGAAATGGTG
* *
18607 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGAAAAGTTTTGAAACTTAAACACAGCTTTGA
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTTGA
*
18672 TTAAAAACTTAATAAAAAGAAATGATACCCAGAGGATTTATCAGAATTAATACCCGGAGGTTTCT
66 TTAAAAACTTAATAAAAAGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCT
18737 GAAATGGTG
131 GAAATGGTG
18746 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTT-A
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTTGA
*
18810 ATAAAAACTTAATAAAAAGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCT
66 TTAAAAACTTAATAAAAAGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCT
*
18875 GAAATTGTG
131 GAAATGGTG
* ** *
18884 CCCGGAGGACTTACAAATGTAAACTTGACCTTGAGCAAGGTTTTGAAACTTAAACACAACTTTGA
1 CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTTGA
18949 TTAAAAACTT
66 TTAAAAACTT
18959 GCCAAAATGG
Statistics
Matches: 334, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
138 131 0.39
139 123 0.37
140 80 0.24
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (139 bp):
CCCGGAGGACTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGAAACTTAAACACAGCTTTGA
TTAAAAACTTAATAAAAAGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCT
GAAATGGTG
Found at i:20264 original size:10 final size:9
Alignment explanation
Indices: 20238--20263 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20228 CGTTTTCTTC
20238 TTTTTTTTG
1 TTTTTTTTG
20247 TTTTTTTTG
1 TTTTTTTTG
20256 TTTTTTTT
1 TTTTTTTT
20264 TTGCATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Done.