Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017247.1 Corchorus olitorius cultivar O-4 contig17280, 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: 58391
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9149 original size:13 final size:13
Alignment explanation
Indices: 9131--9156 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9121 ACAAAAGAAT
9131 TATAACCAACATC
1 TATAACCAACATC
9144 TATAACCAACATC
1 TATAACCAACATC
9157 AGCCTCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAACCAACATC
Found at i:9179 original size:19 final size:19
Alignment explanation
Indices: 9155--9197 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
9145 ATAACCAACA
9155 TCAGCCTCATATATTGCTC
1 TCAGCCTCATATATTGCTC
*
9174 TCAGCCTCATTTATTGCTC
1 TCAGCCTCATATATTGCTC
9193 TCAGC
1 TCAGC
9198 TCCGTACTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.37
Consensus pattern (19 bp):
TCAGCCTCATATATTGCTC
Found at i:17841 original size:205 final size:207
Alignment explanation
Indices: 17488--17876 Score: 613
Period size: 205 Copynumber: 1.9 Consensus size: 207
17478 ACAAAATATA
* * * *
17488 CCAAACTACAATTAGAAAAATTCATGGAATCTACTTTTTAATTGCCAATCAACAAAATTTACCCA
1 CCAAACTACAATTAGAAAAAATCATGAAATCTAATTATTAATTGCCAATCAACAAAATTTACCCA
* * *
17553 AATTCCTTTGCATATTCATATGAATCTTTGAATCCAATTCAAAGCAAACGAATTCTATTTAAAAC
66 AATTCCTTTGCATATTCATATAAATCTTTGAATCAAATTCAAAGCAAACGAATTCTACTTAAAAC
* *
17618 AGAACAGAGCATATTC-AAAACAAATGGGTTTCTCCAGAAGAACCCAAAAAGGTTGAAACACCAT
131 AGAACAGAGCATATTCAAAAAAAAAAGGGTTTCTCCAGAAGAACCCAAAAAGGTTGAAACACCAT
17682 ACCTTGAAACAC
196 ACCTTGAAACAC
* *
17694 CCAAACTACAATT-GAAAAAAATCATGAAATCTAATTATTAATTG-CAGTCTACAAAATTTACCC
1 CCAAACTACAATTAG-AAAAAATCATGAAATCTAATTATTAATTGCCAATCAACAAAATTTACCC
* * *
17757 AAATTCCTTTGCATATTCATATAAATCTTTGAATCAAATTTAAAGCAAACGGATTCTACTTCAAA
65 AAATTCCTTTGCATATTCATATAAATCTTTGAATCAAATTCAAAGCAAACGAATTCTACTTAAAA
17822 CAGAACAGAGCATATTCAAAAAAAAAAAGGGTTTCTCCAGAAGAACCCAAAAAGG
130 CAGAACAGAGCATATTC-AAAAAAAAAAGGGTTTCTCCAGAAGAACCCAAAAAGG
17877 AAAGATTAAC
Statistics
Matches: 166, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
205 94 0.57
206 38 0.23
207 34 0.20
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (207 bp):
CCAAACTACAATTAGAAAAAATCATGAAATCTAATTATTAATTGCCAATCAACAAAATTTACCCA
AATTCCTTTGCATATTCATATAAATCTTTGAATCAAATTCAAAGCAAACGAATTCTACTTAAAAC
AGAACAGAGCATATTCAAAAAAAAAAGGGTTTCTCCAGAAGAACCCAAAAAGGTTGAAACACCAT
ACCTTGAAACAC
Found at i:24529 original size:10 final size:10
Alignment explanation
Indices: 24514--24538 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24504 ACGTACACTT
24514 AAAAAAGAAA
1 AAAAAAGAAA
24524 AAAAAAGAAA
1 AAAAAAGAAA
24534 AAAAA
1 AAAAA
24539 TCAATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:39314 original size:5 final size:5
Alignment explanation
Indices: 39306--39335 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
39296 AATCCCATCC
39306 TTTTA TTTTA TTTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
39336 TTTGGATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:39327 original size:11 final size:11
Alignment explanation
Indices: 39306--39336 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
39296 AATCCCATCC
39306 TTTTA-TTTTA
1 TTTTATTTTTA
39316 TTTTATTTTTA
1 TTTTATTTTTA
39327 TTTTATTTTT
1 TTTTATTTTT
39337 TTGGATGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:44157 original size:29 final size:31
Alignment explanation
Indices: 44125--44191 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
44115 ATGCAATTTG
44125 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
44154 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
44185 GGATATA
1 GGATATA
44192 GTCCGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:44380 original size:33 final size:31
Alignment explanation
Indices: 44310--44392 Score: 112
Period size: 33 Copynumber: 2.6 Consensus size: 31
44300 ACCTAACTGA
**
44310 TTATATCCTTAATTGCTTGAAATCGAAAACC
1 TTATATCCTTAATTGCTTGAAATAAAAAACC
* *
44341 TCATATCCTTAATTGCTTGAAATAAAAAAAACG
1 TTATATCCTTAATTGCTTGAAAT--AAAAAACC
44374 TTATATCCTTAATTGCTTG
1 TTATATCCTTAATTGCTTG
44393 TTTTGTAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 22 0.49
33 23 0.51
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATAAAAAACC
Found at i:44441 original size:31 final size:29
Alignment explanation
Indices: 44369--44448 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
44359 GAAATAAAAA
***
44369 AAACGTTATATCCTTAATTGCTTGTTTTG
1 AAACGTTATATCCTTAATTGCTTGTGCAG
*
44398 TAACGTTATATCCTTAATTGCTTGTGGCAG
1 AAACGTTATATCCTTAATTGCTTGT-GCAG
* *
44428 CAAACATTATATCCTAAATTG
1 -AAACGTTATATCCTTAATTG
44449 ATTATTTGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
30 1 0.02
31 17 0.40
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (29 bp):
AAACGTTATATCCTTAATTGCTTGTGCAG
Found at i:45292 original size:16 final size:16
Alignment explanation
Indices: 45273--45303 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
45263 ATATTCTAAG
45273 AATACATTTTTCTACT
1 AATACATTTTTCTACT
45289 AATACATTTTTCTAC
1 AATACATTTTTCTAC
45304 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:45396 original size:15 final size:17
Alignment explanation
Indices: 45371--45403 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45361 TAAAAAGTTA
45371 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
45387 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
45403 T
1 T
45404 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:45471 original size:31 final size:31
Alignment explanation
Indices: 45431--45574 Score: 148
Period size: 31 Copynumber: 4.7 Consensus size: 31
45421 TATAGATGAT
* *
45431 AAGCAAGCAATTTAGGATATAACGTTTTCTG
1 AAGCAAGCAATTAAGGATATAACGTTTTCTA
** *
45462 CCGCAAGCAATTAAGGATATAACG-TTAC-A
1 AAGCAAGCAATTAAGGATATAACGTTTTCTA
*
45491 AAACAAGCAATTAAGGATATAACGTTTTCTA
1 AAGCAAGCAATTAAGGATATAACGTTTTCTA
*** * *
45522 TTTCAAGCAATTAAGGATATGACGTTTTCGA
1 AAGCAAGCAATTAAGGATATAACGTTTTCTA
***
45553 TTTCAAGCAATTAAGGATATAA
1 AAGCAAGCAATTAAGGATATAA
45575 TCAGTTAAGG
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.22
30 6 0.06
31 69 0.72
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (31 bp):
AAGCAAGCAATTAAGGATATAACGTTTTCTA
Found at i:45508 original size:60 final size:62
Alignment explanation
Indices: 45434--45574 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 62
45424 AGATGATAAG
* *
45434 CAAGCAATTTAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTTACGAAAA
*** * * ***
45494 CAAGCAATTAAGGATATAACGTTTTCTATTTCAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTTACGAAAA
45556 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
45575 TCAGTTAAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
60 46 0.67
61 3 0.04
62 20 0.29
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (62 bp):
CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTTACGAAAA
Found at i:45770 original size:29 final size:31
Alignment explanation
Indices: 45704--45770 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
45694 CATAACGGAC
45704 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
* * *
45735 TATATCCTTAATTGTTTG-TTTT-GTAATGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
45764 TATATCC
1 TATATCC
45771 CAAATCGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:46403 original size:3 final size:3
Alignment explanation
Indices: 46391--46473 Score: 55
Period size: 3 Copynumber: 28.0 Consensus size: 3
46381 TGAATCGCCG
* * * *
46391 CCA CCG CCA CCA -CG CCA CCA CCA CGA GCCA CCA CCA CCC CCA -CA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA -CCA CCA CCA CCA CCA CCA
* * * *
46435 CCT CCA CCA CGA GCCA CCA CCA CC- CCA ACA CCT CCA CCA
1 CCA CCA CCA CCA -CCA CCA CCA CCA CCA CCA CCA CCA CCA
46474 TAACTACGGT
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
2 5 0.08
3 50 0.85
4 4 0.07
ACGTcount: A:0.28, C:0.63, G:0.07, T:0.02
Consensus pattern (3 bp):
CCA
Found at i:46421 original size:27 final size:27
Alignment explanation
Indices: 46390--46458 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 27
46380 ATGAATCGCC
* *
46390 GCCACCGCCACCACGCCACCACCACGA
1 GCCACCACCACCACACCACCACCACGA
*
46417 GCCACCACCACCCCCACACCTCCACCACGA
1 GCCACCACCA---CCACACCACCACCACGA
46447 GCCACCACCACC
1 GCCACCACCACC
46459 CCAACACCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 11 0.31
30 25 0.69
ACGTcount: A:0.26, C:0.62, G:0.10, T:0.01
Consensus pattern (27 bp):
GCCACCACCACCACACCACCACCACGA
Found at i:46422 original size:13 final size:14
Alignment explanation
Indices: 46389--46458 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 14
46379 GATGAATCGC
*
46389 CGCCACCGCCACCA
1 CGCCACCACCACCA
*
46403 CGCCACCACCACGA
1 CGCCACCACCACCA
46417 -GCCACCACCACC-
1 CGCCACCACCACCA
* *
46429 CCCACACCTCCACCA
1 CGC-CACCACCACCA
46444 CGAGCCACCACCACC
1 C--GCCACCACCACC
46459 CCAACACCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 12 0.27
14 21 0.48
15 1 0.02
16 9 0.20
17 1 0.02
ACGTcount: A:0.26, C:0.63, G:0.10, T:0.01
Consensus pattern (14 bp):
CGCCACCACCACCA
Found at i:46442 original size:30 final size:30
Alignment explanation
Indices: 46408--46473 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
46398 CACCACGCCA
*
46408 CCACCACGAGCCACCACCACCCCCACACCT
1 CCACCACGAGCCACCACCACCCCAACACCT
46438 CCACCACGAGCCACCACCACCCCAACACCT
1 CCACCACGAGCCACCACCACCCCAACACCT
46468 CCACCA
1 CCACCA
46474 TAACTACGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.62, G:0.06, T:0.03
Consensus pattern (30 bp):
CCACCACGAGCCACCACCACCCCAACACCT
Found at i:46466 original size:24 final size:24
Alignment explanation
Indices: 46397--46466 Score: 68
Period size: 30 Copynumber: 2.7 Consensus size: 24
46387 GCCGCCACCG
* *
46397 CCACCACGCCACCACCACGAGCCA
1 CCACCACCCCAACACCACGAGCCA
46421 CCACCACCCCCACACCTCCACCACGAGCCA
1 CCACCA-CCCCA-A----CACCACGAGCCA
46451 CCACCACCCCAACACC
1 CCACCACCCCAACACC
46467 TCCACCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
24 10 0.26
25 4 0.11
28 1 0.03
29 5 0.13
30 18 0.47
ACGTcount: A:0.29, C:0.63, G:0.07, T:0.01
Consensus pattern (24 bp):
CCACCACCCCAACACCACGAGCCA
Found at i:56679 original size:13 final size:14
Alignment explanation
Indices: 56661--56693 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
56651 AATTTATGTC
56661 ATATATTAAAT-AA
1 ATATATTAAATAAA
56674 ATATATTAAATAAA
1 ATATATTAAATAAA
56688 ATATAT
1 ATATAT
56694 AATCTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATTAAATAAA
Done.