Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024899.1 Corchorus olitorius cultivar O-4 contig24932, 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: 15947
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:2564 original size:178 final size:177
Alignment explanation
Indices: 2192--2648 Score: 594
Period size: 178 Copynumber: 2.6 Consensus size: 177
2182 AATACAATCC
* * * * * ** * * *
2192 ACCGAAATAACAAATTTTTCAGTAGTATTTTTGGTACTTGAAATATCAAATTTAGCTTTTGAGTT
1 ACCGAAACAACTAATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTC
* * * * * *
2257 CTTCATGAAAGTTGTAGATAACGGAACAACCTTTTAACAGATATTTGAATCACTTAATCGGACAT
66 CTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGAAAATTGAATCACTCAATCAGACAT
* * *
2322 CTGGTGCAAAAGTTATGTAATATTAAGTGAACGGTTCATTCCCAGTA
131 CTGGAGCAAAAGTTATGTAATATTAAGTGAACCGTCCATTCCCAGTA
* * *
2369 ACCGAAACAACTAATTTTTTGGAGGCATTTTTTATATTTGAAACATTAAATTTAGCTTTTGAGTC
1 ACCGAAACAACTAATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTC
* * * * *
2434 CTTTATGATAGTTGTAAATCATGGAACAACCTTTTAAGAGAAAATTGAATCACCTCAATTAGACA
66 CTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGAAAATTGAATCA-CTCAATCAGACA
* *
2499 TTTGGAGCAAAAGTTATGTAATATTAAGTGGACCGTCCATTCCC-GTTA
130 TCTGGAGCAAAAGTTATGTAATATTAAGTGAACCGTCCATTCCCAG-TA
2547 ACCGAAACAACTAATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAG-TTTTAGAGT
1 ACCGAAACAACTAATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTT-GAGT
* *
2611 CCTCCATGAAAGTTGTAGATCATGAAACAACCTTTTAA
65 CCTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAA
2649 TAGACCACTT
Statistics
Matches: 240, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
177 101 0.42
178 139 0.58
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (177 bp):
ACCGAAACAACTAATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTC
CTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGAAAATTGAATCACTCAATCAGACAT
CTGGAGCAAAAGTTATGTAATATTAAGTGAACCGTCCATTCCCAGTA
Found at i:4214 original size:22 final size:22
Alignment explanation
Indices: 4155--4686 Score: 218
Period size: 22 Copynumber: 24.4 Consensus size: 22
4145 TGCTCCAACG
* *
4155 TGATAACCACACTGTGAAAATT
1 TGATAACCACACTATGAAATTT
* ** *
4177 TAATAACCTTATTATGAAATTT
1 TGATAACCACACTATGAAATTT
* * *
4199 CGATAACCACCCTATGAAAATT
1 TGATAACCACACTATGAAATTT
4221 TGATAACCACACTATG-AATTT
1 TGATAACCACACTATGAAATTT
* * *
4242 TGATAACCTCAGTGTGAAATTT
1 TGATAACCACACTATGAAATTT
* *
4264 TGATAATCACA-T-TGTAAA-AT
1 TGATAACCACACTATG-AAATTT
* * *
4284 TGGTAACCGCACTGTGAAAATTT
1 TGATAACCACACTATG-AAATTT
* * *
4307 TGATAACCTC-CTCTTAAAATTT
1 TGATAACCACACT-ATGAAATTT
4329 TGATAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
* * * ** * *
4351 CG--ACCCTATGAGAATGAAACTG
1 TGATAACC-A-CACTATGAAATTT
** * * *
4373 TGATATTCTCTCTATGTAATTT
1 TGATAACCACACTATGAAATTT
* * * * *
4395 TGATAATCTCTCCATAAAATTT
1 TGATAACCACACTATGAAATTT
* * *
4417 TCATAACCTCCCTATGAAATTT
1 TGATAACCACACTATGAAATTT
* * *
4439 TGTTAACCTC-C-ATAGGAATATT
1 TGATAACCACACTAT-GAAAT-TT
* *
4461 CGATAA--GCAC----AAATTT
1 TGATAACCACACTATGAAATTT
*
4477 TGATAACTTCAACCCCTATGAAATTT
1 TGATAAC--C-A-CACTATGAAATTT
* **
4503 TGTTAA-CATTCTTATGAAATTT
1 TGATAACCACAC-TATGAAATTT
* *
4525 TGATAACCACAATATAAAATTT
1 TGATAACCACACTATGAAATTT
* *
4547 TGATAACCTTC-GTATGAAATTT
1 TGATAACC-ACACTATGAAATTT
* * *
4569 TGTTAACCTCCCTATGAAATTT
1 TGATAACCACACTATGAAATTT
* * **
4591 TGGTAACCTCTGTATGAAATTT
1 TGATAACCACACTATGAAATTT
* * *
4613 TGATAACTACATTATGAAGTTT
1 TGATAACCACACTATGAAATTT
* *
4635 TGATAACCTC-CATGTGAAATTT
1 TGATAACCACAC-TATGAAATTT
*
4657 TGGTAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
4679 TGATAACC
1 TGATAACC
4687 TTCCTATATA
Statistics
Matches: 378, Mismatches: 102, Indels: 60
0.70 0.19 0.11
Matches are distributed among these distances:
16 7 0.02
17 3 0.01
20 17 0.04
21 32 0.08
22 289 0.76
23 17 0.04
24 2 0.01
26 11 0.03
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
TGATAACCACACTATGAAATTT
Found at i:4260 original size:43 final size:43
Alignment explanation
Indices: 4155--4347 Score: 158
Period size: 43 Copynumber: 4.4 Consensus size: 43
4145 TGCTCCAACG
* **
4155 TGATAACCACACTGTGAAAATTTAATAACCTTATTATGAAATTT
1 TGATAACCACACTGTGAAAATTTGATAACCACA-TATGAAATTT
* * *
4199 CGATAACCACCCTATGAAAATTTGATAACCACACTATG-AATTT
1 TGATAACCACACTGTGAAAATTTGATAACCACA-TATGAAATTT
* * * * *
4242 TGATAACCTCAGTGTGAAATTTTGATAATCACAT-TGTAAA-AT
1 TGATAACCACACTGTGAAAATTTGATAACCACATATG-AAATTT
* * * * * *
4284 TGGTAACCGCACTGTGAAAATTTTGATAACCTCCTCTTAAAATTT
1 TGATAACCACACTGTGAAAA-TTTGATAACCACAT-ATGAAATTT
*
4329 TGATAACCACACTATGAAA
1 TGATAACCACACTGTGAAA
4348 TTTCGACCCT
Statistics
Matches: 116, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
41 2 0.02
42 18 0.16
43 44 0.38
44 34 0.29
45 18 0.16
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (43 bp):
TGATAACCACACTGTGAAAATTTGATAACCACATATGAAATTT
Found at i:4261 original size:65 final size:65
Alignment explanation
Indices: 4155--4347 Score: 187
Period size: 65 Copynumber: 3.0 Consensus size: 65
4145 TGCTCCAACG
* * * * *
4155 TGATAACCACACTGTGAAAATTTAATAACCTTATTATGAAATTTCGATAACCACCCTATGAAAAT
1 TGATAACCACACTGTGAAATTTTGATAACCTCACTATGAAATTTTGATAACCACCCTATGAAAA-
4220 T
65 T
* * * * *
4221 TGATAACCACACTATG-AATTTTGATAACCTCAGTGTGAAATTTTGATAATCA-CAT-TGTAAAA
1 TGATAACCACACTGTGAAATTTTGATAACCTCACTATGAAATTTTGATAACCACCCTATG-AAAA
4283 T
65 T
* * * * *
4284 TGGTAACCGCACTGTGAAAATTTTGATAACCTC-CTCTTAAAATTTTGATAACCACACTATGAAA
1 TGATAACCACACTGTG-AAATTTTGATAACCTCACT-ATGAAATTTTGATAACCACCCTATGAAA
4348 TTTCGACCCT
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
63 16 0.16
64 7 0.07
65 59 0.57
66 19 0.18
67 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (65 bp):
TGATAACCACACTGTGAAATTTTGATAACCTCACTATGAAATTTTGATAACCACCCTATGAAAAT
Found at i:4573 original size:66 final size:66
Alignment explanation
Indices: 4491--4702 Score: 248
Period size: 66 Copynumber: 3.2 Consensus size: 66
4481 AACTTCAACC
* * * * *
4491 CCTATGAAATTTTGTTAACATTCTTATGAAATTTTGATAACCACAATATAAAATTTTGATAACCT
1 CCTATGAAATTTTGTTAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGATAACCT
4556 T
66 T
* * * **
4557 CGTATGAAATTTTGTTAACCTCCCTATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAA-CT
1 CCTATGAAATTTTGTTAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGATAACCT
*
4621 A
66 T
* * * * *
4622 CATTATGAAGTTTTGATAACCTCCATGTGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
1 C-CTATGAAATTTTGTTAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGATAACC
4687 TT
65 TT
4689 CCTAT-ATAATTTTG
1 CCTATGA-AATTTTG
4703 GTTTGATTGT
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
65 4 0.03
66 115 0.94
67 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (66 bp):
CCTATGAAATTTTGTTAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGATAACCT
T
Found at i:11697 original size:13 final size:13
Alignment explanation
Indices: 11679--11706 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11669 AAGCACTATA
11679 TATCTTATCTTAC
1 TATCTTATCTTAC
11692 TATCTTATCTTAC
1 TATCTTATCTTAC
11705 TA
1 TA
11707 CTATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (13 bp):
TATCTTATCTTAC
Found at i:11951 original size:16 final size:17
Alignment explanation
Indices: 11915--11952 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
11905 TAATTTACTT
* *
11915 TTTATAATTATTTTTAG
1 TTTATAATTATATTTAA
11932 TTTATAA-TATATTTAA
1 TTTATAATTATATTTAA
11948 TTTAT
1 TTTAT
11953 GGGTTTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTATAATTATATTTAA
Done.