Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006645.1 Corchorus olitorius cultivar O-4 contig06670, 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, 664
Length: 1107
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Found at i:577 original size:7 final size:7
Alignment explanation
Indices: 332--576 Score: 328
Period size: 7 Copynumber: 35.0 Consensus size: 7
322 TGAAATGCAG
332 GTTTTGA
1 GTTTTGA
*
339 ATTTTGA
1 GTTTTGA
*
346 TTTTTGA
1 GTTTTGA
***
353 GCCATGA
1 GTTTTGA
*
360 ATTTTGA
1 GTTTTGA
*
367 ATTTTGA
1 GTTTTGA
374 GTTTTGA
1 GTTTTGA
381 GTTTTGA
1 GTTTTGA
388 GTTTTGA
1 GTTTTGA
*
395 GTTTTGC
1 GTTTTGA
402 GTTTTGA
1 GTTTTGA
*
409 ATTTTGA
1 GTTTTGA
416 GTTTTGA
1 GTTTTGA
423 GTTTTGA
1 GTTTTGA
430 GTTTTGA
1 GTTTTGA
437 GTTTTGA
1 GTTTTGA
444 GTTTTGA
1 GTTTTGA
451 GTTTTGA
1 GTTTTGA
458 GTTTTGA
1 GTTTTGA
465 GTTTTGA
1 GTTTTGA
472 GTTTTGA
1 GTTTTGA
479 GTTTTGA
1 GTTTTGA
*
486 ATTTTGA
1 GTTTTGA
493 GTTTTGA
1 GTTTTGA
500 GTTTTGA
1 GTTTTGA
507 GTTTTGA
1 GTTTTGA
*
514 ATTTTGA
1 GTTTTGA
521 GTTTTGA
1 GTTTTGA
*
528 ATTTTGA
1 GTTTTGA
*
535 ATTTTGA
1 GTTTTGA
*
542 ATTTTGA
1 GTTTTGA
*
549 ATTTTGA
1 GTTTTGA
*
556 ATTTTGA
1 GTTTTGA
*
563 ATTTTGA
1 GTTTTGA
*
570 ATTTTGA
1 GTTTTGA
577 AATGAAATGC
Statistics
Matches: 218, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 218 1.00
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.56
Consensus pattern (7 bp):
GTTTTGA
Found at i:756 original size:33 final size:33
Alignment explanation
Indices: 714--791 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
704 AGAAACTATG
* * * *
714 GATTATGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
747 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
780 AATTTTGAACTT
1 GATTTTGAACTT
792 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:918 original size:55 final size:54
Alignment explanation
Indices: 844--1099 Score: 291
Period size: 55 Copynumber: 4.9 Consensus size: 54
834 ATGGAAACCT
* * *
844 TTCTTGGAACGACCGCACTGGATCAATTTAGAGATCAATTCTGATCATCATAAAC
1 TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAACTCTGATCATCA-AAAC
*
899 TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAATTCTGATCATCATAAAC
1 TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAACTCTGATCATCA-AAAC
* *
954 TTCTTGGAATGACCACACTGGATCAA-TTGGAGATCAACTCTTATCATCGAAAAC
1 TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAACTCTGATCATC-AAAAC
* *
1008 TTCTT---A-G---ACACTGGATCAGTTT-GAGATCAACTCCGATCATCCAAAAC
1 TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAACTCTGATCAT-CAAAAC
* * *
1055 TTCTTGGAATGACCGCATTGGATC-ATCT-GAGGATCAACTCTGATC
1 TTCTTGGAATGACCACACTGGATCAATTTAGA-GATCAACTCTGATC
1100 TCTAAAAA
Statistics
Matches: 177, Mismatches: 13, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
47 37 0.21
48 3 0.02
50 2 0.01
51 2 0.01
53 4 0.02
54 49 0.28
55 80 0.45
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
TTCTTGGAATGACCACACTGGATCAATTTAGAGATCAACTCTGATCATCAAAAC
Found at i:1022 original size:47 final size:47
Alignment explanation
Indices: 968--1059 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
958 TGGAATGACC
** *
968 ACACTGGATCAATTGGAGATCAACTCTTATCATCGAAAACTTCTTAG
1 ACACTGGATCAATTGGAGATCAACTCCGATCATCCAAAACTTCTTAG
* *
1015 ACACTGGATCAGTTTGAGATCAACTCCGATCATCCAAAACTTCTT
1 ACACTGGATCAATTGGAGATCAACTCCGATCATCCAAAACTTCTT
1060 GGAATGACCG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (47 bp):
ACACTGGATCAATTGGAGATCAACTCCGATCATCCAAAACTTCTTAG
Found at i:1048 original size:101 final size:104
Alignment explanation
Indices: 844--1099 Score: 292
Period size: 101 Copynumber: 2.4 Consensus size: 104
834 ATGGAAACCT
* *
844 TTCTTGGAACGACCGCACTGGATCAATTTAGAGATCAATTCTGATCATCATAAACTTCTTGGAAT
1 TTCTTGGAATGACCGCACTGGATCAA-TT-GAGATCAACTCTGATCATCATAAACTTCTT-G-AT
* *
909 GACCACACTGGATCAATTTAGAGATCAATTCTGATCAT-CATAAAC
62 G--CACACTGGATCAATTTAGAGATCAACTCCGATCATCCA-AAAC
* *
954 TTCTTGGAATGACCACACTGGATCAATTGGAGATCAACTCTTATCATCGA-AAACTTCTT-A-G-
1 TTCTTGGAATGACCGCACTGGATCAATT-GAGATCAACTCTGATCATC-ATAAACTTCTTGATGC
*
1015 ACACTGGATCAGTTT-GAGATCAACTCCGATCATCCAAAAC
64 ACACTGGATCAATTTAGAGATCAACTCCGATCATCCAAAAC
*
1055 TTCTTGGAATGACCGCATTGGATC-ATCTGAGGATCAACTCTGATC
1 TTCTTGGAATGACCGCACTGGATCAAT-TGA-GATCAACTCTGATC
1100 TCTAAAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
100 4 0.03
101 56 0.43
102 16 0.12
105 1 0.01
106 1 0.01
109 28 0.21
110 25 0.19
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (104 bp):
TTCTTGGAATGACCGCACTGGATCAATTGAGATCAACTCTGATCATCATAAACTTCTTGATGCAC
ACTGGATCAATTTAGAGATCAACTCCGATCATCCAAAAC
Done.