Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014443.1 Corchorus olitorius cultivar O-4 contig14476, 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: 25884
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:910 original size:18 final size:18
Alignment explanation
Indices: 884--918 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
874 TATTTATATT
*
884 ATTTTAAAAAAACTACCC
1 ATTTAAAAAAAACTACCC
902 ATTTAAAAAAAACTACC
1 ATTTAAAAAAAACTACC
919 AAAAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTTAAAAAAAACTACCC
Found at i:5568 original size:19 final size:19
Alignment explanation
Indices: 5540--5588 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5530 TTAAAATTAT
5540 TAAT-TATATAAATGA-ATA
1 TAATATATATAAAT-ATATA
*
5558 TAATATATATATATATATA
1 TAATATATATAAATATATA
5577 TAA-A-ATATAAAT
1 TAATATATATAAAT
5589 TATTGTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAATATATATAAATATATA
Found at i:9975 original size:29 final size:29
Alignment explanation
Indices: 9902--9974 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
9892 TACACACAAC
** *
9902 AGCCAAATAAGCCCCTGAACTCTAATTAC
1 AGCCAAATAAGCCCCTGAACTCTAAGAAA
* *
9931 AGTCAAATAAGCCCCTGAACTCTTAGAAA
1 AGCCAAATAAGCCCCTGAACTCTAAGAAA
9960 AGGCCAAATAAGCCC
1 A-GCCAAATAAGCCC
9975 TTTTCGAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.18
Consensus pattern (29 bp):
AGCCAAATAAGCCCCTGAACTCTAAGAAA
Found at i:10414 original size:30 final size:30
Alignment explanation
Indices: 10378--10454 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
10368 GTCAGAAAAT
*
10378 GGCTTATTTGGCCTTTTCTAAGAGTTCAGG
1 GGCTTATTTGGCCTTTTATAAGAGTTCAGG
*** *
10408 GGCTTATTTGG-CTGCAATTAGAGTTCAGG
1 GGCTTATTTGGCCTTTTATAAGAGTTCAGG
*
10437 CGCTTATTTGGCCATTTT
1 GGCTTATTTGGCC-TTTT
10455 GTGTAAGTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 23 0.64
30 12 0.33
31 1 0.03
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (30 bp):
GGCTTATTTGGCCTTTTATAAGAGTTCAGG
Found at i:18677 original size:53 final size:53
Alignment explanation
Indices: 18614--18722 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
18604 TCTTTAAATC
* *
18614 CAATAGTTCATTACATTTTGTATTATTTGGTATATGTGCTTATTTAATATGTT
1 CAATAATTCATTACATTTTGTATTATTTGGTATATGTGCTTATTTAATAGGTT
* *
18667 CAATAATTCATTACGTTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAATTCATTACATTTTGTATTATTTGGTATATGTGCTTATTTAATAGGTT
18720 CAA
1 CAA
18723 CTGAATAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (53 bp):
CAATAATTCATTACATTTTGTATTATTTGGTATATGTGCTTATTTAATAGGTT
Found at i:21360 original size:14 final size:15
Alignment explanation
Indices: 21326--21363 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
21316 GGTTAGATTT
*
21326 ACTGATTAATTTCAT
1 ACTGATTAATTTCAA
*
21341 ACTGATTGATTT-AA
1 ACTGATTAATTTCAA
21355 ACTGATTAA
1 ACTGATTAA
21364 AAGTTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (15 bp):
ACTGATTAATTTCAA
Found at i:23536 original size:35 final size:36
Alignment explanation
Indices: 23475--23550 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 36
23465 CTAAGACTTC
**
23475 TATATATTTTTTAATTTTGTTATCTATAATCCATTG
1 TATATATCATTTAATTTTGTTATCTATAATCCATTG
*
23511 TATATATCATTTAA-TTTGTTATCTATAATCTATTG
1 TATATATCATTTAATTTTGTTATCTATAATCCATTG
23546 TATAT
1 TATAT
23551 TAGTATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (36 bp):
TATATATCATTTAATTTTGTTATCTATAATCCATTG
Found at i:24507 original size:18 final size:18
Alignment explanation
Indices: 24484--24518 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
24474 CCTGGGTCGC
24484 TATCGGTACCAAGAGGAA
1 TATCGGTACCAAGAGGAA
24502 TATCGGTACCAAGAGGA
1 TATCGGTACCAAGAGGA
24519 GTAAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (18 bp):
TATCGGTACCAAGAGGAA
Found at i:24786 original size:24 final size:24
Alignment explanation
Indices: 24759--24806 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
24749 AAATTACTTC
24759 TTTTCAATTTTAATGGAAATGAAA
1 TTTTCAATTTTAATGGAAATGAAA
24783 TTTTCAATTTTAATGGAAATGAAA
1 TTTTCAATTTTAATGGAAATGAAA
24807 AAATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (24 bp):
TTTTCAATTTTAATGGAAATGAAA
Found at i:24824 original size:12 final size:12
Alignment explanation
Indices: 24804--24847 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
24794 AATGGAAATG
*
24804 AAAAA-ATTAAT
1 AAAAATATTATT
24815 AAAAATATTATT
1 AAAAATATTATT
*
24827 GAAAATATTATT
1 AAAAATATTATT
*
24839 GAAAATATT
1 AAAAATATT
24848 GAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 5 0.17
12 25 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:24829 original size:24 final size:24
Alignment explanation
Indices: 24802--24847 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24792 TTAATGGAAA
24802 TGAAAAAATTAATAAAAATATTAT
1 TGAAAAAATTAATAAAAATATTAT
* * *
24826 TGAAAATATTATTGAAAATATT
1 TGAAAAAATTAATAAAAATATT
24848 GAAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (24 bp):
TGAAAAAATTAATAAAAATATTAT
Done.