Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008763.1 Corchorus capsularis cultivar CVL-1 contig08784, 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: 22834
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:218 original size:24 final size:24
Alignment explanation
Indices: 186--231 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
176 TGGGAAAAAA
186 TATATGACGGCGTCTAAACGCCTC
1 TATATGACGGCGTCTAAACGCCTC
* *
210 TATATGACGGCGTGTAGACGCC
1 TATATGACGGCGTCTAAACGCC
232 GTAATCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
TATATGACGGCGTCTAAACGCCTC
Found at i:669 original size:6 final size:6
Alignment explanation
Indices: 660--686 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
650 AAAGCAAAGC
660 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
687 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:720 original size:12 final size:13
Alignment explanation
Indices: 694--722 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
684 AAAGCAGATT
694 ATAAAGCAAATCA
1 ATAAAGCAAATCA
707 ATAAAGCAAA-CA
1 ATAAAGCAAATCA
719 ATAA
1 ATAA
723 TTATGGATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (13 bp):
ATAAAGCAAATCA
Found at i:1616 original size:10 final size:10
Alignment explanation
Indices: 1601--1625 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1591 GAGGACTCTA
1601 GAATTTTCTG
1 GAATTTTCTG
1611 GAATTTTCTG
1 GAATTTTCTG
1621 GAATT
1 GAATT
1626 GTGCAGGAAC
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:6556 original size:32 final size:31
Alignment explanation
Indices: 6497--6569 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 31
6487 AAATTAGCAG
* *
6497 AAACAGAAAATAAAAATATTTTTTTAAAAGGAA
1 AAACGGAAAAGAAAAATATTTTTTT-AAA-GAA
*
6530 AAACGGAAAAGAAAAA-CTTTTTTTAAAGAA
1 AAACGGAAAAGAAAAATATTTTTTTAAAGAA
6560 AAATCGGAAA
1 AAA-CGGAAA
6570 CCCTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.17
31 9 0.25
32 7 0.19
33 14 0.39
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.23
Consensus pattern (31 bp):
AAACGGAAAAGAAAAATATTTTTTTAAAGAA
Found at i:7858 original size:10 final size:10
Alignment explanation
Indices: 7843--7867 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7833 GAGGACTCTA
7843 GAATTTTCTG
1 GAATTTTCTG
7853 GAATTTTCTG
1 GAATTTTCTG
7863 GAATT
1 GAATT
7868 GTGCAGGAAC
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:8491 original size:12 final size:12
Alignment explanation
Indices: 8456--8495 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 12
8446 TAAAAACACA
8456 TATAAAAATAGC
1 TATAAAAATAGC
8468 -A-AAAAATA--
1 TATAAAAATAGC
8476 TATAAAAATAGC
1 TATAAAAATAGC
8488 TATAAAAA
1 TATAAAAA
8496 CATGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.04
10 14 0.58
11 1 0.04
12 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (12 bp):
TATAAAAATAGC
Found at i:10863 original size:10 final size:10
Alignment explanation
Indices: 10848--10877 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
10838 GCCCAATCGA
10848 TGGCCGGTTG
1 TGGCCGGTTG
10858 TGGCCGGTTG
1 TGGCCGGTTG
10868 TGGCCGGTTG
1 TGGCCGGTTG
10878 GTGCACCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.50, T:0.30
Consensus pattern (10 bp):
TGGCCGGTTG
Found at i:10940 original size:33 final size:32
Alignment explanation
Indices: 10899--10997 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 32
10889 GATGACCAGT
* *
10899 TGTT-GCCGGACATGTCCATGTCGCGTGGCCGG
1 TGTTGGCCGGGCATCTCCA-GTCGCGTGGCCGG
*
10931 TGTTGGCCGGGCATCTCCGAGTCACGTGGCCGG
1 TGTTGGCCGGGCATCTCC-AGTCGCGTGGCCGG
* *
10964 TGTTGGCCGGGCTTCTCCAAGTCGCATGGCCGG
1 TGTTGGCCGGGCATCTCC-AGTCGCGTGGCCGG
10997 T
1 T
10998 CACTAGTGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
32 4 0.07
33 53 0.91
34 1 0.02
ACGTcount: A:0.09, C:0.29, G:0.37, T:0.24
Consensus pattern (32 bp):
TGTTGGCCGGGCATCTCCAGTCGCGTGGCCGG
Found at i:16924 original size:30 final size:30
Alignment explanation
Indices: 16888--16950 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
16878 TCTTCAAGGG
* *
16888 GGAGGGAATTATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT
16918 GGAGGGAATGAAGCGCCAAGGACTTATCAT
1 GGAGGGAATGAAGCGCCAAGGACTTATCAT
16948 GGA
1 GGA
16951 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGAAGCGCCAAGGACTTATCAT
Found at i:18792 original size:30 final size:30
Alignment explanation
Indices: 18756--18818 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
18746 CTTCAAGGGG
* *
18756 GGAGGGAATTATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT
18786 GGAGGGAATGAAGCGCCAAGGACTTATCAT
1 GGAGGGAATGAAGCGCCAAGGACTTATCAT
18816 GGA
1 GGA
18819 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGAAGCGCCAAGGACTTATCAT
Found at i:20658 original size:30 final size:30
Alignment explanation
Indices: 20622--20684 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
20612 CTTCAAGGGG
* *
20622 GGAGGGAATTATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT
20652 GGAGGGAATGAAGCGCCAAGGACTTATCAT
1 GGAGGGAATGAAGCGCCAAGGACTTATCAT
20682 GGA
1 GGA
20685 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGAAGCGCCAAGGACTTATCAT
Found at i:22526 original size:30 final size:30
Alignment explanation
Indices: 22490--22552 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
22480 CTTCAAGGGG
* *
22490 GGAGGGAATTATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT
22520 GGAGGGAATGAAGCGCCAAGGACTTATCAT
1 GGAGGGAATGAAGCGCCAAGGACTTATCAT
22550 GGA
1 GGA
22553 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGAAGCGCCAAGGACTTATCAT
Done.