Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013154.1 Corchorus olitorius cultivar O-4 contig13187, 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: 16108
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:526 original size:6 final size:6
Alignment explanation
Indices: 515--540 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
505 CCTTCCGCCA
515 TTGCCG TTGCCG TTGCCG TTGCCG TT
1 TTGCCG TTGCCG TTGCCG TTGCCG TT
541 ACCATTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38
Consensus pattern (6 bp):
TTGCCG
Found at i:6374 original size:42 final size:44
Alignment explanation
Indices: 6323--6416 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
6313 AGTGCATTAT
*
6323 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
*
6364 TTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAG
6409 CTAATATT
1 CTAATATT
6417 AATTGTTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
44 1 0.02
45 36 0.78
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:9179 original size:36 final size:37
Alignment explanation
Indices: 9136--9208 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
9126 TTTCAAATTT
9136 AATATTGTAATTAG-TTAATTACCTTCGTTAGTTTTA
1 AATATTGTAATTAGTTTAATTACCTTCGTTAGTTTTA
* *
9172 AATATTGTAATTAGTTTTATTACCTTTGTTAGTTTTA
1 AATATTGTAATTAGTTTAATTACCTTCGTTAGTTTTA
9209 TATTAGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 14 0.41
37 20 0.59
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (37 bp):
AATATTGTAATTAGTTTAATTACCTTCGTTAGTTTTA
Found at i:10996 original size:22 final size:23
Alignment explanation
Indices: 10965--11010 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
10955 TAATATCCAC
10965 ACACAATTAAT-ATGAAAT-TAAA
1 ACACAATTAATCAT-AAATATAAA
*
10987 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
11010 A
1 A
11011 TATATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:12956 original size:98 final size:98
Alignment explanation
Indices: 12820--13016 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
12810 AACCCCAAAG
12820 CATAAGGCCATGAGAAGTGAATAAATTCATGTGTGACACTTGTCACGGTCAATGGCTAAAAAATG
1 CATAAGGCCATGAGAAGTGAATAAATTCATGTGTGACACTTGTCACGGTCAATGGCTAAAAAATG
12885 ATTATTTGTGAATAATTCGGTTGATTTATGGTT
66 ATTATTTGTGAATAATTCGGTTGATTTATGGTT
12918 CATAAGGCCATGAGAAGTGAATAAATTCATGTGTGACACTTGTCACGGTCAATGGCTAAAAAATG
1 CATAAGGCCATGAGAAGTGAATAAATTCATGTGTGACACTTGTCACGGTCAATGGCTAAAAAATG
12983 ATTATTTGTGAATAATTCGGTTGATTTATGGTT
66 ATTATTTGTGAATAATTCGGTTGATTTATGGTT
13016 C
1 C
13017 GAATCTAAGC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (98 bp):
CATAAGGCCATGAGAAGTGAATAAATTCATGTGTGACACTTGTCACGGTCAATGGCTAAAAAATG
ATTATTTGTGAATAATTCGGTTGATTTATGGTT
Found at i:14673 original size:17 final size:18
Alignment explanation
Indices: 14640--14677 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
14630 CCCAAATTAC
*
14640 TTATGGAAATTAGGGAAA
1 TTATGAAAATTAGGGAAA
14658 TTATGAAAATTA-GGAAA
1 TTATGAAAATTAGGGAAA
14675 TTA
1 TTA
14678 AATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (18 bp):
TTATGAAAATTAGGGAAA
Found at i:15638 original size:18 final size:18
Alignment explanation
Indices: 15615--15652 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
15605 CCAGTTCAAA
15615 TCAATCAAGCCCAATGCT
1 TCAATCAAGCCCAATGCT
*
15633 TCAATCAAGCCCAGTGCT
1 TCAATCAAGCCCAATGCT
15651 TC
1 TC
15653 TTTTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (18 bp):
TCAATCAAGCCCAATGCT
Found at i:16052 original size:48 final size:49
Alignment explanation
Indices: 15977--16082 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 49
15967 CAAGCAATCC
* **
15977 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTCCCACAAAATTGATCT
1 TTTACTTTTTCCTTGCACTTTTTCTCAATTTTTAACACAAAATTGATCT
* *
16025 TTTA-TTTTTCCTTGCACTTTTTCTCAATTTTTAAGATAAAATTGATCT
1 TTTACTTTTTCCTTGCACTTTTTCTCAATTTTTAACACAAAATTGATCT
16073 TTTACTTTTT
1 TTTACTTTTT
16083 ATTGTTCCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
47 6 0.12
48 40 0.78
49 5 0.10
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (49 bp):
TTTACTTTTTCCTTGCACTTTTTCTCAATTTTTAACACAAAATTGATCT
Done.