Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023142.1 Corchorus olitorius cultivar O-4 contig23175, 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: 30317
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6073 original size:21 final size:21
Alignment explanation
Indices: 6059--6096 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6049 ACGCAGATAT
6059 TTTTTTTTATGACGCAAAAAC
1 TTTTTTTTATGACGCAAAAAC
6080 TTTTTTTTAT--CGCAAAA
1 TTTTTTTTATGACGCAAAA
6097 CCGAGAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (21 bp):
TTTTTTTTATGACGCAAAAAC
Found at i:6470 original size:15 final size:16
Alignment explanation
Indices: 6450--6482 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6440 TAAGAAGAAT
6450 AATTAAA-AAGAAAAC
1 AATTAAACAAGAAAAC
*
6465 AATTAAACTAGAAAAC
1 AATTAAACAAGAAAAC
6481 AA
1 AA
6483 AGCAGAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (16 bp):
AATTAAACAAGAAAAC
Found at i:7856 original size:19 final size:18
Alignment explanation
Indices: 7823--7858 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7813 TTGAAATTAT
7823 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
7841 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
7859 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:12998 original size:21 final size:21
Alignment explanation
Indices: 12974--13041 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
12964 GGAATGGCGA
12974 TGGCACGGGCATGGCCGGTAG
1 TGGCACGGGCATGGCCGGTAG
* ** * *
12995 TGGCACGGGCTTAACCGATGG
1 TGGCACGGGCATGGCCGGTAG
* *
13016 TGGCACGGTGAATGGCCGGTAA
1 TGGCACGG-GCATGGCCGGTAG
13038 TGGC
1 TGGC
13042 TTAGTAGTGG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 24 0.71
22 10 0.29
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGGTAG
Found at i:17508 original size:11 final size:11
Alignment explanation
Indices: 17492--17517 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17482 CCTTGCCTAA
17492 AAAACTAGAAG
1 AAAACTAGAAG
17503 AAAACTAGAAG
1 AAAACTAGAAG
17514 AAAA
1 AAAA
17518 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:20842 original size:16 final size:16
Alignment explanation
Indices: 20823--20857 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20813 ATTGGGCGGG
* *
20823 TTCGGGTTTGGGTTTT
1 TTCGGGTTCGGGTATT
20839 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
20855 TTC
1 TTC
20858 AGGCTCGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.34, T:0.51
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:21128 original size:22 final size:22
Alignment explanation
Indices: 21082--21128 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
21072 ATAATATAAT
*
21082 AATATAATATAACATGATTATC
1 AATATAATATAACATGATTAAC
21104 AATATATATATAA-A-GATTGAAC
1 AATATA-ATATAACATGATT-AAC
21126 AAT
1 AAT
21129 TGTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (22 bp):
AATATAATATAACATGATTAAC
Found at i:21843 original size:23 final size:23
Alignment explanation
Indices: 21813--21891 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
21803 TCAAATTATT
* **
21813 TCGGGTTCGGCCTCGGGTTGGGA
1 TCGGGTTCGGTCTCGGGTCAGGA
21836 TCGGGTTCGGTCTCGGGTCAGGA
1 TCGGGTTCGGTCTCGGGTCAGGA
*
21859 TCGGATTCGGTCTCGGGTCAGGA
1 TCGGGTTCGGTCTCGGGTCAGGA
*
21882 TCGGGCTCGG
1 TCGGGTTCGG
21892 GCTACCCTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.08, C:0.23, G:0.44, T:0.25
Consensus pattern (23 bp):
TCGGGTTCGGTCTCGGGTCAGGA
Found at i:24791 original size:6 final size:6
Alignment explanation
Indices: 24780--24814 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
24770 AGCAAAAGCC
24780 GCCGCA GCCGCA GCCGCA GCCGCA GCCGCA GCCGC
1 GCCGCA GCCGCA GCCGCA GCCGCA GCCGCA GCCGC
24815 CACAAGAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.51, G:0.34, T:0.00
Consensus pattern (6 bp):
GCCGCA
Done.