Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013247.1 Corchorus olitorius cultivar O-4 contig13280, 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: 12393
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:3356 original size:42 final size:42
Alignment explanation
Indices: 3304--3392 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
3294 GCCACAACCG
*
3304 GCCAACCGCGCCGCCTGCCCGGTCGAGCC-TGCCTTCTTCCGC
1 GCCATCCGCGCCGCCTGCCCGGT-GAGCCGTGCCTTCTTCCGC
* *
3346 GCCATCCGCGCCGCCTGCCCGGTTATCCGTGCCTTCTTCCGC
1 GCCATCCGCGCCGCCTGCCCGGTGAGCCGTGCCTTCTTCCGC
3388 GCCAT
1 GCCAT
3393 TCCAGACGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 3 0.07
42 40 0.93
ACGTcount: A:0.07, C:0.48, G:0.25, T:0.20
Consensus pattern (42 bp):
GCCATCCGCGCCGCCTGCCCGGTGAGCCGTGCCTTCTTCCGC
Found at i:3612 original size:21 final size:21
Alignment explanation
Indices: 3588--3642 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3578 CAGCCATTCA
**
3588 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
* *
3609 CCGTGCCACCCCCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
3630 CCGTGCCATCACC
1 CCGTGCCACCACC
3643 ATTCCAAGCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.51, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:5473 original size:11 final size:11
Alignment explanation
Indices: 5457--5504 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
5447 GAAGTTCGTG
5457 TTTGAAGACCA
1 TTTGAAGACCA
5468 TTTGAAGACCA
1 TTTGAAGACCA
5479 TTTGAAGA-C-
1 TTTGAAGACCA
5488 -TTGAAGACCA
1 TTTGAAGACCA
5498 -TTGAAGA
1 TTTGAAGA
5505 TTTATTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:5493 original size:19 final size:18
Alignment explanation
Indices: 5469--5504 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5459 TGAAGACCAT
5469 TTGAAGACCATTTGAAGAC
1 TTGAAGACCA-TTGAAGAC
5488 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
5505 TTTATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAC
Found at i:6909 original size:15 final size:16
Alignment explanation
Indices: 6878--6917 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6868 TTACTTTGCT
6878 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
6894 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
6909 TTGCTTTCT
1 TTGTTTTCT
6918 GTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:7153 original size:55 final size:55
Alignment explanation
Indices: 7087--7192 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
7077 GTTCTCCATA
*
7087 ATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCG
1 ATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCG
* *
7142 ATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGTAGACCGTCT
1 ATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCT
7193 CCGGTGTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (55 bp):
ATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCG
Found at i:7247 original size:66 final size:67
Alignment explanation
Indices: 7141--7272 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 67
7131 ACCGTCTTCC
*
7141 GATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGT-AGACCGTC-TCCGGTGTACTT
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTA-TCAAACCGTCTTCCGGTGTACTT
7204 CTT
65 CTT
* * * *
7207 GATGAGATTG-CTTTCTAATCATCTTTTGAAAATTCTTTCTATCAAACCGTCTTCCGGTGTACTT
1 GATGAGATTGTC-TTCCAATCAACATTTGAAAATCCTTTCTATCAAACCGTCTTCCGGTGTACTT
7271 CT
65 CT
7273 AAAATCCTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
65 2 0.03
66 42 0.72
67 14 0.24
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (67 bp):
GATGAGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTATCAAACCGTCTTCCGGTGTACTTC
TT
Done.