Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012158.1 Corchorus olitorius cultivar O-4 contig12191, 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: 25309
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:1967 original size:11 final size:12
Alignment explanation
Indices: 1951--1982 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1941 GAAGTTCGTG
1951 TTTGAAGACT-A
1 TTTGAAGACTAA
1962 TTTGAAGA-TAA
1 TTTGAAGACTAA
1973 TTTGAAGACT
1 TTTGAAGACT
1983 TGAAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:1987 original size:19 final size:18
Alignment explanation
Indices: 1963--1998 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1953 TGAAGACTAT
1963 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
1982 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
1999 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:6717 original size:21 final size:20
Alignment explanation
Indices: 6693--6732 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
6683 AGCGAAGTCA
6693 CCTGCCCGGTCATCCGCGCCG
1 CCTGCCCGGTCATCC-CGCCG
6714 CCTGCCCGGTCATCCCGCC
1 CCTGCCCGGTCATCCCGCC
6733 TTCCTCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.05, C:0.55, G:0.25, T:0.15
Consensus pattern (20 bp):
CCTGCCCGGTCATCCCGCCG
Found at i:6968 original size:21 final size:22
Alignment explanation
Indices: 6930--6975 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
6920 CCAAGCCCCA
*
6930 ACCGGCCATTCACCGTGCCACC
1 ACCGGCCATGCACCGTGCCACC
*
6952 ACCGGCCATGC-CCGTGCCATC
1 ACCGGCCATGCACCGTGCCACC
6973 ACC
1 ACC
6976 ATTCCAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (22 bp):
ACCGGCCATGCACCGTGCCACC
Found at i:14566 original size:21 final size:23
Alignment explanation
Indices: 14532--14575 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
14522 TTGCTCAGTT
14532 TTCTCTCTGTCTTCAC-CATCATC
1 TTCTCTCTGTCTTC-CTCATCATC
14555 TTCT-TCT-TCTTCCTCATCATC
1 TTCTCTCTGTCTTCCTCATCATC
14576 ATCAGGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.05
21 12 0.60
22 3 0.15
23 4 0.20
ACGTcount: A:0.11, C:0.39, G:0.02, T:0.48
Consensus pattern (23 bp):
TTCTCTCTGTCTTCCTCATCATC
Found at i:18079 original size:19 final size:18
Alignment explanation
Indices: 18055--18090 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18045 TGAAGACCAT
18055 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
18074 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
18091 TCTATTTCAA
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:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:18928 original size:21 final size:21
Alignment explanation
Indices: 18914--18993 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
18904 ATTGGAACAA
18914 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
18935 GTTCCAAGTTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
18956 GTTCCAAGATCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
18977 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
18994 ATTGCCTAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:18945 original size:42 final size:41
Alignment explanation
Indices: 18898--18994 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
18888 AAGATGCTAG
*
18898 AAGTTCATTGGAACAAGTTCCAAGCTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAA-AAGTTCCAAGATCATTGGAGAAGGTTCC
* *
18940 AAGTTCATTGGAGAAGGTTCCAAGATCATTGGAGAAGGTTTC
1 AAGTTCATTGGA-AAAGTTCCAAGATCATTGGAGAAGGTTCC
*
18982 AAGCTCATTGGAA
1 AAGTTCATTGGAA
18995 TTGCCTAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.02
42 48 0.96
43 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (41 bp):
AAGTTCATTGGAAAAGTTCCAAGATCATTGGAGAAGGTTCC
Done.