Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015329.1 Corchorus olitorius cultivar O-4 contig15362, 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: 72510
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1504 original size:3 final size:3
Alignment explanation
Indices: 1496--1520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1486 CACCATCACC
1496 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
1521 TTGAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:3577 original size:1 final size:1
Alignment explanation
Indices: 3571--3601 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3561 CGGATGGGAT
3571 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3602 GAATAGCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5815 original size:2 final size:2
Alignment explanation
Indices: 5808--5836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5798 GACTTTGCAC
5808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5837 GCTTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6938 original size:2 final size:2
Alignment explanation
Indices: 6931--6964 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6921 GGAATTTTGG
6931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6965 CTGATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10673 original size:62 final size:62
Alignment explanation
Indices: 10597--10715 Score: 161
Period size: 62 Copynumber: 1.9 Consensus size: 62
10587 GTGGCATATC
* *
10597 ACGTGTCACTTTTTGAAACACA-TGGCATGTCACGTGTC-ATTTTTGGATACACATGGCGTGAT
1 ACGTGTCACTTTTTGAAACA-AGTGGCATGCCACATGTCGATTTTTGG-TACACATGGCGTGAT
* * *
10659 ACGTGTCACTTTTTGATACAAGTGGCATGCCACATGTCGCTTTTTGGTACACGTGGC
1 ACGTGTCACTTTTTGAAACAAGTGGCATGCCACATGTCGATTTTTGGTACACATGGC
10716 ATGCCACGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 1 0.02
62 42 0.84
63 7 0.14
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (62 bp):
ACGTGTCACTTTTTGAAACAAGTGGCATGCCACATGTCGATTTTTGGTACACATGGCGTGAT
Found at i:10677 original size:31 final size:31
Alignment explanation
Indices: 10588--10724 Score: 145
Period size: 31 Copynumber: 4.4 Consensus size: 31
10578 TTTGTGTACG
* *
10588 TGGCATATCACGTGTCACTTTTTGAAACACA
1 TGGCATGTCACGTGTCACTTTTTGATACACA
10619 TGGCATGTCACGTGTCA-TTTTTGGATACACA
1 TGGCATGTCACGTGTCACTTTTT-GATACACA
*
10650 TGGCGTGAT-ACGTGTCACTTTTTGATACA-A
1 TGGCATG-TCACGTGTCACTTTTTGATACACA
* * * * *
10680 GTGGCATGCCACATGTCGCTTTTTGGTACACG
1 -TGGCATGTCACGTGTCACTTTTTGATACACA
*
10712 TGGCATGCCACGT
1 TGGCATGTCACGT
10725 CGGACACCAT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
30 6 0.07
31 78 0.87
32 6 0.07
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (31 bp):
TGGCATGTCACGTGTCACTTTTTGATACACA
Found at i:18924 original size:23 final size:23
Alignment explanation
Indices: 18892--18944 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
18882 GGTTAAATGA
*
18892 TATATATTCATTTTAAAATCCTAT
1 TATA-ATTCATTCTAAAATCCTAT
18916 TATAATTCATTCTAAAATCCTAT
1 TATAATTCATTCTAAAATCCTAT
*
18939 CATAAT
1 TATAAT
18945 CAATGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATTCATTCTAAAATCCTAT
Found at i:19022 original size:30 final size:30
Alignment explanation
Indices: 18978--19061 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
18968 CCTATAAAAT
*
18978 AAATTCATTTGAGACTAAACTTAATATAAA
1 AAATTTATTTGAGACTAAACTTAATATAAA
* *
19008 AAATTTATTCGAGACTAAATTTAATATAAA
1 AAATTTATTTGAGACTAAACTTAATATAAA
*
19038 AAGTTTATTTGAGACTAAAACTTA
1 AAATTTATTTGAGACT-AAACTTA
19062 TTGGCCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 41 0.87
31 6 0.13
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AAATTTATTTGAGACTAAACTTAATATAAA
Found at i:23874 original size:12 final size:12
Alignment explanation
Indices: 23857--23883 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23847 TCCTTGTATC
23857 TGATAGTCATAT
1 TGATAGTCATAT
23869 TGATAGTCATAT
1 TGATAGTCATAT
23881 TGA
1 TGA
23884 CTCTGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (12 bp):
TGATAGTCATAT
Found at i:34111 original size:6 final size:6
Alignment explanation
Indices: 34100--34126 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34090 AGCACTCTAT
34100 TGAAAA TGAAAA TGAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGA
34127 GATGCTTGTG
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:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:41154 original size:31 final size:31
Alignment explanation
Indices: 41092--41154 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
41082 TCGATCGGAT
* * * *
41092 TCAATTGATCGAAACTTGTGAGTATATAGAC
1 TCAATTAATCGAAACTTATGAGTACAGAGAC
* *
41123 TCAATTAATCTAATCTTATGAGTACAGAGAC
1 TCAATTAATCGAAACTTATGAGTACAGAGAC
41154 T
1 T
41155 TTTATATCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (31 bp):
TCAATTAATCGAAACTTATGAGTACAGAGAC
Found at i:63146 original size:8 final size:8
Alignment explanation
Indices: 63135--63166 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
63125 CAAAAACAGA
63135 AAAAAAAT
1 AAAAAAAT
63143 AAAAAAAAT
1 -AAAAAAAT
63152 AAAAAAAT
1 AAAAAAAT
63160 AAAAAAA
1 AAAAAAA
63167 ATCAGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAAAAT
Found at i:63146 original size:9 final size:9
Alignment explanation
Indices: 63134--63168 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
63124 TCAAAAACAG
63134 AAAAAAAAT
1 AAAAAAAAT
63143 AAAAAAAAT
1 AAAAAAAAT
63152 -AAAAAAAT
1 AAAAAAAAT
63160 AAAAAAAAT
1 AAAAAAAAT
63169 CAGTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:63155 original size:17 final size:17
Alignment explanation
Indices: 63135--63168 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
63125 CAAAAACAGA
63135 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
63152 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
63169 CAGTATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Done.