Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011308.1 Corchorus olitorius cultivar O-4 contig11341, 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: 11899
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Found at i:4482 original size:36 final size:36
Alignment explanation
Indices: 4441--4514 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
4431 TTAAAAATTA
4441 TTGTGTTTATAACTTAATTTATATTGATTAATAGTT
1 TTGTGTTTATAACTTAATTTATATTGATTAATAGTT
*
4477 TTGTGTTTATAATTTAATTTATATTGATTAATAGTT
1 TTGTGTTTATAACTTAATTTATATTGATTAATAGTT
4513 TT
1 TT
4515 ATTGATTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (36 bp):
TTGTGTTTATAACTTAATTTATATTGATTAATAGTT
Found at i:8036 original size:178 final size:175
Alignment explanation
Indices: 7739--8059 Score: 475
Period size: 178 Copynumber: 1.8 Consensus size: 175
7729 TACACTGTAA
* * *
7739 GTGTAAATTTTTGACTCCATAAGCGGGTTAAAAGGTTGACACATACCCATTTCATAATTAATTAA
1 GTGTAAAGTTTGGACTCCATAA-CGGGTTAAAAGGTTAACACATACCCATTTCATAATTAATTAA
* *
7804 ATATTTAATAGTAATACATATTCCCTAAGGGGACACATGCCAACCCTTAAACCCCGCATGTGCAG
65 ATATTTAATAGTAATACATATTCCCTAAGGGCACACATGCCAACCCTTAAACCCCGCACGTGCAG
7869 TCTGCTAAACTCCACTGACTGTGTATTGCATAATTTTTCACTGTCG
130 TCTGCTAAACTCCACTGACTGTGTATTGCATAATTTTTCACTGTCG
* *
7915 GTGTAAAGTTTGGACTCCATAA-GTGTTAAGAA-GTTAACACATACCCGTTTCATAATTAATTAA
1 GTGTAAAGTTTGGACTCCATAACGGGTTAA-AAGGTTAACACATACCCATTTCATAATTAATT--
* * * *
7978 ATATATATTTAATATTAATACATATTTCCTAAGGGCTCACATGTCAACCCTTAAACCCCGCACGT
63 A-A-ATATTTAATAGTAATACATATTCCCTAAGGGCACACATGCCAACCCTTAAACCCCGCACGT
8043 GCAGTCTGCTAAACTCC
126 GCAGTCTGCTAAACTCC
8060 TTAAACCCCG
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
174 33 0.26
175 2 0.02
176 21 0.16
177 1 0.01
178 72 0.56
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (175 bp):
GTGTAAAGTTTGGACTCCATAACGGGTTAAAAGGTTAACACATACCCATTTCATAATTAATTAAA
TATTTAATAGTAATACATATTCCCTAAGGGCACACATGCCAACCCTTAAACCCCGCACGTGCAGT
CTGCTAAACTCCACTGACTGTGTATTGCATAATTTTTCACTGTCG
Found at i:8067 original size:32 final size:32
Alignment explanation
Indices: 8026--8091 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
8016 ACATGTCAAC
8026 CCTTAAACCCCGCACGTGCAGTCTGCTAAACT
1 CCTTAAACCCCGCACGTGCAGTCTGCTAAACT
*
8058 CCTTAAACCCCGCATGTGCAGTCTGCTAAACT
1 CCTTAAACCCCGCACGTGCAGTCTGCTAAACT
8090 CC
1 CC
8092 ACTGACTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (32 bp):
CCTTAAACCCCGCACGTGCAGTCTGCTAAACT
Found at i:11091 original size:6 final size:6
Alignment explanation
Indices: 11080--11154 Score: 75
Period size: 6 Copynumber: 12.3 Consensus size: 6
11070 TAGTTATTTT
*
11080 TTTTCC TTTTCC TTTTCC TTTTCC TTTTTCC -TTT-C TTTTTC TTTTCTTC
1 TTTTCC TTTTCC TTTTCC TTTTCC -TTTTCC TTTTCC TTTTCC TTTTC--C
*
11129 TTTTCC TTTTTC TTTT-C TTCTTCC TT
1 TTTTCC TTTTCC TTTTCC TT-TTCC TT
11155 ATGGGCCAGG
Statistics
Matches: 60, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
4 1 0.02
5 9 0.15
6 35 0.58
7 9 0.15
8 6 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCC
Found at i:11135 original size:31 final size:29
Alignment explanation
Indices: 11085--11154 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
11075 ATTTTTTTTC
11085 CTTTTCCTTTTCCTTTTCCTTTTTCCTTT
1 CTTTTCCTTTTCCTTTTCCTTTTTCCTTT
* *
11114 CTTTTTCTTTTCTTCTTTTCCTTTTTCTTTT
1 CTTTTCCTTTTC--CTTTTCCTTTTTCCTTT
11145 CTTCTTCCTT
1 CTT-TTCCTT
11155 ATGGGCCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 11 0.31
31 19 0.54
32 5 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
CTTTTCCTTTTCCTTTTCCTTTTTCCTTT
Found at i:11202 original size:16 final size:14
Alignment explanation
Indices: 11174--11216 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
11164 GCCCACACTC
11174 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
*
11188 TTTCTTCTCCTTTTT
1 TTTCTT-TCTTTTTT
11203 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
11217 GGCTGTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTCTTTTTT
Done.