Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018729.1 Corchorus olitorius cultivar O-4 contig18762, 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: 8411
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Found at i:3499 original size:43 final size:43
Alignment explanation
Indices: 3438--3525 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
3428 AATAATCTGA
3438 AATCTCATTGCAATAAGATATCTTTTATGTTTAAACAGTGAAT
1 AATCTCATTGCAATAAGATATCTTTTATGTTTAAACAGTGAAT
3481 AATCTCATTGCAATAAGATATCTTTTATGTTTAAACAGTGAAT
1 AATCTCATTGCAATAAGATATCTTTTATGTTTAAACAGTGAAT
3524 AA
1 AA
3526 GAAATCACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (43 bp):
AATCTCATTGCAATAAGATATCTTTTATGTTTAAACAGTGAAT
Found at i:3587 original size:21 final size:21
Alignment explanation
Indices: 3548--3591 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3538 ACAATCTAAT
* *
3548 AAACTAAGAAAGCTAATGAGA
1 AAACTAAGAAAACCAATGAGA
*
3569 AAACTAAGAAAACCCATGAGA
1 AAACTAAGAAAACCAATGAGA
3590 AA
1 AA
3592 TTACAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (21 bp):
AAACTAAGAAAACCAATGAGA
Found at i:3669 original size:21 final size:21
Alignment explanation
Indices: 3643--3685 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3633 CCCACAAGCA
*
3643 CACATAAAAAGGCACAAAAAT
1 CACATAAAAAGGCAAAAAAAT
*
3664 CACATAAAATGGCAAAAAAAT
1 CACATAAAAAGGCAAAAAAAT
3685 C
1 C
3686 CGCATATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.12
Consensus pattern (21 bp):
CACATAAAAAGGCAAAAAAAT
Found at i:4165 original size:18 final size:19
Alignment explanation
Indices: 4144--4191 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
4134 ACTTTCTTAA
4144 TTTCTCCCTTTCC-TTTCC
1 TTTCTCCCTTTCCTTTTCC
* * *
4162 TTTCTTCTTTTCCTTTTTC
1 TTTCTCCCTTTCCTTTTCC
*
4181 TTTCTCTCTTT
1 TTTCTCCCTTT
4192 GCTGCGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTCTCCCTTTCCTTTTCC
Found at i:4185 original size:19 final size:19
Alignment explanation
Indices: 4152--4191 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4142 AATTTCTCCC
4152 TTTCCTTTCCTTTCT-TCT
1 TTTCCTTTCCTTTCTCTCT
*
4170 TTTCCTTTTTCTTTCTCTCT
1 TTTCC-TTTCCTTTCTCTCT
4190 TT
1 TT
4192 GCTGCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCCTTTCCTTTCTCTCT
Found at i:4551 original size:6 final size:6
Alignment explanation
Indices: 4542--4570 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4532 GCAACAGCAG
4542 CAAGAA CAAGAA CAAGAA CAAGAA CAAGA
1 CAAGAA CAAGAA CAAGAA CAAGAA CAAGA
4571 TCAAATTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
CAAGAA
Found at i:4904 original size:3 final size:3
Alignment explanation
Indices: 4896--4925 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4886 AAATTACCTC
*
4896 CTT CTT CTT CTT CTT CTT CTT CCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
4926 GTTTCCACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:7279 original size:11 final size:11
Alignment explanation
Indices: 7263--7297 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
7253 TAATGTGAGT
7263 TTAGTTTGTAA
1 TTAGTTTGTAA
7274 TTAGTTTGTAA
1 TTAGTTTGTAA
*
7285 TTTGTTTGTAA
1 TTAGTTTGTAA
7296 TT
1 TT
7298 TATTTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (11 bp):
TTAGTTTGTAA
Found at i:7408 original size:21 final size:21
Alignment explanation
Indices: 7383--7424 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7373 ATGTTTGAGC
7383 ATATAGAAATTTATTCATGTT
1 ATATAGAAATTTATTCATGTT
7404 ATATAGAAATTTATTCATGTT
1 ATATAGAAATTTATTCATGTT
7425 GTAAATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (21 bp):
ATATAGAAATTTATTCATGTT
Done.