Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021655.1 Corchorus olitorius cultivar O-4 contig21688, 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: 15294
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:84 original size:22 final size:23
Alignment explanation
Indices: 57--103 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
47 TTGAACAAAC
57 CTCTCAAAT-AACCAAACAGTTT
1 CTCTCAAATAAACCAAACAGTTT
*
79 CTCTCAAATAAACCAAACGGTTT
1 CTCTCAAATAAACCAAACAGTTT
102 CT
1 CT
104 ATTAGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (23 bp):
CTCTCAAATAAACCAAACAGTTT
Found at i:1090 original size:8 final size:9
Alignment explanation
Indices: 1054--1091 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
1044 CCCAAATTAC
1054 TTATGGAAA
1 TTATGGAAA
*
1063 TTAAGGAAA
1 TTATGGAAA
1072 TTATGGAAA
1 TTATGGAAA
1081 TTAT-GAAA
1 TTATGGAAA
1089 TTA
1 TTA
1092 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:2447 original size:49 final size:47
Alignment explanation
Indices: 2370--2510 Score: 169
Period size: 49 Copynumber: 2.9 Consensus size: 47
2360 CAAGCAATCC
* *
2370 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* *
2418 TTTAATTTT-ACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
2467 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
2511 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
47 11 0.14
48 27 0.33
49 41 0.51
50 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:3699 original size:2 final size:2
Alignment explanation
Indices: 3692--3724 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3682 ATTCTGCCAA
3692 AT AT 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 AT AT A
3725 CATGTTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7850 original size:19 final size:18
Alignment explanation
Indices: 7821--7857 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
7811 AATTAATTAA
7821 TTATTAATAATTATTATT
1 TTATTAATAATTATTATT
7839 TTATTGAATAATTATTATT
1 TTATT-AATAATTATTATT
7858 AAAAATCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTAATAATTATTATT
Found at i:7990 original size:31 final size:31
Alignment explanation
Indices: 7955--8052 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
7945 AGAACCTAAA
* *
7955 TAGTCCCTGTACTATTGAAAAAAGATCATTT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
* * ***
7986 TAGTCCCTCCATTA-TGAAATCTG-TCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
*
8015 TAGTCCCTCTACTATTGAAAAGAGATCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
8046 TAGTCCC
1 TAGTCCC
8053 ACCGTGAAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 17 0.32
30 12 0.23
31 24 0.45
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (31 bp):
TAGTCCCTCTACTATTGAAAAAAGATCAATT
Found at i:11709 original size:10 final size:9
Alignment explanation
Indices: 11685--11742 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
11675 ATTTCTTACC
*
11685 CTTATCTTT
1 CTTATTTTT
11694 -TTATTTTT
1 CTTATTTTT
11702 CGTTATTTTT
1 C-TTATTTTT
11712 CTT-TTTCTT
1 CTTATTT-TT
11721 -TTATTTTT
1 CTTATTTTT
*
11729 GTTTATTTTT
1 -CTTATTTTT
11739 CTTA
1 CTTA
11743 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:11716 original size:16 final size:17
Alignment explanation
Indices: 11691--11728 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
11681 TACCCTTATC
11691 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
11707 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
11724 TTTTT
1 TTTTT
11729 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:12906 original size:21 final size:21
Alignment explanation
Indices: 12867--12915 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12857 TCAATGCTTT
**
12867 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
12889 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
12910 A-GAAGC
1 AGGAAGC
12916 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.