Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012142.1 Corchorus olitorius cultivar O-4 contig12175, 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: 33037
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3575 original size:35 final size:35
Alignment explanation
Indices: 3529--3605 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
3519 GAAACCGCTA
3529 ACGGTTTTTTGCGATTATGTCAAACCGCGGTTTAG
1 ACGGTTTTTTGCGATTATGTCAAACCGCGGTTTAG
*
3564 ACGGTTTTTTGCGGTTATGTCAAACCGCGGTTTAG
1 ACGGTTTTTTGCGATTATGTCAAACCGCGGTTTAG
3599 ACGGTTT
1 ACGGTTT
3606 GGCGGTTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (35 bp):
ACGGTTTTTTGCGATTATGTCAAACCGCGGTTTAG
Found at i:3733 original size:23 final size:23
Alignment explanation
Indices: 3706--3781 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 23
3696 TAGTAATATT
3706 TATAATTAAATATATATTTTATA
1 TATAATTAAATATATATTTTATA
* *
3729 TATAA-AAAATA-ATATTAGATATA
1 TATAATTAAATATATATT--TTATA
* * *
3752 TATAATTACATATATA-ATAATA
1 TATAATTAAATATATATTTTATA
3774 TATAATTA
1 TATAATTA
3782 TTAAACGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.12
22 16 0.38
23 14 0.33
24 4 0.10
25 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (23 bp):
TATAATTAAATATATATTTTATA
Found at i:3743 original size:21 final size:22
Alignment explanation
Indices: 3713--3753 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3703 ATTTATAATT
**
3713 AAATATATATTTTATATATAAA
1 AAATATATATTAGATATATAAA
3735 AAATA-ATATTAGATATATA
1 AAATATATATTAGATATATA
3754 TAATTACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATATATATTAGATATATAAA
Found at i:3766 original size:12 final size:11
Alignment explanation
Indices: 3749--3781 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
3739 AATATTAGAT
3749 ATATATAATTA
1 ATATATAATTA
3760 CATATATAA-TA
1 -ATATATAATTA
3771 ATATATAATTA
1 ATATATAATTA
3782 TTAAACGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAATTA
Found at i:4312 original size:26 final size:26
Alignment explanation
Indices: 4283--4332 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4273 AATAATAATA
4283 ATAAGATAATAAGATAGTAAGATAAG
1 ATAAGATAATAAGATAGTAAGATAAG
* *
4309 ATAAGATAGTAAGATAGTATGATA
1 ATAAGATAATAAGATAGTAAGATA
4333 TTGCTTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (26 bp):
ATAAGATAATAAGATAGTAAGATAAG
Found at i:4325 original size:8 final size:8
Alignment explanation
Indices: 4284--4332 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
4274 ATAATAATAA
*
4284 TAAGATAA
1 TAAGATAG
4292 TAAGATAG
1 TAAGATAG
4300 TAAGATAAG
1 TAAGAT-AG
4309 ATAAGATAG
1 -TAAGATAG
4318 TAAGATAG
1 TAAGATAG
*
4326 TATGATA
1 TAAGATA
4333 TTGCTTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 27 0.73
9 4 0.11
10 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (8 bp):
TAAGATAG
Found at i:10439 original size:7 final size:7
Alignment explanation
Indices: 10427--10451 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10417 CTTTATAGGA
10427 TTTTTAT
1 TTTTTAT
10434 TTTTTAT
1 TTTTTAT
10441 TTTTTAT
1 TTTTTAT
10448 TTTT
1 TTTT
10452 CAACATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:10885 original size:14 final size:14
Alignment explanation
Indices: 10862--10892 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10852 TAATAATTGT
10862 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
10876 AAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG
10890 AAA
1 AAA
10893 GAACTAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:16438 original size:5 final size:5
Alignment explanation
Indices: 16428--16466 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
16418 TGCAATCTTT
*
16428 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTG TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
16467 TGTGGGGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:29248 original size:137 final size:137
Alignment explanation
Indices: 29002--29276 Score: 532
Period size: 137 Copynumber: 2.0 Consensus size: 137
28992 TGGGTTTTGG
*
29002 ATAAAAGTTGAGGCCCGTTCTTCGAGTCGGGCTGGGCTTGGGCAAGCATAAATTATATAATTACT
1 ATAAAAGTTGAGGCCCGTTCTTCGAGTCGGGCTGGGCTTGGACAAGCATAAATTATATAATTACT
29067 AAACAAAATCCGGCTCGAACCCGATCCGGCCATGAACACCTCTAGTCGCCACTAGCTAATATTCC
66 AAACAAAATCCGGCTCGAACCCGATCCGGCCATGAACACCTCTAGTCGCCACTAGCTAATATTCC
29132 ATTTTTC
131 ATTTTTC
*
29139 ATAAAAGTTGAGGCCCGTTCTTTGAGTCGGGCTGGGCTTGGACAAGCATAAATTATATAATTACT
1 ATAAAAGTTGAGGCCCGTTCTTCGAGTCGGGCTGGGCTTGGACAAGCATAAATTATATAATTACT
29204 AAACAAAATCCGGCTCGAACCCGATCCGGCCATGAACACCTCTAGTCGCCACTAGCTAATATTCC
66 AAACAAAATCCGGCTCGAACCCGATCCGGCCATGAACACCTCTAGTCGCCACTAGCTAATATTCC
29269 ATTTTTC
131 ATTTTTC
29276 A
1 A
29277 AGACATACAA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (137 bp):
ATAAAAGTTGAGGCCCGTTCTTCGAGTCGGGCTGGGCTTGGACAAGCATAAATTATATAATTACT
AAACAAAATCCGGCTCGAACCCGATCCGGCCATGAACACCTCTAGTCGCCACTAGCTAATATTCC
ATTTTTC
Done.