Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023388.1 Corchorus olitorius cultivar O-4 contig23421, 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: 13369
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:2465 original size:21 final size:21
Alignment explanation
Indices: 2441--2481 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2431 TTCGACAGGC
*
2441 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
*
2462 CAACATCTGGGCCGAAGTTG
1 CAACATCTGGGCAGAAGTTG
2482 TCCTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (21 bp):
CAACATCTGGGCAGAAGTTGA
Found at i:3729 original size:29 final size:29
Alignment explanation
Indices: 3659--3745 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
3649 CAAAGCTTTG
*
3659 ACACGAGTGCA-AACCCACAC-TCAAAACAA
1 ACACAAGTGCACAACCCACACTTC--AACAA
* * *
3688 TCCCAAG-GTACAACCCACACTTCAACAA
1 ACACAAGTGCACAACCCACACTTCAACAA
* *
3716 ACACAAGTGCACAACCCGCACTTAAACAA
1 ACACAAGTGCACAACCCACACTTCAACAA
3745 A
1 A
3746 AATCAGAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 12 0.26
29 32 0.70
30 2 0.04
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.10
Consensus pattern (29 bp):
ACACAAGTGCACAACCCACACTTCAACAA
Found at i:7875 original size:19 final size:19
Alignment explanation
Indices: 7851--7890 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
7841 GTGTGCTTCG
*
7851 TGGTGGTGGTGGTGGTG-GT
1 TGGTGGAGG-GGTGGTGTGT
7870 TGGTGGAGGGGTGGTGTGT
1 TGGTGGAGGGGTGGTGTGT
7889 TG
1 TG
7891 TAGTTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.03, C:0.00, G:0.62, T:0.35
Consensus pattern (19 bp):
TGGTGGAGGGGTGGTGTGT
Found at i:8673 original size:75 final size:78
Alignment explanation
Indices: 8582--8775 Score: 340
Period size: 75 Copynumber: 2.5 Consensus size: 78
8572 CACACCATAA
*
8582 TCCTCATCCTGTCCTATATCTTCTTCAGTATCATCATCATCTTCATCCCCCTCATCTCCTTCAAT
1 TCCTCCTCCTGTCCTATATCTTCTTCAGTATCATCATCATCTTCATCCCCCTCATCTCCTTCAAT
8647 TTTATC-TC-CAC
66 TTTATCTTCACAC
8658 -CCTCCTCCTGTCCTATATCTTCTTCAGTATCATCATCATCTTCATCCCCCTCATCTCCTTCAAT
1 TCCTCCTCCTGTCCTATATCTTCTTCAGTATCATCATCATCTTCATCCCCCTCATCTCCTTCAAT
*
8722 TTTATCTTCACCC
66 TTTATCTTCACAC
*
8735 TCCTCCTCCTGTCCTATATCTTCTTCAGTATCATCACCATC
1 TCCTCCTCCTGTCCTATATCTTCTTCAGTATCATCATCATC
8776 CACACACTGT
Statistics
Matches: 112, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
75 69 0.62
76 2 0.02
77 2 0.02
78 39 0.35
ACGTcount: A:0.18, C:0.39, G:0.03, T:0.40
Consensus pattern (78 bp):
TCCTCCTCCTGTCCTATATCTTCTTCAGTATCATCATCATCTTCATCCCCCTCATCTCCTTCAAT
TTTATCTTCACAC
Found at i:9168 original size:18 final size:18
Alignment explanation
Indices: 9147--9206 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
9137 ATCTCTGCAA
9147 TCCTCATCCTCTCCTCCT
1 TCCTCATCCTCTCCTCCT
* **
9165 TCCTC-TCCCTTTGTTCCT
1 TCCTCAT-CCTCTCCTCCT
* * *
9183 TCCTCTTGCTCTCCTTCT
1 TCCTCATCCTCTCCTCCT
9201 TCCTCA
1 TCCTCA
9207 CCGATCCCTC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.03, C:0.48, G:0.03, T:0.45
Consensus pattern (18 bp):
TCCTCATCCTCTCCTCCT
Found at i:10257 original size:7 final size:7
Alignment explanation
Indices: 10245--10282 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
10235 TTAGTACATC
10245 TCTCTCT
1 TCTCTCT
10252 TCTCTCT
1 TCTCTCT
*
10259 TCTTTC-
1 TCTCTCT
10265 TCTCTCT
1 TCTCTCT
10272 TCTCTCT
1 TCTCTCT
10279 TCTC
1 TCTC
10283 ACAGCACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTCTCT
Found at i:10257 original size:9 final size:9
Alignment explanation
Indices: 10243--10278 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
10233 TTTTAGTACA
10243 TCTCTCTCT
1 TCTCTCTCT
10252 TCTCTCTTCTT
1 TCTCTC-TC-T
10263 TCTCTCTCT
1 TCTCTCTCT
10272 TCTCTCT
1 TCTCTCT
10279 TCTCACAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 14 0.56
10 4 0.16
11 7 0.28
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTCTCTCT
Found at i:10268 original size:20 final size:20
Alignment explanation
Indices: 10243--10281 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10233 TTTTAGTACA
10243 TCTCTCTCTTCTCTCTTCTT
1 TCTCTCTCTTCTCTCTTCTT
10263 TCTCTCTCTTCTCTCTTCT
1 TCTCTCTCTTCTCTCTTCT
10282 CACAGCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (20 bp):
TCTCTCTCTTCTCTCTTCTT
Done.