Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018998.1 Corchorus olitorius cultivar O-4 contig19031, 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: 30605
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:469 original size:2 final size:2
Alignment explanation
Indices: 458--495 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
448 AGTTTAGACT
458 TA TA TA -A TA TA TA TA T- TA TGA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
496 CATAATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:483 original size:12 final size:11
Alignment explanation
Indices: 458--495 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
448 AGTTTAGACT
*
458 TATATAATATA
1 TATATTATATA
469 TATATTATGATA
1 TATATTAT-ATA
481 TATA-TATATA
1 TATATTATATA
491 TATAT
1 TATAT
496 CATAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.29
11 10 0.42
12 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TATATTATATA
Found at i:11486 original size:17 final size:18
Alignment explanation
Indices: 11459--11496 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11449 CGCCACCTCC
*
11459 TTCTCCTTGTATGGAGTT
1 TTCTCCTTGTAAGGAGTT
11477 TTCT-CTTGTAAGGAGTT
1 TTCTCCTTGTAAGGAGTT
11494 TTC
1 TTC
11497 CATGAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (18 bp):
TTCTCCTTGTAAGGAGTT
Found at i:12980 original size:18 final size:19
Alignment explanation
Indices: 12947--12985 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12937 AAATATCTCT
12947 AATTAGGGCTAATTGCACA
1 AATTAGGGCTAATTGCACA
*
12966 AATTAGGTC-AATTGCACA
1 AATTAGGGCTAATTGCACA
12984 AA
1 AA
12986 AACAAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
AATTAGGGCTAATTGCACA
Found at i:15324 original size:13 final size:13
Alignment explanation
Indices: 15306--15330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15296 AGATATCGAT
15306 GGATATATCGAAC
1 GGATATATCGAAC
15319 GGATATATCGAA
1 GGATATATCGAA
15331 AAATCGATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
GGATATATCGAAC
Found at i:17836 original size:51 final size:51
Alignment explanation
Indices: 17756--17856 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
17746 GCTAAGTTAC
*
17756 AAGTAATGATAAATTTTAAGATTAATAAAGCCGGATAAGATCAAAATGCTT
1 AAGTAATGATAAATTTTAAGATTAATAAAGCCAGATAAGATCAAAATGCTT
* * *
17807 AAGTAATGATAAATTTTAAGATTATTAAAGCTAGATAAGATGAAAATGCT
1 AAGTAATGATAAATTTTAAGATTAATAAAGCCAGATAAGATCAAAATGCT
17857 ATTGAAGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.31
Consensus pattern (51 bp):
AAGTAATGATAAATTTTAAGATTAATAAAGCCAGATAAGATCAAAATGCTT
Found at i:21412 original size:34 final size:34
Alignment explanation
Indices: 21364--21447 Score: 141
Period size: 34 Copynumber: 2.5 Consensus size: 34
21354 GCTATAAGAA
*
21364 TTCTTCAGCTTTGTTTAATAAAAACTTGGGGTGC
1 TTCTTCAGCCTTGTTTAATAAAAACTTGGGGTGC
* *
21398 TTCTTCAACCTTGTTTAATAAAGACTTGGGGTGC
1 TTCTTCAGCCTTGTTTAATAAAAACTTGGGGTGC
21432 TTCTTCAGCCTTGTTT
1 TTCTTCAGCCTTGTTT
21448 GTTGTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (34 bp):
TTCTTCAGCCTTGTTTAATAAAAACTTGGGGTGC
Found at i:29876 original size:8 final size:8
Alignment explanation
Indices: 29863--29899 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
29853 AGAAAGGGGA
29863 AAAAAAAG
1 AAAAAAAG
29871 AAAAAAAG
1 AAAAAAAG
29879 AAAAAGAA-
1 AAAAA-AAG
29887 AAAAAAAG
1 AAAAAAAG
29895 AAAAA
1 AAAAA
29900 GGAAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 2 0.07
8 23 0.85
9 2 0.07
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:29880 original size:24 final size:24
Alignment explanation
Indices: 29862--29913 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
29852 AAGAAAGGGG
29862 AAAAAAAAGAAAAAAAGAAAAAGA
1 AAAAAAAAGAAAAAAAGAAAAAGA
* *
29886 AAAAAAAAG-AAAAAGGAAAAAGG
1 AAAAAAAAGAAAAAAAGAAAAAGA
29909 AAAAA
1 AAAAA
29914 GGAAATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAGAAAAAGA
Found at i:29882 original size:14 final size:14
Alignment explanation
Indices: 29865--29914 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
29855 AAAGGGGAAA
29865 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
29879 AAAAAGAAAAAAAAAG
1 AAAAAG--AAAAAAAG
* *
29895 AAAAAGGAAAAAGG
1 AAAAAGAAAAAAAG
29909 AAAAAG
1 AAAAAG
29915 GAAATAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 18 0.56
16 14 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:29882 original size:16 final size:16
Alignment explanation
Indices: 29861--29906 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
29851 AAAGAAAGGG
*
29861 GAAAAAAAAGAAAAAAA
1 GAAAAAGAA-AAAAAAA
29878 GAAAAAGAAAAAAAAA
1 GAAAAAGAAAAAAAAA
29894 GAAAAAGGAAAAA
1 GAAAAA-GAAAAA
29907 GGAAAAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
GAAAAAGAAAAAAAAA
Found at i:29929 original size:30 final size:29
Alignment explanation
Indices: 29862--29939 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
29852 AAGAAAGGGG
29862 AAAAAAAAGAAAAAAAGAAAAAGAAAAAA
1 AAAAAAAAGAAAAAAAGAAAAAGAAAAAA
* * *
29891 AAAGAAAAAGGAAAAAGGAAAAAGGAAATAACT
1 AAA-AAAAAGAAAAAAAGAAAAA-GAAA-AA-A
*
29924 AAAAAAAATAAAAAAA
1 AAAAAAAAGAAAAAAA
29940 ATAAAAAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 3 0.08
30 17 0.44
31 4 0.10
32 12 0.31
33 3 0.08
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.04
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAGAAAAAGAAAAAA
Found at i:29938 original size:8 final size:9
Alignment explanation
Indices: 29923--29947 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29913 AGGAAATAAC
29923 TAAAAAAAA
1 TAAAAAAAA
29932 TAAAAAAAA
1 TAAAAAAAA
29941 TAAAAAA
1 TAAAAAA
29948 GGAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:29957 original size:18 final size:17
Alignment explanation
Indices: 29860--29958 Score: 55
Period size: 17 Copynumber: 5.6 Consensus size: 17
29850 AAAAGAAAGG
29860 GGAAA-AAAAAGAAAAAA
1 GGAAATAAAAA-AAAAAA
*
29877 AGAAA-AAGAAAAAAAAA
1 GGAAATAA-AAAAAAAAA
*
29894 -GAAAAAGGAAAAAGGAAAAA
1 GGAAATA--AAAAA--AAAAA
*
29914 GGAAATAACTAAAAAAAA
1 GGAAATAA-AAAAAAAAA
*
29932 -TAAA-AAAAATAAAAAA
1 GGAAATAAAAA-AAAAAA
29948 GGAAATAAAAA
1 GGAAATAAAAA
29959 GGAAAATTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
15 2 0.03
16 12 0.18
17 19 0.29
18 17 0.26
19 2 0.03
20 8 0.12
21 5 0.08
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (17 bp):
GGAAATAAAAAAAAAAA
Done.