Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021479.1 Corchorus olitorius cultivar O-4 contig21512, 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: 40120
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7684 original size:21 final size:21
Alignment explanation
Indices: 7655--7699 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
7645 CTTTCTTGAG
*
7655 CATTGTCTTTCAGAGGAAGTT
1 CATTATCTTTCAGAGGAAGTT
7676 CATTATCTTTCAGAGGAAGTT
1 CATTATCTTTCAGAGGAAGTT
7697 CAT
1 CAT
7700 AAGTTGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (21 bp):
CATTATCTTTCAGAGGAAGTT
Found at i:15631 original size:27 final size:27
Alignment explanation
Indices: 15593--15649 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
15583 AAGGGAAAAA
*
15593 GAGGTTGAGGCTGCTCAGATGTATAGG
1 GAGGCTGAGGCTGCTCAGATGTATAGG
*
15620 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCAGATGTATAGG
15647 GAG
1 GAG
15650 AAGGAGGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.44, T:0.23
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCAGATGTATAGG
Found at i:15656 original size:27 final size:27
Alignment explanation
Indices: 15599--15660 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
15589 AAAAGAGGTT
***
15599 GAGGCTGCTCAGATGTATAGGGAGGCT
1 GAGGCTGCTCAGATGTATAGGGAGAAG
*
15626 GAGGCTGCTCGGATGTATAGGGAGAAG
1 GAGGCTGCTCAGATGTATAGGGAGAAG
15653 GAGGCTGC
1 GAGGCTGC
15661 CGCTGGTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.44, T:0.19
Consensus pattern (27 bp):
GAGGCTGCTCAGATGTATAGGGAGAAG
Found at i:15957 original size:20 final size:20
Alignment explanation
Indices: 15932--15973 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
15922 TATTATGTGA
*
15932 TATTATAAATTGAAATTAAT
1 TATTATAAATTGAAATAAAT
15952 TATTATAAATTGAAATAAAT
1 TATTATAAATTGAAATAAAT
15972 TA
1 TA
15974 AATAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATTATAAATTGAAATAAAT
Found at i:19301 original size:12 final size:12
Alignment explanation
Indices: 19286--19310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19276 ATACATTAAT
19286 AAATAATAATAA
1 AAATAATAATAA
19298 AAATAATAATAA
1 AAATAATAATAA
19310 A
1 A
19311 TATTACAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:19304 original size:19 final size:19
Alignment explanation
Indices: 19282--19334 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
19272 ATGAATACAT
19282 TAATAAATAATAATAAAAA
1 TAATAAATAATAATAAAAA
* * *
19301 TAAT-AATAAATATTACAAC
1 TAATAAAT-AATAATAAAAA
*
19320 TATTAAATAATAATA
1 TAATAAATAATAATA
19335 CCACCTGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAATAATAATAAAAA
Found at i:21740 original size:2 final size:2
Alignment explanation
Indices: 21733--21759 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21723 AATTACTAGA
21733 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 A
21760 CCAATAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22006 original size:19 final size:20
Alignment explanation
Indices: 21984--22023 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
21974 TCTCCTATCT
21984 AATTAAA-GTTA-CTAAAACA
1 AATTAAAGGTTATC-AAAACA
22003 AATTAAAGGTTATCAAAACA
1 AATTAAAGGTTATCAAAACA
22023 A
1 A
22024 TAATGATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 11 0.58
21 1 0.05
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (20 bp):
AATTAAAGGTTATCAAAACA
Found at i:23063 original size:7 final size:7
Alignment explanation
Indices: 23048--23078 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
23038 GATTGAACTT
*
23048 TTTAGTA
1 TTTAATA
23055 TTTAATA
1 TTTAATA
23062 TTTAATA
1 TTTAATA
23069 TTTAATA
1 TTTAATA
23076 TTT
1 TTT
23079 TTTTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:23696 original size:40 final size:42
Alignment explanation
Indices: 23602--23699 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
23592 TCAATGTAAG
* * *
23602 TTGTTTATTTTTTTAAAAAAAAAATTGGTAATGGAGTGGAGTT
1 TTGTTTATTTTTTT-AAAAAAAAATTGGTAACGAAATGGAGTT
**
23645 TTGTTTATTTTTTTAAAAAAATTTTGGTAACGAAATGGA-TT
1 TTGTTTATTTTTTTAAAAAAAAATTGGTAACGAAATGGAGTT
*
23686 TT-TTTCTTTTTTTA
1 TTGTTTATTTTTTTA
23700 GGAAAAGTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
40 11 0.22
41 4 0.08
42 20 0.41
43 14 0.29
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (42 bp):
TTGTTTATTTTTTTAAAAAAAAATTGGTAACGAAATGGAGTT
Found at i:25304 original size:18 final size:19
Alignment explanation
Indices: 25272--25307 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25262 AATTTTCTTC
*
25272 TTTTTGTCTTCTCTTTTAG
1 TTTTTCTCTTCTCTTTTAG
25291 TTTTTCTCTT-TCTTTTA
1 TTTTTCTCTTCTCTTTTA
25308 AGTGTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (19 bp):
TTTTTCTCTTCTCTTTTAG
Found at i:32894 original size:56 final size:56
Alignment explanation
Indices: 32774--32895 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 56
32764 GGTGGGCATG
* * * *
32774 TGCCCACACTCACTTTCTTAATCTCTACAAATTTCACTATAATTTTAGATGGTGCC
1 TGCCCACCCTCACTTTCTAAATCTCTACAAATTTCACTATAATTTTAGATGATGCA
** * * * * *
32830 CACTCACCCTCACTTTCTAAATCTCTTCACATTTCACTATAATTTTGGATGATTCA
1 TGCCCACCCTCACTTTCTAAATCTCTACAAATTTCACTATAATTTTAGATGATGCA
32886 TGCCCACCCT
1 TGCCCACCCT
32896 TATTTGATCT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.37
Consensus pattern (56 bp):
TGCCCACCCTCACTTTCTAAATCTCTACAAATTTCACTATAATTTTAGATGATGCA
Found at i:34634 original size:49 final size:49
Alignment explanation
Indices: 34562--34659 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
34552 GATCCACTTT
34562 CAGTGTTGTGAGTGTGGTGGAGTGTGATATCACATAGCAAGCATAGTGA
1 CAGTGTTGTGAGTGTGGTGGAGTGTGATATCACATAGCAAGCATAGTGA
*
34611 CAGTGTTGTGAGTGTGGTGGAGTGTGATATCACATAGTAAGCATAGTGA
1 CAGTGTTGTGAGTGTGGTGGAGTGTGATATCACATAGCAAGCATAGTGA
34660 ATATCATATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.27, C:0.09, G:0.35, T:0.30
Consensus pattern (49 bp):
CAGTGTTGTGAGTGTGGTGGAGTGTGATATCACATAGCAAGCATAGTGA
Done.