Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012666.1 Corchorus olitorius cultivar O-4 contig12699, 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: 40879
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--41 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 GTAAAG
7 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42 TCCTTTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8064 original size:16 final size:16
Alignment explanation
Indices: 8026--8064 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
8016 GCTTAATCAA
8026 ATGTTTTTATTAGCAC
1 ATGTTTTTATTAGCAC
*
8042 ATAGTTTTTCTTAGCAC
1 AT-GTTTTTATTAGCAC
*
8059 GTGTTT
1 ATGTTT
8065 CTCAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (16 bp):
ATGTTTTTATTAGCAC
Found at i:16155 original size:17 final size:17
Alignment explanation
Indices: 16114--16155 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16104 AACCCATTTT
*
16114 AGAGAGAGAAAGGGGAA
1 AGAGAGAGAAAGGAGAA
*
16131 AGAAAGAGAAATGGAGAA
1 AGAGAGAGAAA-GGAGAA
16149 AG-GAGAG
1 AGAGAGAG
16156 TTTTTTGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (17 bp):
AGAGAGAGAAAGGAGAA
Found at i:17994 original size:16 final size:16
Alignment explanation
Indices: 17944--17996 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
17934 GTAGTATTTG
17944 ATTTATTTATGTAAGA
1 ATTTATTTATGTAAGA
* * ** *
17960 ATTTTTTTTTGGCACA
1 ATTTATTTATGTAAGA
17976 ATTTATTTATGTAAGA
1 ATTTATTTATGTAAGA
17992 ATTTA
1 ATTTA
17997 GGAGCAGCTT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (16 bp):
ATTTATTTATGTAAGA
Found at i:21461 original size:18 final size:18
Alignment explanation
Indices: 21438--21477 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
21428 GGACTTTCCC
21438 CTAGAGTTTTAAGCTAAG
1 CTAGAGTTTTAAGCTAAG
21456 CTAGAGTTTTAAGCTAAG
1 CTAGAGTTTTAAGCTAAG
21474 CTAG
1 CTAG
21478 TCGTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (18 bp):
CTAGAGTTTTAAGCTAAG
Found at i:21984 original size:14 final size:14
Alignment explanation
Indices: 21965--21991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21955 GCAATAGAGG
21965 CAGATAGAGGCAGA
1 CAGATAGAGGCAGA
21979 CAGATAGAGGCAG
1 CAGATAGAGGCAG
21992 GGGGCAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.37, T:0.07
Consensus pattern (14 bp):
CAGATAGAGGCAGA
Found at i:24181 original size:21 final size:22
Alignment explanation
Indices: 24152--24194 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
24142 CTCGCTCGCT
*
24152 TAATCTTTCTTTTCTTTTCTTG
1 TAATCTTTCTTTTCCTTTCTTG
24174 TAAT-TTTCTTTTCCTTTCTTG
1 TAATCTTTCTTTTCCTTTCTTG
24195 GGTTCAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (22 bp):
TAATCTTTCTTTTCCTTTCTTG
Found at i:28895 original size:1 final size:1
Alignment explanation
Indices: 28889--28916 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28879 TCTTAATGTC
28889 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
28917 CTAATCCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32428 original size:23 final size:23
Alignment explanation
Indices: 32397--32443 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
32387 ATGAAATGCT
*
32397 TACCTTGATGCTTTGGCCCGTAA
1 TACCATGATGCTTTGGCCCGTAA
* * *
32420 TACCATGATGTTTTTGCCTGTAA
1 TACCATGATGCTTTGGCCCGTAA
32443 T
1 T
32444 GTTCTGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (23 bp):
TACCATGATGCTTTGGCCCGTAA
Found at i:37112 original size:16 final size:16
Alignment explanation
Indices: 37093--37124 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
37083 AAAAGCATAT
37093 CCACATAAAAATTTAA
1 CCACATAAAAATTTAA
*
37109 CCACATAAAGATTTAA
1 CCACATAAAAATTTAA
37125 AGTGATTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (16 bp):
CCACATAAAAATTTAA
Done.