Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014181.1 Corchorus olitorius cultivar O-4 contig14214, 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: 74967
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6204 original size:12 final size:12
Alignment explanation
Indices: 6187--6213 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6177 TTTTTCCTTC
6187 TGCCTATCACAT
1 TGCCTATCACAT
6199 TGCCTATCACAT
1 TGCCTATCACAT
6211 TGC
1 TGC
6214 AGCAGGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (12 bp):
TGCCTATCACAT
Found at i:10908 original size:108 final size:109
Alignment explanation
Indices: 10713--10908 Score: 263
Period size: 108 Copynumber: 1.8 Consensus size: 109
10703 AGATTTAACC
* ** * *
10713 CCAATTATAAAAATATTTTATTTTTTAAAAGGGTAAATCTTGAATTCAAGACCTATTATTATAGG
1 CCAATTATAAAAATATTTTATTTCTTAAAAGGGTAAATCTCAAATTCAAGACCCATTATCATAGG
* * *
10778 GTTTTAGAAAAATAAGTTTAAATATTTATTAATAAGGTTTAGCA
66 GTTTTAGAAAAAAAAATATAAATATTTATTAATAAGGTTTAGCA
* *
10822 CCAATTAT-AAAAT-TTTTATTTCTTAAAAGGGTAAATCTCAAATTTTGAA-ACCCATTATCATG
1 CCAATTATAAAAATATTTTATTTCTTAAAAGGGTAAATCTCAAA--TTCAAGACCCATTATCATA
10884 GGGTTTTAGAAAAAAAAATATAAAT
64 GGGTTTTAGAAAAAAAAATATAAAT
10909 CATTCCTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
107 26 0.35
108 37 0.49
109 12 0.16
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (109 bp):
CCAATTATAAAAATATTTTATTTCTTAAAAGGGTAAATCTCAAATTCAAGACCCATTATCATAGG
GTTTTAGAAAAAAAAATATAAATATTTATTAATAAGGTTTAGCA
Found at i:15931 original size:27 final size:27
Alignment explanation
Indices: 15863--15949 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
15853 ACCAATTCTA
* **
15863 GGGTAAAATGGTAAATTCCTCATTAT-AG
1 GGGTAAAATAGTAAATTTATCA--ATCAG
* *
15891 GGGTAAAATCGTAATTTTATCAATCAG
1 GGGTAAAATAGTAAATTTATCAATCAG
* * * *
15918 GGGTAATATAGTAAATTTGTCCATCAC
1 GGGTAAAATAGTAAATTTATCAATCAG
15945 GGGTA
1 GGGTA
15950 TTTTGGTAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 2 0.04
27 28 0.58
28 18 0.38
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (27 bp):
GGGTAAAATAGTAAATTTATCAATCAG
Found at i:20777 original size:16 final size:16
Alignment explanation
Indices: 20730--20771 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20720 TTAATTTCCA
*
20730 TAGTTTAGATTTA-ATT
1 TAGTTT-GATTTATTTT
*
20746 TAGTTTGCTTTATTTT
1 TAGTTTGATTTATTTT
20762 TAGTTTGATT
1 TAGTTTGATT
20772 GTTTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.62
Consensus pattern (16 bp):
TAGTTTGATTTATTTT
Found at i:29958 original size:16 final size:17
Alignment explanation
Indices: 29937--29971 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29927 CAATTCACAA
*
29937 TTCTCTTCATCTA-TTT
1 TTCTCTTAATCTAGTTT
29953 TTCTCTTAATCTAGTTT
1 TTCTCTTAATCTAGTTT
29970 TT
1 TT
29972 AAGTGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.14, C:0.20, G:0.03, T:0.63
Consensus pattern (17 bp):
TTCTCTTAATCTAGTTT
Found at i:40539 original size:7 final size:7
Alignment explanation
Indices: 40527--40551 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40517 GGCGAAAGGC
40527 TGCTGGA
1 TGCTGGA
40534 TGCTGGA
1 TGCTGGA
40541 TGCTGGA
1 TGCTGGA
40548 TGCT
1 TGCT
40552 AGCTGGTAAC
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:0.16, G:0.40, T:0.32
Consensus pattern (7 bp):
TGCTGGA
Found at i:44857 original size:11 final size:11
Alignment explanation
Indices: 44841--44867 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
44831 CACGGATGGT
44841 CGGGCCATAGC
1 CGGGCCATAGC
44852 CGGGCCATAGC
1 CGGGCCATAGC
44863 CGGGC
1 CGGGC
44868 ATTGGCCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.37, G:0.41, T:0.07
Consensus pattern (11 bp):
CGGGCCATAGC
Found at i:48871 original size:11 final size:11
Alignment explanation
Indices: 48855--48880 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48845 CCTTGCCGAA
48855 AAAACTAGAAG
1 AAAACTAGAAG
48866 AAAACTAGAAG
1 AAAACTAGAAG
48877 AAAA
1 AAAA
48881 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:60833 original size:30 final size:30
Alignment explanation
Indices: 60774--60834 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
60764 TTGAAGAAGA
* *
60774 GGCATTAGTGGCAGTAGGCATATATATAGT
1 GGCATTAGTGGCAGTAGGCACAGATATAGT
60804 GGCATTAGTGGCAGTAGGCACAGGA-ATAGT
1 GGCATTAGTGGCAGTAGGCACA-GATATAGT
60834 G
1 G
60835 TTTATGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (30 bp):
GGCATTAGTGGCAGTAGGCACAGATATAGT
Found at i:65855 original size:30 final size:30
Alignment explanation
Indices: 65819--65877 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
65809 CATGGGTGAG
65819 TTCCACAAATTTGATCAAATCATTGATCAT
1 TTCCACAAATTTGATCAAATCATTGATCAT
65849 TTCCACAAATTTGATCAAATCATTGATCA
1 TTCCACAAATTTGATCAAATCATTGATCA
65878 AATGCAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (30 bp):
TTCCACAAATTTGATCAAATCATTGATCAT
Done.