Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013491.1 Corchorus olitorius cultivar O-4 contig13524, 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: 18478
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7484 original size:17 final size:16
Alignment explanation
Indices: 7444--7490 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
7434 CATTTAATCT
*
7444 TTGATCACCAGTGATC
1 TTGATCACTAGTGATC
*
7460 TTGCATCACTGGTGATC
1 TTG-ATCACTAGTGATC
7477 TTAGATCACTAGTG
1 TT-GATCACTAGTG
7491 GTTATCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 22 0.85
18 1 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:11950 original size:110 final size:110
Alignment explanation
Indices: 11747--11958 Score: 327
Period size: 110 Copynumber: 1.9 Consensus size: 110
11737 GATCTGCTCA
* * * * * *
11747 CGCTGACTCGTCGAGCATTTTTTATTTGTGGCTAGCAAATCATTTTAGTTTTAGAGTTTTTTTTT
1 CGCTGACGCGTCAAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAGTTTTTTTTT
* **
11812 TCCTCTCGGTTCTTACATATATTTGAGTAGGTGGTTATCGACTCG
66 TCCTCTCGGTTCTTACATACATGCGAGTAGGTGGTTATCGACTCG
11857 CGCTGACGCGTCAAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAGTTTTTTTTT
1 CGCTGACGCGTCAAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAGTTTTTTTTT
11922 T-CTCTCGGTTCTTATCATACATGCGAGTAGGTGGTTA
66 TCCTCTCGGTTCTTA-CATACATGCGAGTAGGTGGTTA
11959 GCAAATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 13 0.14
110 79 0.86
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (110 bp):
CGCTGACGCGTCAAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAGTTTTTTTTT
TCCTCTCGGTTCTTACATACATGCGAGTAGGTGGTTATCGACTCG
Found at i:14940 original size:132 final size:131
Alignment explanation
Indices: 14734--14997 Score: 420
Period size: 132 Copynumber: 2.0 Consensus size: 131
14724 CATTGTTCAA
* * *
14734 ACTTTTATAGTTTTACTCAACTAAAAATTTTATTTTTATTTAATTAAATTTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
* * * *
14799 TATTATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
66 TATTATATTTTTACCATTTTAATAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATA
14864 T
131 T
* *
14865 ACTTTTATAGTTTTACTCAACTAAAGACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAA
* *
14930 CTATTTTATTTTTATCATTTTAATAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAT
65 CTATTATATTTTTACCATTTTAATAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAT
14995 AT
130 AT
14997 A
1 A
14998 TTTCTTAAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
131 29 0.24
132 92 0.76
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.50
Consensus pattern (131 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTATATTTTTACCATTTTAATAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATA
T
Found at i:17840 original size:30 final size:30
Alignment explanation
Indices: 17804--17862 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
17794 CATGGATGAG
17804 TTCCACAAATTTGATCAAATCATTGATCAT
1 TTCCACAAATTTGATCAAATCATTGATCAT
*
17834 TTCCACAAATTTGATCACATCATTGATCA
1 TTCCACAAATTTGATCAAATCATTGATCA
17863 AATGCAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (30 bp):
TTCCACAAATTTGATCAAATCATTGATCAT
Done.