Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020330.1 Corchorus olitorius cultivar O-4 contig20363, 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: 15597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1019 original size:132 final size:133
Alignment explanation
Indices: 862--1161 Score: 532
Period size: 132 Copynumber: 2.3 Consensus size: 133
852 TTGTTTAGAC
* *
862 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTA-AGA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATACAATATATCCTTATA-A
* *
926 CTATTTAATTTTTACCATTTTACTATTTTAATTAGAAAAATTATATATATTAGAATTTTTTAAAT
65 CTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAACTTTTTAAAT
991 ATA-
130 ATAT
994 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATACAATATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATACAATATATCCTTATAAC
1059 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAACTTTTTAAATA
66 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAACTTTTTAAATA
1124 TAT
131 TAT
*
1127 TTTTATAGTTTTATTCAACTAAAAACTCTATTTTT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTT
1162 TGGCCAAAAA
Statistics
Matches: 161, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
132 126 0.78
133 35 0.22
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (133 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATACAATATATCCTTATAAC
TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAACTTTTTAAATA
TAT
Found at i:1922 original size:31 final size:31
Alignment explanation
Indices: 1865--1923 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1855 TTCAGCTCAT
* *
1865 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
1896 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
1924 TTTGACCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:8878 original size:31 final size:31
Alignment explanation
Indices: 8840--8919 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
8830 CTCTAGGGAT
* *
8840 TGATTTGAGCTG-ATTCTACAACGGT-AGGAAC
1 TGATTTGAGCCGAATT-TACAACAGTAAGG-AC
*
8871 TGATTTGAGCCGAATTTACAACATTAAGGAC
1 TGATTTGAGCCGAATTTACAACAGTAAGGAC
8902 TGATTTGAGCCGAATTTA
1 TGATTTGAGCCGAATTTA
8920 TAATATTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 38 0.86
32 6 0.14
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (31 bp):
TGATTTGAGCCGAATTTACAACAGTAAGGAC
Found at i:8928 original size:31 final size:31
Alignment explanation
Indices: 8869--8929 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
8859 AACGGTAGGA
8869 ACTGATTTGAGCCGAATTTACAACATTAAGG
1 ACTGATTTGAGCCGAATTTACAACATTAAGG
* *
8900 ACTGATTTGAGCCGAATTTATAATATTAAG
1 ACTGATTTGAGCCGAATTTACAACATTAAG
8930 AACTTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (31 bp):
ACTGATTTGAGCCGAATTTACAACATTAAGG
Found at i:13782 original size:12 final size:12
Alignment explanation
Indices: 13767--13791 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13757 TACTTTCTTT
13767 TTCACTTCCTTC
1 TTCACTTCCTTC
13779 TTCACTTCCTTC
1 TTCACTTCCTTC
13791 T
1 T
13792 CCGCTACTTT
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:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCACTTCCTTC
Done.