Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021024.1 Corchorus olitorius cultivar O-4 contig21057, 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: 11565
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:118 original size:16 final size:16
Alignment explanation
Indices: 94--137 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
84 CGGGTCAGGA
* *
94 TCGGATTCGGGTATTT
1 TCGGGTTCGGGTAATT
*
110 TCGGGTTCGGCTAATT
1 TCGGGTTCGGGTAATT
126 TCGGGTTCGGGT
1 TCGGGTTCGGGT
138 TCGGGCGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.36, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:2911 original size:39 final size:38
Alignment explanation
Indices: 2785--2932 Score: 235
Period size: 38 Copynumber: 3.9 Consensus size: 38
2775 TCGAGTCTAG
2785 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
2822 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
2860 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
2899 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
2933 ATGCACAGCC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
37 7 0.07
38 62 0.60
39 34 0.33
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:2919 original size:77 final size:75
Alignment explanation
Indices: 2785--2932 Score: 233
Period size: 77 Copynumber: 1.9 Consensus size: 75
2775 TCGAGTCTAG
2785 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
2850 TCCACTCTTA
66 TCCACTCTTA
* * * * *
2860 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG
2925 GGTCCACT
64 GGTCCACT
2933 ATGCACAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 7 0.11
76 24 0.36
77 35 0.53
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:6325 original size:6 final size:6
Alignment explanation
Indices: 6288--6324 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
6278 AGGCTGCACA
* *
6288 ACAATA ACAATC ACAATC ACAATC ACAATC ATAATC A
1 ACAATC ACAATC ACAATC ACAATC ACAATC ACAATC A
6325 TCCGTTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (6 bp):
ACAATC
Found at i:6479 original size:77 final size:75
Alignment explanation
Indices: 6354--6501 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 75
6344 TCGAGTCTAG
* *
6354 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAAACCCCTGAGGCACGGGTCCACTCTTACCAACACTTTAACCCCCTGAGGCACGGG
6419 TCCACTCTTA
66 TCCACTCTTA
* * * * * *
6429 CCAACAGTTTAAACCCCTGTGGTATGGGTCCACTATTTACCATCACTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAAACCCCTGAGGCACGGGTCCACT-CTTACCAACACTTTAACCCCCTGAGGCACG
6494 GGTCCACT
64 GGTCCACT
6502 ATGCACAGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 7 0.11
76 22 0.35
77 34 0.54
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAAACCCCTGAGGCACGGGTCCACTCTTACCAACACTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:6503 original size:39 final size:38
Alignment explanation
Indices: 6354--6501 Score: 208
Period size: 38 Copynumber: 3.9 Consensus size: 38
6344 TCGAGTCTAG
6354 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
6391 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * * *
6429 CCAACAGTTTAAACCCCTGTGGTATGGGTCCACTATTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT-CTTA
* * *
6468 CCATCACTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
6502 ATGCACAGCC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
37 7 0.07
38 60 0.61
39 32 0.32
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Done.