Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016393.1 Corchorus olitorius cultivar O-4 contig16426, 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: 58228
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:13052 original size:20 final size:20
Alignment explanation
Indices: 13029--13066 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13019 TAGTAATAAA
13029 ATTACTATCTAGAAAATATT
1 ATTACTATCTAGAAAATATT
* *
13049 ATTATTATCTAGATAATA
1 ATTACTATCTAGAAAATA
13067 GTAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTACTATCTAGAAAATATT
Found at i:23288 original size:22 final size:22
Alignment explanation
Indices: 23263--23310 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
23253 CTTAACTGCT
23263 TATAACACGCCGAATATCTCTA
1 TATAACACGCCGAATATCTCTA
* *
23285 TAT-A-ACGCCGAATGTCTTTA
1 TATAACACGCCGAATATCTCTA
23305 TATAAC
1 TATAAC
23311 TAGGGTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.77
21 2 0.09
22 3 0.14
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.31
Consensus pattern (22 bp):
TATAACACGCCGAATATCTCTA
Found at i:23292 original size:20 final size:20
Alignment explanation
Indices: 23269--23310 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
23259 TGCTTATAAC
23269 ACGCCGAATATCTCTATATA
1 ACGCCGAATATCTCTATATA
* *
23289 ACGCCGAATGTCTTTATATA
1 ACGCCGAATATCTCTATATA
23309 AC
1 AC
23311 TAGGGTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (20 bp):
ACGCCGAATATCTCTATATA
Found at i:26894 original size:24 final size:24
Alignment explanation
Indices: 26867--26920 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
26857 AATATTGGCT
26867 AAAAAGAA-AAAAAAAAGAAAGCAC
1 AAAAAGAACAAAAAAAA-AAAGCAC
* *
26891 AAAATA-AACAAAGAAAAAAAGCAT
1 AAAA-AGAACAAAAAAAAAAAGCAC
26915 AAAAAG
1 AAAAAG
26921 CTATCCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.04
24 16 0.64
25 8 0.32
ACGTcount: A:0.78, C:0.07, G:0.11, T:0.04
Consensus pattern (24 bp):
AAAAAGAACAAAAAAAAAAAGCAC
Found at i:49272 original size:2 final size:2
Alignment explanation
Indices: 49265--49295 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49255 ATTTTGTGAC
49265 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 T
49296 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50231 original size:3 final size:3
Alignment explanation
Indices: 50223--50264 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
50213 TACAAGGTTT
50223 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50265 GGGTAATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:50805 original size:2 final size:2
Alignment explanation
Indices: 50800--50840 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
50790 TGACATGAAC
50800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50841 ACCAATATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54191 original size:19 final size:19
Alignment explanation
Indices: 54167--54203 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54157 GTACAGTACC
54167 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
54186 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
54204 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:58200 original size:2 final size:2
Alignment explanation
Indices: 58193--58227 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58183 AATACTCTTA
58193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58228 A
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.