Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017588.1 Corchorus olitorius cultivar O-4 contig17621, 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: 20839
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:3430 original size:9 final size:9
Alignment explanation
Indices: 3416--3442 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3406 CAACAAACAT
3416 CAAAACAAA
1 CAAAACAAA
3425 CAAAACAAA
1 CAAAACAAA
3434 CAAAACAAA
1 CAAAACAAA
3443 TCAACCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAACAAA
Found at i:6826 original size:39 final size:39
Alignment explanation
Indices: 6766--6859 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
6756 AGTGAACTGC
* * *
6766 AAAATGCATATGGCTAGGTTTTGAGATG-ATGTGGATTGA
1 AAAATGCATATAGCTAAGTTTTGAGATGTA-ATGGATTGA
* *
6805 AAAATGCATATAGCTAAGTTTTGTGTTGTAATGGATTGA
1 AAAATGCATATAGCTAAGTTTTGAGATGTAATGGATTGA
6844 AAAATGCATATAGCTA
1 AAAATGCATATAGCTA
6860 GGTCTTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 48 0.98
40 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (39 bp):
AAAATGCATATAGCTAAGTTTTGAGATGTAATGGATTGA
Found at i:8401 original size:28 final size:27
Alignment explanation
Indices: 8315--8412 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 27
8305 GGTGTCCCTG
* * *
8315 AAATGACCAAAATGCCCCCTAGCCTAGCA
1 AAATGACCAAAATG-CCCATGGCAT-GCA
8344 AAATGACCAAAATGCCCATGG-ATGTACA
1 AAATGACCAAAATGCCCATGGCATG--CA
*
8372 AAATGACCAAAATGCCCTTGGTCATGCA
1 AAATGACCAAAATGCCCATGG-CATGCA
*
8400 AAATGAGCAAAAT
1 AAATGACCAAAAT
8413 AAAAGTAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 41 0.68
29 14 0.23
30 3 0.05
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCATGGCATGCA
Found at i:13025 original size:2 final size:2
Alignment explanation
Indices: 13018--13058 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
13008 TGATAGGAGA
*
13018 AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT CT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
13059 TAAAAAGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13242 original size:78 final size:79
Alignment explanation
Indices: 13153--13315 Score: 256
Period size: 79 Copynumber: 2.1 Consensus size: 79
13143 AACTTTTATA
* *
13153 ATTTTATTCAACTAAAAACTATATTTTTATTTAATTACATCT-AATATCATTATAACTATTTTAT
1 ATTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAAATATCATTATAACTATTTTAT
13217 TTTACCATTTTACT
66 TTTACCATTTTACT
* * * *
13231 GTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAAATATCCTTATAACTATTTTAT
1 ATTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAAATATCATTATAACTATTTTAT
*
13296 TTTGCCATTTTACT
66 TTTACCATTTTACT
13310 ATTTTA
1 ATTTTA
13316 ATTAAACAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
78 37 0.49
79 39 0.51
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.52
Consensus pattern (79 bp):
ATTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAAATATCATTATAACTATTTTAT
TTTACCATTTTACT
Found at i:14946 original size:2 final size:2
Alignment explanation
Indices: 14939--14968 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14929 GCATGTGGCA
14939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14969 TTTTTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17220 original size:40 final size:41
Alignment explanation
Indices: 17169--17247 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
17159 TTTTATAATT
* *
17169 TTTTGAAGAAAATTCAGTTAAGAAATGAAATTTATAAGTGC
1 TTTTGAAGAAAATTCAGTTAAGAAAAGAAAGTTATAAGTGC
*
17210 TTTT-AAGAAAATTTAGTTAAGAAAAGAAAGTTATAAGT
1 TTTTGAAGAAAATTCAGTTAAGAAAAGAAAGTTATAAGT
17248 TATTGTGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (41 bp):
TTTTGAAGAAAATTCAGTTAAGAAAAGAAAGTTATAAGTGC
Found at i:17827 original size:15 final size:14
Alignment explanation
Indices: 17802--17853 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
17792 CTCATAAGAT
17802 TAATAGTATGTATAA
1 TAATA-TATGTATAA
17817 TAATATAATGTATAA
1 TAATAT-ATGTATAA
17832 T-ATATATGTATATA
1 TAATATATGTATA-A
17846 TAAT-TATG
1 TAATATATG
17854 GAAGAACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.21
14 11 0.32
15 16 0.47
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
TAATATATGTATAA
Found at i:17831 original size:12 final size:12
Alignment explanation
Indices: 17816--17849 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
17806 AGTATGTATA
17816 ATAATATAATGT
1 ATAATATAATGT
17828 ATAATATATATGT
1 ATAATATA-ATGT
17841 AT-ATATAAT
1 ATAATATAAT
17850 TATGGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 13 0.62
13 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (12 bp):
ATAATATAATGT
Found at i:20802 original size:2 final size:2
Alignment explanation
Indices: 20795--20839 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20785 GGAGTCAAGA
20795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20837 AT A
1 AT A
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.