Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024165.1 Corchorus olitorius cultivar O-4 contig24198, 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: 9504
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3416 original size:21 final size:21
Alignment explanation
Indices: 3390--3444 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3380 CGGCCATTCA
**
3390 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
3411 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
3432 CCGTGCCATCACC
1 CCGTGCCACCACC
3445 ATTCCATGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:5347 original size:29 final size:30
Alignment explanation
Indices: 5288--5347 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
5278 GAAGTTCGTG
* *
5288 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
*
5319 TTTGAAGA-CATTGAAGAATTTTTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
5348 GGAAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:6744 original size:15 final size:15
Alignment explanation
Indices: 6726--6755 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6716 TTTTGTTCCT
*
6726 AGTTTAATTGTTTTC
1 AGTTTAATTGCTTTC
6741 AGTTTAATTGCTTTC
1 AGTTTAATTGCTTTC
6756 TTTCAACCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
AGTTTAATTGCTTTC
Found at i:8065 original size:16 final size:16
Alignment explanation
Indices: 8031--8166 Score: 152
Period size: 16 Copynumber: 8.6 Consensus size: 16
8021 TGGGCTCGGG
* *
8031 CGGGTTCGGCTA-CTT
1 CGGGTTCGGGTATTTT
* *
8046 CGGGTTCGGATTTTTT
1 CGGGTTCGGGTATTTT
8062 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
8078 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
8094 CGGGCTCGGG-ATAAGT
1 CGGGTTCGGGTAT-TTT
8110 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
8126 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
8142 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
8158 CGGGTTCGG
1 CGGGTTCGG
8167 TCTCAGGTAG
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
15 13 0.13
16 85 0.84
17 3 0.03
ACGTcount: A:0.07, C:0.16, G:0.39, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:8084 original size:32 final size:33
Alignment explanation
Indices: 8045--8166 Score: 169
Period size: 32 Copynumber: 3.8 Consensus size: 33
8035 TTCGGCTACT
* * *
8045 TCGGGTTCGGATTTTTTCGGGTTCGGGTAT-TT
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATATG
* *
8077 TCGGGTTCGGGTATTTTCGGGCTCGGG-ATAAG
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATATG
*
8109 TCGGGTTCGGGTATTTTCGGGCTCGGGT-TATG
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATATG
8141 TCGGGTTCGGGTATTTTCGGGTTCGG
1 TCGGGTTCGGGTATTTTCGGGTTCGG
8167 TCTCAGGTAG
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
31 2 0.02
32 79 0.98
ACGTcount: A:0.07, C:0.15, G:0.39, T:0.39
Consensus pattern (33 bp):
TCGGGTTCGGGTATTTTCGGGTTCGGGTATATG
Found at i:8346 original size:13 final size:12
Alignment explanation
Indices: 8323--8369 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
8313 AAGTTTATTG
8323 ATAATATATAAT
1 ATAATATATAAT
8335 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
8348 ATAACAT-TATT
1 ATAATATATAAT
8359 ATCAATATATA
1 AT-AATATATA
8370 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:9020 original size:140 final size:140
Alignment explanation
Indices: 8768--9049 Score: 510
Period size: 140 Copynumber: 2.0 Consensus size: 140
8758 ACAAGATTGA
**
8768 ATAAGGATAGAACTTCCGGTTTAAACCTTTGCTTCTGTTTCATCATCTGCTTTTGTAGACTCTTT
1 ATAAGGATAGAACTTCCGGTTTAAACCTTTGCTTCCATTTCATCATCTGCTTTTGTAGACTCTTT
* *
8833 ATTTCCTTTAAAAAAATTAAAATTTCATGTATTTAATTAATAATAGTTTAATTAGTTATAAGGGT
66 ATTTCCTTAAAAAAAATTAAAATTTCATGTATTTAATTAATAATAGTTTAATTAGTTATAAGAGT
8898 ACTTTTTAGT
131 ACTTTTTAGT
*
8908 ATAAGGATAGAACTTTCGGTTTAAACCTTTGCTTCCATTTCATCATCTGCTTTTGTAGACTCTTT
1 ATAAGGATAGAACTTCCGGTTTAAACCTTTGCTTCCATTTCATCATCTGCTTTTGTAGACTCTTT
*
8973 ATTTGCTTAAAAAAAATTAAAATTTCATGTATTTAATTAATAATAGTTTAATTAGTTATAAGAGT
66 ATTTCCTTAAAAAAAATTAAAATTTCATGTATTTAATTAATAATAGTTTAATTAGTTATAAGAGT
9038 ACTTTTTAGT
131 ACTTTTTAGT
9048 AT
1 AT
9050 TTTGCTTTAA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (140 bp):
ATAAGGATAGAACTTCCGGTTTAAACCTTTGCTTCCATTTCATCATCTGCTTTTGTAGACTCTTT
ATTTCCTTAAAAAAAATTAAAATTTCATGTATTTAATTAATAATAGTTTAATTAGTTATAAGAGT
ACTTTTTAGT
Done.