Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005966.1 Corchorus capsularis cultivar CVL-1 contig05984, 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: 12517
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Found at i:2488 original size:21 final size:21
Alignment explanation
Indices: 2464--2504 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2454 ATTGAGACAG
2464 TCACAAGAAGAAATGAGGCAT
1 TCACAAGAAGAAATGAGGCAT
*
2485 TCACAAGAAGAGATGAGGCA
1 TCACAAGAAGAAATGAGGCA
2505 AGAACAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (21 bp):
TCACAAGAAGAAATGAGGCAT
Found at i:2511 original size:21 final size:21
Alignment explanation
Indices: 2466--2512 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2456 TGAGACAGTC
***
2466 ACAAGAAGAAATGAGGCATTC
1 ACAAGAAGAAATGAGGCAAGA
*
2487 ACAAGAAGAGATGAGGCAAGA
1 ACAAGAAGAAATGAGGCAAGA
2508 ACAAG
1 ACAAG
2513 GCGTTATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.28, T:0.09
Consensus pattern (21 bp):
ACAAGAAGAAATGAGGCAAGA
Found at i:10666 original size:35 final size:35
Alignment explanation
Indices: 10567--11133 Score: 825
Period size: 35 Copynumber: 16.2 Consensus size: 35
10557 TCTAGAGCGG
* * *
10567 TCATTTTAAGAAGCTTTCAGAGGTCAGAGTCGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
10602 TCATATCAAAAAGTTTTACAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-CAGAGGTCAGAGTTGATC
10638 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
10673 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTAATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
10708 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
10743 TCATTTCAAAAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
10778 TCATTCCAGGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* * *
10813 TCATTTCAGGAAGTTTTTAGAGGTCAGACTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
10848 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
10883 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
10918 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* * *
10953 TCATTCCAATAAGTTTTCAGAGGACAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
10988 TCATTTCAAGAAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
11023 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTAATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
11058 TCATTTCAAGAAGTTTCCA-ACGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
* * * *
11093 GCATTTTC-AGTA-TTTTCAAACGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
*
11128 GCATTT
1 TCATTT
11134 TCAGTATTTT
Statistics
Matches: 490, Mismatches: 38, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
34 9 0.02
35 445 0.91
36 36 0.07
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
Found at i:11134 original size:35 final size:35
Alignment explanation
Indices: 11071--11405 Score: 487
Period size: 35 Copynumber: 9.6 Consensus size: 35
11061 TTTCAAGAAG
11071 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
*
11106 TTTCAAACGATCAGAGTTGATCGCATTTTCAGTAT
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
* *
11141 TTTCC-ATGATCAGAGTTGATCGCATTTTCAGTAG
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
11175 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
*
11210 TTTCCAACGATCAGAGTTGGTCGCATTTTCAGTAT
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
* * *
11245 TTTCC-ATGATCATAGTTGATCGCATTTTCAGTAG
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
11279 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
* *
11314 TTTCCAACGATCAGAGTTGATCACATTTTCAGTAG
1 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
* * * * * *
11349 TTTCCAACAATAAGAGGTGATCTCA-TTTCAAGAAA
1 TTTCCAACGATCAGAGTTGATCGCATTTTC-AGTAT
* *
11384 TTTCCGATGATCAGAGTTGATC
1 TTTCCAACGATCAGAGTTGATC
11406 CAGAGGAGTT
Statistics
Matches: 270, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
34 66 0.24
35 204 0.76
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (35 bp):
TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAT
Found at i:11162 original size:69 final size:70
Alignment explanation
Indices: 11046--11405 Score: 494
Period size: 69 Copynumber: 5.2 Consensus size: 70
11036 TTTTCAGAGG
* * *
11046 TCAGAGTTAATCTCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
*
11110 AAACGA
65 CAACGA
* * *
11116 TCAGAGTTGATCGCATTTTCAGTATTTTCC-ATGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
11180 AACGA
66 AACGA
* *
11185 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGGTCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
*
11250 -ATGA
66 AACGA
*
11254 TCATAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
11319 AACGA
66 AACGA
* * * * * * *
11324 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATAAGAGGTGATCTCA-TTTCAAGAAATTTC
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTATTTTC
* *
11388 CGATGA
65 CAACGA
11394 TCAGAGTTGATC
1 TCAGAGTTGATC
11406 CAGAGGAGTT
Statistics
Matches: 261, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
69 135 0.52
70 122 0.47
71 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (70 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
AACGA
Found at i:11378 original size:104 final size:105
Alignment explanation
Indices: 11046--11405 Score: 530
Period size: 104 Copynumber: 3.5 Consensus size: 105
11036 TTTTCAGAGG
* *
11046 TCAGAGTTAATCTCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
*
11110 AAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCATGA
66 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCATGA
*
11150 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
*
11214 CAACGATCAGAGTTGGTCGCATTTTCAGTATTTTCCATGA
66 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCATGA
* *
11254 TCATAGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
* * **
11318 CAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
66 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC-ATGA
* * * * * *
11359 TAAGAGGTGATCTCA-TTTCAAGAAATTTCCGATGATCAGAGTTGATC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATC
11406 CAGAGGAGTT
Statistics
Matches: 234, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
104 194 0.83
105 40 0.17
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (105 bp):
TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCATGA
Found at i:11866 original size:2 final size:2
Alignment explanation
Indices: 11859--11891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11849 CATACACAAA
11859 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11892 CGCACACGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.