Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013105.1 Corchorus capsularis cultivar CVL-1 contig13126, 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: 7007
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1060 original size:58 final size:58
Alignment explanation
Indices: 970--1085 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
960 CAGAGGAGAC
970 GTCACAAATAGAGCAAAGGGATATGGAGGAGGCGACAAAGAGGAAGACCGGAGCAGAT
1 GTCACAAATAGAGCAAAGGGATATGGAGGAGGCGACAAAGAGGAAGACCGGAGCAGAT
1028 GTCACAAATAGAGCAAAGGGATATGGAGGAGGCGACAAAGAGGAAGACCGGAGCAGAT
1 GTCACAAATAGAGCAAAGGGATATGGAGGAGGCGACAAAGAGGAAGACCGGAGCAGAT
1086 CTCAGTGAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.09
Consensus pattern (58 bp):
GTCACAAATAGAGCAAAGGGATATGGAGGAGGCGACAAAGAGGAAGACCGGAGCAGAT
Found at i:3530 original size:77 final size:76
Alignment explanation
Indices: 3449--3644 Score: 315
Period size: 75 Copynumber: 2.6 Consensus size: 76
3439 TTGATATTTT
*
3449 CTAAATCTCCCACAGTTTGGCAAGATTTAGAGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCATTCTTTATTATTAT-TTTATTT
3513 CTTAAAATATCTC
64 CTTAAAATATCTC
* *
3526 CTAAATCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCA-ACTTTATTATTATTTTATTTCT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTCTTTATTATTATTTTATTTCT
3590 TAAAATATCTC
66 TAAAATATCTC
* *
3601 TTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCACATT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATT
3645 ATTATTTTAA
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 69 0.63
76 12 0.11
77 29 0.26
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (76 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTCTTTATTATTATTTTATTTCT
TAAAATATCTC
Found at i:4141 original size:35 final size:35
Alignment explanation
Indices: 4091--4277 Score: 245
Period size: 35 Copynumber: 5.4 Consensus size: 35
4081 TATTATAATG
* * *
4091 CGATCAACTCCGATCATTGGAAACTACTGAAAATA
1 CGATCAACTCTGATCGTTGGAAAATACTGAAAATA
* *
4126 CGATCAACTCTGATC-ATGGAAAATACTGAAAATG
1 CGATCAACTCTGATCGTTGGAAAATACTGAAAATA
*
4160 CGATCAACTCTGATCGTTGGAAAATACTGAAAATG
1 CGATCAACTCTGATCGTTGGAAAATACTGAAAATA
*
4195 CGATCAACTATGATCGTTGGAAAATACTGAAAATA
1 CGATCAACTCTGATCGTTGGAAAATACTGAAAATA
* * *
4230 TGATCAACTCTGATCGTTGGAAACTTCTTG-AAATGA
1 CGATCAACTCTGATCGTTGGAAAATAC-TGAAAAT-A
4266 -GATCAACTCTGA
1 CGATCAACTCTGA
4278 CCCCTAAAAA
Statistics
Matches: 138, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
34 31 0.22
35 104 0.75
36 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (35 bp):
CGATCAACTCTGATCGTTGGAAAATACTGAAAATA
Found at i:4289 original size:35 final size:35
Alignment explanation
Indices: 4231--4404 Score: 244
Period size: 35 Copynumber: 5.0 Consensus size: 35
4221 CTGAAAATAT
* *
4231 GATCAACTCTGATCGT-TGGAAACTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * *
4266 GATCAACTCTGACCCCTAAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
4301 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
4336 GATCAACTCTGACCTCTGAAAACTTCTTG-GATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
4370 GATCAACTCTGACCTCTGAAAGCTTCTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
4405 CCGCTCTGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
34 32 0.26
35 92 0.74
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:5290 original size:23 final size:23
Alignment explanation
Indices: 5264--5313 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
5254 ACCCCTCCCT
5264 TTTTTCT-TCTTTTTTTTTGAAAC
1 TTTTTCTCTCTTTTTTTTT-AAAC
5287 -TTTTCTCTCTTTTTTTTTAAAC
1 TTTTTCTCTCTTTTTTTTTAAAC
5309 TTTTT
1 TTTTT
5314 TTTTTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTCTCTCTTTTTTTTTAAAC
Found at i:5292 original size:22 final size:21
Alignment explanation
Indices: 5265--5319 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
5255 CCCCTCCCTT
5265 TTTTCTTCTTTTTTTTTGAAAC
1 TTTTCTTCTTTTTTTTT-AAAC
5287 TTTTCTCTCTTTTTTTTTAAAC
1 TTTTCT-TCTTTTTTTTTAAAC
5309 TTTT-TT-TTTTT
1 TTTTCTTCTTTTT
5320 GGAAACCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 1 0.03
21 1 0.03
22 14 0.44
23 11 0.34
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTCTTTTTTTTTAAAC
Done.