Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011266.1 Corchorus capsularis cultivar CVL-1 contig11287, 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: 23288
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2779 original size:20 final size:21
Alignment explanation
Indices: 2735--2780 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
2725 AAGAAGAAAG
2735 GAGAACTCTCACAAAAGGAGA
1 GAGAACTCTCACAAAAGGAGA
*
2756 GAGAAGCTCTCACAAGAGGAGA
1 GAGAA-CTCTCACAAAAGGAGA
2778 GAG
1 GAG
2781 TTTGTCCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.43, C:0.17, G:0.30, T:0.09
Consensus pattern (21 bp):
GAGAACTCTCACAAAAGGAGA
Found at i:4055 original size:20 final size:20
Alignment explanation
Indices: 4030--4084 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
4020 TTGAAATCAC
*
4030 AAACTTGCTCCTAACGAAAT
1 AAACTTGCTGCTAACGAAAT
*
4050 AAACTTGCTGCTAACGTAAT
1 AAACTTGCTGCTAACGAAAT
4070 AAACTTGCTGCTAAC
1 AAACTTGCTGCTAAC
4085 ACAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (20 bp):
AAACTTGCTGCTAACGAAAT
Found at i:4090 original size:20 final size:19
Alignment explanation
Indices: 4030--4092 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
4020 TTGAAATCAC
*
4030 AAACTTGCTCCTAACGAAAT
1 AAACTTGCTGCTAAC-AAAT
*
4050 AAACTTGCTGCTAACGTAAT
1 AAACTTGCTGCTAAC-AAAT
4070 AAACTTGCTGCTAACACAAT
1 AAACTTGCTGCTAACA-AAT
4090 AAA
1 AAA
4093 TAACCAAGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (19 bp):
AAACTTGCTGCTAACAAAT
Found at i:8870 original size:20 final size:20
Alignment explanation
Indices: 8845--8899 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
8835 TTGAAATCAC
*
8845 AAACTTGCTCCTAACGAAAT
1 AAACTTGCTGCTAACGAAAT
*
8865 AAACTTGCTGCTAACGTAAT
1 AAACTTGCTGCTAACGAAAT
8885 AAACTTGCTGCTAAC
1 AAACTTGCTGCTAAC
8900 ACAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (20 bp):
AAACTTGCTGCTAACGAAAT
Found at i:8905 original size:20 final size:19
Alignment explanation
Indices: 8845--8907 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
8835 TTGAAATCAC
*
8845 AAACTTGCTCCTAACGAAAT
1 AAACTTGCTGCTAAC-AAAT
*
8865 AAACTTGCTGCTAACGTAAT
1 AAACTTGCTGCTAAC-AAAT
8885 AAACTTGCTGCTAACACAAT
1 AAACTTGCTGCTAACA-AAT
8905 AAA
1 AAA
8908 TAACCAAGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (19 bp):
AAACTTGCTGCTAACAAAT
Found at i:9618 original size:22 final size:22
Alignment explanation
Indices: 9588--9630 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9578 CATAAATTAA
*
9588 AATTTGGAGTAAAAAGAAATTT
1 AATTGGGAGTAAAAAGAAATTT
* *
9610 AATTGGGAGTGAAAATAAATT
1 AATTGGGAGTAAAAAGAAATT
9631 AAATGGAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (22 bp):
AATTGGGAGTAAAAAGAAATTT
Found at i:9641 original size:22 final size:22
Alignment explanation
Indices: 9593--9641 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
9583 ATTAAAATTT
*
9593 GGAGTAAAAAGAAATTTAATTG
1 GGAGTAAAAAGAAATTTAAATG
* *
9615 GGAGTGAAAATAAA-TTAAATG
1 GGAGTAAAAAGAAATTTAAATG
9636 GAGAGT
1 G-GAGT
9642 TTTGTGACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (22 bp):
GGAGTAAAAAGAAATTTAAATG
Found at i:20123 original size:2 final size:2
Alignment explanation
Indices: 20116--20147 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20106 CATTTACTAG
20116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20148 AATGAGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.