Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010294.1 Corchorus capsularis cultivar CVL-1 contig10315, 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: 35648
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7526 original size:39 final size:39
Alignment explanation
Indices: 7472--7549 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
7462 AGAGGGGGGA
* *
7472 GGTGGTGGAGGAGGACTGG-CCTTACTTGGGACAGGAGGT
1 GGTGGAGGAGGAGGACTGGCCCTGA-TTGGGACAGGAGGT
*
7511 GGTGGAGGAGGAGGACTGGCCCTGATTGGGGCAGGAGGT
1 GGTGGAGGAGGAGGACTGGCCCTGATTGGGACAGGAGGT
7550 TCAGGAGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 31 0.89
40 4 0.11
ACGTcount: A:0.18, C:0.13, G:0.51, T:0.18
Consensus pattern (39 bp):
GGTGGAGGAGGAGGACTGGCCCTGATTGGGACAGGAGGT
Found at i:8288 original size:6 final size:6
Alignment explanation
Indices: 8279--8305 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8269 GAGGCTGGGC
8279 CTGGAG CTGGAG CTGGAG CTGGAG CTG
1 CTGGAG CTGGAG CTGGAG CTGGAG CTG
8306 AACCTGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.48, T:0.19
Consensus pattern (6 bp):
CTGGAG
Found at i:20952 original size:2 final size:2
Alignment explanation
Indices: 20945--20969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20935 ATAGTATTAT
20945 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20970 GAAATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30145 original size:13 final size:14
Alignment explanation
Indices: 30123--30155 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30113 GCAAGAATAC
*
30123 AAGAACTAGTATT-
1 AAGAATTAGTATTA
30136 AAGAATTAGTATTA
1 AAGAATTAGTATTA
30150 AAGAAT
1 AAGAAT
30156 ATATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (14 bp):
AAGAATTAGTATTA
Found at i:35043 original size:21 final size:21
Alignment explanation
Indices: 35004--35044 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34994 AAGGAGAAGA
*
35004 AGTATAACAGGTGACTGGAGT
1 AGTATAACAGGAGACTGGAGT
* *
35025 AGTATAATAGGAGATTGGAG
1 AGTATAACAGGAGACTGGAG
35045 AACGTTGGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (21 bp):
AGTATAACAGGAGACTGGAGT
Found at i:35208 original size:24 final size:24
Alignment explanation
Indices: 35176--35226 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
35166 CTCATAATCG
35176 GGATTATAATCATAAGAAGGTGGA
1 GGATTATAATCATAAGAAGGTGGA
35200 GGATTATAATCATAAGAAGGTGGA
1 GGATTATAATCATAAGAAGGTGGA
35224 GGA
1 GGA
35227 CAGAGACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.31, T:0.24
Consensus pattern (24 bp):
GGATTATAATCATAAGAAGGTGGA
Found at i:35237 original size:24 final size:24
Alignment explanation
Indices: 35186--35239 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
35176 GGATTATAAT
* * *
35186 CATAAGAAGGTGGAGGATTATAAT
1 CATAAGAAGGTGGAGGATCAGAAC
35210 CATAAGAAGGTGGAGGA-CAGAGAC
1 CATAAGAAGGTGGAGGATCAGA-AC
35234 CATAAG
1 CATAAG
35240 GATGGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (24 bp):
CATAAGAAGGTGGAGGATCAGAAC
Found at i:35508 original size:27 final size:27
Alignment explanation
Indices: 35472--35527 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
35462 TAGTATTGGA
35472 AGCCTCTCGTCGAAGGGGAAAAGGTGG
1 AGCCTCTCGTCGAAGGGGAAAAGGTGG
* * *
35499 AGCCTTTCGTCGAAGGGTAGAAGGTGG
1 AGCCTCTCGTCGAAGGGGAAAAGGTGG
35526 AG
1 AG
35528 AAACGGCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.41, T:0.18
Consensus pattern (27 bp):
AGCCTCTCGTCGAAGGGGAAAAGGTGG
Found at i:35565 original size:30 final size:30
Alignment explanation
Indices: 35529--35585 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
35519 AAGGTGGAGA
*
35529 AACGGCGGAGGAGACCATAGTGTTGGGGGC
1 AACGGCGGAGGAGACCACAGTGTTGGGGGC
35559 AACGGCGGAGGAGACCACAGTGTTGGG
1 AACGGCGGAGGAGACCACAGTGTTGGG
35586 AGAAGGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.46, T:0.12
Consensus pattern (30 bp):
AACGGCGGAGGAGACCACAGTGTTGGGGGC
Done.