Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017130.1 Corchorus olitorius cultivar O-4 contig17163, 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: 9364
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Found at i:141 original size:21 final size:21
Alignment explanation
Indices: 115--158 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
105 GGATATGGAC
*
115 GATAACGATCCATCGACGCCA
1 GATAACGAGCCATCGACGCCA
136 GATAACGAGCCATCGACGCCA
1 GATAACGAGCCATCGACGCCA
157 GA
1 GA
159 CGGGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.32, G:0.23, T:0.11
Consensus pattern (21 bp):
GATAACGAGCCATCGACGCCA
Found at i:459 original size:20 final size:19
Alignment explanation
Indices: 436--475 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
426 GTTTTAATTA
436 AATTAATTTTAATATTTATT
1 AATTAATTTTAATA-TTATT
* *
456 AATTTATTTTTATATTATT
1 AATTAATTTTAATATTATT
475 A
1 A
476 GGCAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTAATTTTAATATTATT
Found at i:466 original size:21 final size:19
Alignment explanation
Indices: 432--475 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
422 TTTTGTTTTA
432 ATTAAATTAATTTTAATATTT
1 ATTAAATTAATTTT-ATA-TT
* *
453 ATTAATTTATTTTTATATT
1 ATTAAATTAATTTTATATT
472 ATTA
1 ATTA
476 GGCAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTAAATTAATTTTATATT
Found at i:2604 original size:28 final size:30
Alignment explanation
Indices: 2533--2595 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
2523 CTAAATACTT
* * *
2533 AAAAAAATCCCTCATGTTTTTCGTTTTGGAC
1 AAAATAATCCCTTATGTTTTTC-TTTAGGAC
2564 AAAATAATCCCTTATGTTTTT-TTTAGGAC
1 AAAATAATCCCTTATGTTTTTCTTTAGGAC
2593 AAA
1 AAA
2596 TTACTCCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
31 19 0.66
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
AAAATAATCCCTTATGTTTTTCTTTAGGAC
Found at i:2611 original size:29 final size:28
Alignment explanation
Indices: 2556--2611 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
2546 ATGTTTTTCG
*
2556 TTTTGGACAAAATAATCCCTTATGTTTT
1 TTTTGGACAAAATAATCCCTTACGTTTT
* * *
2584 TTTTAGGACAAATTACTCCTTTACGTTT
1 TTTT-GGACAAAATAATCCCTTACGTTT
2612 CAAAAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (28 bp):
TTTTGGACAAAATAATCCCTTACGTTTT
Found at i:7792 original size:1 final size:1
Alignment explanation
Indices: 7786--7819 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
7776 CATTGTCCTT
7786 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7820 CTCAATTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7954 original size:12 final size:12
Alignment explanation
Indices: 7937--7969 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7927 ACTAATGATC
7937 TGAAAAATAATT
1 TGAAAAATAATT
*
7949 TGAAAAACAATT
1 TGAAAAATAATT
7961 T-AAAAATAA
1 TGAAAAATAA
7970 AAAGACATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (12 bp):
TGAAAAATAATT
Found at i:8305 original size:13 final size:13
Alignment explanation
Indices: 8287--8316 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
8277 GGCCCAACAA
8287 CAACAAAATACCC
1 CAACAAAATACCC
8300 CAACAAAATACCC
1 CAACAAAATACCC
8313 CAAC
1 CAAC
8317 CCCAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (13 bp):
CAACAAAATACCC
Done.