Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007344.1 Corchorus capsularis cultivar CVL-1 contig07365, 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: 56741
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7660 original size:12 final size:12
Alignment explanation
Indices: 7643--7684 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
7633 GCAAAAAGCC
7643 CTGCTGCCGCCG
1 CTGCTGCCGCCG
7655 CTGCTGCCGCCG
1 CTGCTGCCGCCG
7667 CTGCTGCCGCCG
1 CTGCTGCCGCCG
7679 CTGCTG
1 CTGCTG
7685 GTGGGTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.00, C:0.48, G:0.33, T:0.19
Consensus pattern (12 bp):
CTGCTGCCGCCG
Found at i:20425 original size:3 final size:3
Alignment explanation
Indices: 20370--20409 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20360 GCCGCCCTGC
20370 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20410 AATTTGTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28254 original size:17 final size:17
Alignment explanation
Indices: 28232--28267 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
28222 TAAAAAATAA
28232 AAAGAAG-AAGAAAGGAG
1 AAAGAAGAAAGAAA-GAG
28249 AAAGAAGAAAGAAAGAG
1 AAAGAAGAAAGAAAGAG
28266 AA
1 AA
28268 CCATGGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAGAAAGAG
Found at i:34741 original size:6 final size:6
Alignment explanation
Indices: 34730--34759 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
34720 CACGCTTTTC
34730 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
34760 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:46129 original size:7 final size:7
Alignment explanation
Indices: 46117--46141 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
46107 TTAAAAAATT
46117 ACATTAA
1 ACATTAA
46124 ACATTAA
1 ACATTAA
46131 ACATTAA
1 ACATTAA
46138 ACAT
1 ACAT
46142 AGTCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATTAA
Found at i:47574 original size:23 final size:23
Alignment explanation
Indices: 47548--47591 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
47538 ATTTAAACTT
47548 TTATAGTTTTACTTAACTAAAAA
1 TTATAGTTTTACTTAACTAAAAA
* * *
47571 TTATATTTTTATTTAATTAAA
1 TTATAGTTTTACTTAACTAAA
47592 TCCAATATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAGTTTTACTTAACTAAAAA
Found at i:48320 original size:2 final size:2
Alignment explanation
Indices: 48308--48342 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
48298 TGAAGACTAG
*
48308 TA TA TA CA TA 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 TA TA TA TA TA T
48343 TACACACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:52255 original size:31 final size:31
Alignment explanation
Indices: 52220--52313 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
52210 GGACGAAATA
52220 AAAGGTTTGATACTAAGTAAGTATCAAACAT
1 AAAGGTTTGATACTAAGTAAGTATCAAACAT
* * * *
52251 AAAGGTTTGGTAC-CA--AA-T-T--GAGAT
1 AAAGGTTTGATACTAAGTAAGTATCAAACAT
52275 -AAGGTTTGATACTAAGTAAGTATCAAACAT
1 AAAGGTTTGATACTAAGTAAGTATCAAACAT
52305 AAAGGTTTG
1 AAAGGTTTG
52314 GTACCAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
23 11 0.23
24 4 0.09
26 3 0.06
27 2 0.04
28 3 0.06
30 4 0.09
31 20 0.43
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (31 bp):
AAAGGTTTGATACTAAGTAAGTATCAAACAT
Found at i:52303 original size:54 final size:54
Alignment explanation
Indices: 52221--52328 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
52211 GACGAAATAA
52221 AAGGTTTGATACTAAGTAAGTATCAAACATAAAGGTTTGGTACCAAATTGAGAT
1 AAGGTTTGATACTAAGTAAGTATCAAACATAAAGGTTTGGTACCAAATTGAGAT
52275 AAGGTTTGATACTAAGTAAGTATCAAACATAAAGGTTTGGTACCAAATTGAGAT
1 AAGGTTTGATACTAAGTAAGTATCAAACATAAAGGTTTGGTACCAAATTGAGAT
52329 TTCAGCCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (54 bp):
AAGGTTTGATACTAAGTAAGTATCAAACATAAAGGTTTGGTACCAAATTGAGAT
Found at i:53570 original size:34 final size:34
Alignment explanation
Indices: 53522--53592 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
53512 CGATTTTGAC
** *
53522 ATATGGGAATAAGATGATTTTAAAGATGAAGGAT
1 ATATGGGAATAAGATGATTGCAAAGATAAAGGAT
* *
53556 ATATTGGAATAAGATGATTGCAAAGATAAAGGGT
1 ATATGGGAATAAGATGATTGCAAAGATAAAGGAT
53590 ATA
1 ATA
53593 CAAACAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.01, G:0.25, T:0.28
Consensus pattern (34 bp):
ATATGGGAATAAGATGATTGCAAAGATAAAGGAT
Found at i:56415 original size:2 final size:2
Alignment explanation
Indices: 56403--56502 Score: 51
Period size: 2 Copynumber: 54.5 Consensus size: 2
56393 AATAAATTAT
* *
56403 TA TA AA TA TA TA TA -A TA TA TA TA -A TA -A TA TA TA GA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
56440 TA AA TA AA TA T- TA TA TA TA T- TA CTA TA TC TGA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA
*
56481 TA -A TA TA TT TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
56503 TAATAAACGG
Statistics
Matches: 74, Mismatches: 11, Indels: 26
0.67 0.10 0.23
Matches are distributed among these distances:
1 11 0.15
2 60 0.81
3 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56488 original size:33 final size:33
Alignment explanation
Indices: 56408--56501 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
56398 ATTATTATAA
56408 ATATATATAATATATATAATAATATATAGAATT
1 ATATATATAATATATATAATAATATATAGAATT
* * * * * *
56441 AAATAAATATTATATATATTACTATATCTG-ATT
1 ATATATATAATATATATAATAATATAT-AGAATT
* *
56474 ATATATATAATATATTTAATTATATATA
1 ATATATATAATATATATAATAATATATA
56502 TTAATAAACG
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (33 bp):
ATATATATAATATATATAATAATATATAGAATT
Done.