Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014006.1 Corchorus olitorius cultivar O-4 contig14039, 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: 18931
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:10812 original size:19 final size:19
Alignment explanation
Indices: 10790--10840 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
10780 GGGCTGAAAT
10790 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
10809 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
10828 TAATT-ATTATTAA
1 TAATTAATTATTAA
10841 AAATAGCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:10845 original size:16 final size:16
Alignment explanation
Indices: 10794--10845 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
10784 TGAAATTAAT
10794 TAATTATTAATTAAATAA
1 TAATTATT-ATTAAA-AA
**
10812 TAATTATT-TTATTGAA
1 TAATTATTATTA-AAAA
10828 TAATTATTATTAAAAA
1 TAATTATTATTAAAAA
10844 TA
1 TA
10846 GCACATGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 17 0.61
17 3 0.11
18 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTATTATTAAAAA
Found at i:18305 original size:61 final size:60
Alignment explanation
Indices: 18239--18399 Score: 164
Period size: 62 Copynumber: 2.6 Consensus size: 60
18229 GCTAATTGCT
* * * * *
18239 CAAATAAGGGTCTAA-TATTTGTCAAAATGCTCAAATGAGAACCTGATCTTTTAATTTGGC
1 CAAATAAGGGACTAACT-TTTGCCAAAATACTCAAATAAGAACATGATCTTTTAATTTGGC
* * **
18299 CAAAATAAGAGCCTAACGTTTTGCCAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGC
1 C-AAATAAGGGACTAAC-TTTTGCCAAAATACTCAAATAAGAACATGATCTTTTAATTTGGC
* * *
18361 CAAATAAGGGACTAACGTTAT-CGAAAATGCTCAAATAAG
1 CAAATAAGGGACTAAC-TTTTGCCAAAATACTCAAATAAG
18400 GGCCTAGCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
60 17 0.20
61 29 0.34
62 38 0.45
63 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGACTAACTTTTGCCAAAATACTCAAATAAGAACATGATCTTTTAATTTGGC
Found at i:18327 original size:62 final size:61
Alignment explanation
Indices: 18256--18399 Score: 182
Period size: 62 Copynumber: 2.4 Consensus size: 61
18246 GGGTCTAATA
* * * *
18256 TTTGTCAAAATGCTCAAATGAGAACCTGATCTTTTAATTTGGCCAAAATAAGAGCCTAACGT
1 TTTGCCAAAATGCTCAAATAAGAACATGATCTTTTAATTTGGCC-AAATAAGAGACTAACGT
* ** *
18318 TTTGCCAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGCCAAATAAGGGACTAACGT
1 TTTGCCAAAATGCTCAAATAAGAACATGATCTTTTAATTTGGCCAAATAAGAGACTAACGT
* *
18379 TAT-CGAAAATGCTCAAATAAG
1 TTTGCCAAAATGCTCAAATAAG
18400 GGCCTAGCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 16 0.23
61 17 0.24
62 38 0.54
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (61 bp):
TTTGCCAAAATGCTCAAATAAGAACATGATCTTTTAATTTGGCCAAATAAGAGACTAACGT
Found at i:18540 original size:60 final size:60
Alignment explanation
Indices: 18447--18583 Score: 202
Period size: 60 Copynumber: 2.3 Consensus size: 60
18437 AATGTCAGGC
* * *
18447 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCGGGT
1 CCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAGAT
* * * *
18507 CCTTATTTGAGTATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTATAAGATCAGAT
1 CCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAGAT
*
18567 CATTATTTGAGCATTTT
1 CCTTATTTGAGCATTTT
18584 GGCAAACGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAGAT
Found at i:18545 original size:31 final size:31
Alignment explanation
Indices: 18426--18546 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 31
18416 GGATGACACG
*
18426 TGAGAATTTTCAAT---GTCAGGCCCTTATT
1 TGAGAATTTTCAATAACGTTAGGCCCTTATT
* *
18454 TGAGCATTTTCGATAACGTTAGGCCCTTATT
1 TGAGAATTTTCAATAACGTTAGGCCCTTATT
* * ** * * *
18485 TGGACAAATTAAAAGACCG---GGTCCTTATT
1 T-GAGAATTTTCAATAACGTTAGGCCCTTATT
*
18514 TGAGTATTTTCAATAACGTTAGGCCCTTATT
1 TGAGAATTTTCAATAACGTTAGGCCCTTATT
18545 TG
1 TG
18547 GCCAAATTAT
Statistics
Matches: 66, Mismatches: 20, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
28 22 0.33
29 10 0.15
31 25 0.38
32 9 0.14
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (31 bp):
TGAGAATTTTCAATAACGTTAGGCCCTTATT
Found at i:18698 original size:21 final size:21
Alignment explanation
Indices: 18672--18712 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18662 AAGAAGGGTA
*
18672 TTACTAAATACCGCCCCCTTT
1 TTACTAAACACCGCCCCCTTT
**
18693 TTACTAGCCACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
18713 GGATTATTTT
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:0.20, C:0.44, G:0.07, T:0.29
Consensus pattern (21 bp):
TTACTAAACACCGCCCCCTTT
Done.