Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016850.1 Corchorus olitorius cultivar O-4 contig16883, 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: 18276
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:501 original size:58 final size:57
Alignment explanation
Indices: 392--573 Score: 231
Period size: 58 Copynumber: 3.1 Consensus size: 57
382 GACTTTCAAT
*
392 CAGAGACCTC-AATCAGGATTTTAAAACAAGACAAGATTTGAATTGAAAACTCTCTAC
1 CAGAGACCTCGAA-CAGGATTTTAAAACAAGATAAGATTTGAATTGAAAACTCTCTAC
* * *
449 CAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTGGATTGGAAACTCTTTAC
1 CAGAGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTGAATTGAAAACTCTCTAC
* * *
507 CAGAAACCTCGAACAGGATTTTTTTTAAAATAAGATAAGATTTTGAATTGAAAACTCACTAC
1 CAGAGACCTCGAACAGGA----TTTTAAAACAAGATAAGA-TTTGAATTGAAAACTCTCTAC
569 CAGAG
1 CAGAG
574 TTGATTCCAA
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
57 19 0.18
58 50 0.47
61 13 0.12
62 25 0.23
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (57 bp):
CAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTGAATTGAAAACTCTCTAC
Found at i:11809 original size:59 final size:59
Alignment explanation
Indices: 11584--11960 Score: 513
Period size: 58 Copynumber: 6.5 Consensus size: 59
11574 ACTTTCAATT
*
11584 AGAGACCTC-AATCAGGATTTT-AAAACAAGACAAGA-TTTGAATTGAAAACTCTCTACC
1 AGAGACCTCGAA-CAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
* *
11641 AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGA-TTTGAATTGGAAACTCTTTACC
1 AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
** * * *
11699 AGAGACCTTTAATAGGATTTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCACTATC
1 AGAGACCTCGAACAGGA---TTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
*
11761 AGAGACCTCGAGCAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
1 AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
* ** *
11820 AGAGACCTCAAACAGGATTTT-AATGCAAGATAAGATTTTGAATTGAAAACTCTCTACT
1 AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
*
11878 AGAGACCTCGAACAAGATTTT----A-AAGATAAGATTTTGAATTGAAAACTCTCTACC
1 AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
*
11932 AGAGACCTCGAACAGGATTTTAACAACAA
1 AGAGACCTCGAACAGGATTTTAAAAACAA
11961 AAAAAGGGGA
Statistics
Matches: 283, Mismatches: 26, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
54 51 0.18
57 18 0.06
58 103 0.36
59 61 0.22
61 19 0.07
62 31 0.11
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (59 bp):
AGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACC
Found at i:11884 original size:179 final size:170
Alignment explanation
Indices: 11584--11960 Score: 499
Period size: 179 Copynumber: 2.2 Consensus size: 170
11574 ACTTTCAATT
11584 AGAGACCTC-AATCAGGATTTT-AAAACAAGACAAGATTTGAATTGAAAACTCTCTACCAGAGAC
1 AGAGACCTCGAA-CAGGATTTTAAAAACAAGACAAGATTTGAATTGAAAACTCTCTACCAGAGAC
* * * ** *
11647 CTCGAACAGGATTTTAAAAACAAGATAAGATTTGAATTGGAAACTCTTTACCAGAGACCTTTAAT
65 CTCAAACAGGATTTTAAAAACAAGATAAGATTTGAATTGAAAACTCTCTACCAGAGACCTCGAAC
* *
11712 AGGATTTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCACTATC
130 AAGA---TTTT----A-AAGATAAGATTTTGAATTGAAAACTCACTACC
* *
11761 AGAGACCTCGAGCAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGAC
1 AGAGACCTCGAACAGGATTTTAAAAACAAGACAAGA-TTTGAATTGAAAACTCTCTACCAGAGAC
** *
11826 CTCAAACAGGATTTT-AATGCAAGATAAGATTTTGAATTGAAAACTCTCTACTAGAGACCTCGAA
65 CTCAAACAGGATTTTAAAAACAAGATAAGA-TTTGAATTGAAAACTCTCTACCAGAGACCTCGAA
*
11890 CAAGATTTTAAAGATAAGATTTTGAATTGAAAACTCTCTACC
129 CAAGATTTTAAAGATAAGATTTTGAATTGAAAACTCACTACC
*
11932 AGAGACCTCGAACAGGATTTTAACAACAA
1 AGAGACCTCGAACAGGATTTTAAAAACAA
11961 AAAAAGGGGA
Statistics
Matches: 180, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
171 57 0.32
172 1 0.01
176 4 0.02
177 18 0.10
178 26 0.14
179 74 0.41
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (170 bp):
AGAGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTGAATTGAAAACTCTCTACCAGAGACC
TCAAACAGGATTTTAAAAACAAGATAAGATTTGAATTGAAAACTCTCTACCAGAGACCTCGAACA
AGATTTTAAAGATAAGATTTTGAATTGAAAACTCACTACC
Found at i:12832 original size:38 final size:37
Alignment explanation
Indices: 12790--12904 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
12780 TTTTTATTTA
* * * *
12790 TTTCTTTTTCTGACCTCTTCCTGTTTTAAGCCCAGTTT
1 TTTCTTTTTC-GACCTCTTTCTATTTTAGGTCCAGTTT
*
12828 TTTCTTTTCCGACCTCTTTCTATTTTAGGTCCAGTTT
1 TTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTT
12865 TTAT-TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTT
1 TT-TCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTT
12902 TTT
1 TTT
12905 TTTAGCTCCT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
36 1 0.01
37 59 0.84
38 10 0.14
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.56
Consensus pattern (37 bp):
TTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTT
Found at i:12869 original size:18 final size:18
Alignment explanation
Indices: 12848--12909 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
12838 GACCTCTTTC
12848 TATTTTAGGTCCAGTTTT
1 TATTTTAGGTCCAGTTTT
** * ** *
12866 TATTTTTTCGACCTCTTTC
1 TA-TTTTAGGTCCAGTTTT
12885 TATTTTAGGTCCAGTTTT
1 TATTTTAGGTCCAGTTTT
12903 T-TTTTAG
1 TATTTTAG
12910 CTCCTTTTAG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
17 6 0.19
18 13 0.42
19 12 0.39
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.58
Consensus pattern (18 bp):
TATTTTAGGTCCAGTTTT
Found at i:17583 original size:15 final size:15
Alignment explanation
Indices: 17563--17592 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17553 TCAAAACCTA
17563 GAAAATATTTTCCCT
1 GAAAATATTTTCCCT
17578 GAAAATATTTTCCCT
1 GAAAATATTTTCCCT
17593 TTTAATTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
GAAAATATTTTCCCT
Found at i:17671 original size:17 final size:17
Alignment explanation
Indices: 17641--17683 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
17631 CATCCAATTT
* * *
17641 ATTTGGTAGGCATTTTA
1 ATTTGTTAGACATTTAA
17658 ATTTGTTAGACATTTAA
1 ATTTGTTAGACATTTAA
*
17675 ATTTATTAG
1 ATTTGTTAG
17684 TTTCGCATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (17 bp):
ATTTGTTAGACATTTAA
Done.