Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014087.1 Corchorus olitorius cultivar O-4 contig14120, 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: 10591
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:1108 original size:51 final size:50
Alignment explanation
Indices: 1007--1108 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
997 GTTCTTCATA
* **
1007 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
1057 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
1108 T
1 T
1109 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:2952 original size:15 final size:16
Alignment explanation
Indices: 2919--2952 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2909 GAAGAACAAC
*
2919 AAATACTTTTCTCGAAA
1 AAATACTTCTCTC-AAA
2936 AAATACTTCTCTCAAA
1 AAATACTTCTCTCAAA
2952 A
1 A
2953 TTGTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATACTTCTCTCAAA
Found at i:4501 original size:13 final size:13
Alignment explanation
Indices: 4483--4511 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4473 AGTGTCTCTC
4483 TTTTTTTT-TTCT
1 TTTTTTTTGTTCT
4495 TTTTTTTTGTTCT
1 TTTTTTTTGTTCT
4508 TTTT
1 TTTT
4512 GAATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (13 bp):
TTTTTTTTGTTCT
Found at i:6877 original size:18 final size:18
Alignment explanation
Indices: 6856--6907 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
6846 CTGCAAAATT
*
6856 AAGAAAAACACAAAAACA
1 AAGAAAAAAACAAAAACA
6874 AAGAAACAAAAC-AAAACA
1 AAGAAA-AAAACAAAAACA
6892 AA-AACAAAATACAAAA
1 AAGAA-AAAA-ACAAAA
6908 CTAAACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.17
18 17 0.59
19 7 0.24
ACGTcount: A:0.79, C:0.15, G:0.04, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAACAAAAACA
Found at i:6896 original size:24 final size:23
Alignment explanation
Indices: 6865--6913 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6855 TAAGAAAAAC
6865 ACAAAAACAAAGAAACAAAACAAA
1 ACAAAAACAAA-AAACAAAACAAA
* *
6889 ACAAAAACAAAATACAAAACTAA
1 ACAAAAACAAAAAACAAAACAAA
6912 AC
1 AC
6914 TAAACTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.76, C:0.18, G:0.02, T:0.04
Consensus pattern (23 bp):
ACAAAAACAAAAAACAAAACAAA
Found at i:8794 original size:15 final size:15
Alignment explanation
Indices: 8774--8812 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
8764 CCAGTAAGGT
8774 ACGGCATGGAACGGG
1 ACGGCATGGAACGGG
*
8789 ACGGCATGAAACGGG
1 ACGGCATGGAACGGG
*
8804 ACGGGATGG
1 ACGGCATGG
8813 GAGGTCCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.18, G:0.46, T:0.08
Consensus pattern (15 bp):
ACGGCATGGAACGGG
Found at i:9847 original size:13 final size:14
Alignment explanation
Indices: 9829--9861 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
9819 TACTATTTCT
9829 CAAAAAAAAA-AAA
1 CAAAAAAAAAGAAA
9842 CAAAAAAAAAGAAA
1 CAAAAAAAAAGAAA
9856 -AAAAAA
1 CAAAAAA
9862 CTTAATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAGAAA
Found at i:9848 original size:10 final size:10
Alignment explanation
Indices: 9833--9862 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
9823 ATTTCTCAAA
9833 AAAAAAAAAC
1 AAAAAAAAAC
*
9843 AAAAAAAAAG
1 AAAAAAAAAC
9853 AAAAAAAAAC
1 AAAAAAAAAC
9863 TTAATGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Done.