Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017008.1 Corchorus olitorius cultivar O-4 contig17041, 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: 28895
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3914 original size:2 final size:2
Alignment explanation
Indices: 3902--3942 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
3892 GGGTTCTGAA
*
3902 AT AT A- AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
3943 AGTCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4572 original size:26 final size:27
Alignment explanation
Indices: 4543--4593 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
4533 CAAATTAATT
4543 ATCATTAAATTTTAAACAC-TTAAAAA
1 ATCATTAAATTTTAAACACATTAAAAA
4569 ATCATTAAATTTTAAACACATTAAA
1 ATCATTAAATTTTAAACACATTAAA
4594 TTATAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATCATTAAATTTTAAACACATTAAAAA
Found at i:4592 original size:16 final size:16
Alignment explanation
Indices: 4545--4595 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
4535 AATTAATTAT
4545 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
*
4561 C-TTAAA----AAA-T
1 CATTAAATTTTAAACA
4571 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
4587 CATTAAATT
1 CATTAAATT
4596 ATAGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
15 8 0.30
16 10 0.37
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
CATTAAATTTTAAACA
Found at i:5118 original size:23 final size:24
Alignment explanation
Indices: 5071--5119 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
5061 GTCTTTCTAC
5071 TTTTTTACTTCAATTTAGTCACAAT
1 TTTTTTACTTCAATTTAGT-ACAAT
*
5096 TTTTTTACTTCCATTTAGT-CAAT
1 TTTTTTACTTCAATTTAGTACAAT
5119 T
1 T
5120 GAGAGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
25 18 0.78
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTTTACTTCAATTTAGTACAAT
Found at i:8939 original size:129 final size:134
Alignment explanation
Indices: 8775--9030 Score: 335
Period size: 135 Copynumber: 1.9 Consensus size: 134
8765 CTTCAAAAAC
* * * *
8775 CTTAATTTGAAATATATAAAACACCAATTTTAATATTAAACATTAGTTTTAACCTTT-G-GTT-G
1 CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAGAGTTAA
* * *
8837 T-TA-GTAGTTTAATATACCAATCTAAAATATATTAAATATAGCAAATA-TCTTTAAAATACCAT
66 TATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAA-AGTATTTAAAATACCAT
8899 ATAAA
130 ATAAA
* * ** *
8904 CTTAATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCTTTAGTAGTTA
1 CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAG-AGTTA
*
8969 ATATATATAATTTAATATATCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
65 ATATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
9031 GTGCAATGCA
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
129 49 0.46
130 1 0.01
132 3 0.03
133 1 0.01
134 3 0.03
135 50 0.47
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (134 bp):
CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAGAGTTAA
TATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATACCATA
TAAA
Found at i:17487 original size:29 final size:29
Alignment explanation
Indices: 17429--17487 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
17419 ACTTGTACAG
* * *
17429 TTTAATTTTGGACGCTTTGCCCCTTGAAC
1 TTTAATTTTGAACGCTTTGCCCCATAAAC
* *
17458 TTTAATTTTGAACGTTTTGTCCCATAAAC
1 TTTAATTTTGAACGCTTTGCCCCATAAAC
17487 T
1 T
17488 CTCAATTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTAATTTTGAACGCTTTGCCCCATAAAC
Found at i:17520 original size:18 final size:18
Alignment explanation
Indices: 17497--17532 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17487 TCTCAATTTG
17497 GACGTTGTAGTCCCTCTC
1 GACGTTGTAGTCCCTCTC
* *
17515 GACGTTTTAGTCTCTCTC
1 GACGTTGTAGTCCCTCTC
17533 AGACATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.39
Consensus pattern (18 bp):
GACGTTGTAGTCCCTCTC
Done.