Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018208.1 Corchorus olitorius cultivar O-4 contig18241, 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: 11218
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:6774 original size:12 final size:12
Alignment explanation
Indices: 6757--6781 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6747 CACAACATAA
6757 GAAGCAAAATTT
1 GAAGCAAAATTT
6769 GAAGCAAAATTT
1 GAAGCAAAATTT
6781 G
1 G
6782 GTTGAGAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAGCAAAATTT
Found at i:6892 original size:22 final size:23
Alignment explanation
Indices: 6862--6915 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
6852 GTCGACAAGT
*
6862 GGAAG-AAAAATTGTCGA-TTAA
1 GGAAGCAAAAATAGTCGATTTAA
*
6883 GGAAGCAAAACTAGTCGATTTAA
1 GGAAGCAAAAATAGTCGATTTAA
6906 GGAAGCAAAA
1 GGAAGCAAAA
6916 CCATCGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.17
22 10 0.34
23 14 0.48
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.19
Consensus pattern (23 bp):
GGAAGCAAAAATAGTCGATTTAA
Found at i:6909 original size:23 final size:22
Alignment explanation
Indices: 6874--6916 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
6864 AAGAAAAATT
6874 GTCGATTAAGGAAGCAAAACTA
1 GTCGATTAAGGAAGCAAAACTA
6896 GTCGATTTAAGGAAGCAAAAC
1 GTCGA-TTAAGGAAGCAAAAC
6917 CATCGACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (22 bp):
GTCGATTAAGGAAGCAAAACTA
Found at i:6922 original size:22 final size:22
Alignment explanation
Indices: 6874--6922 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
6864 AAGAAAAATT
*
6874 GTCGATTAAGGAAGCAAAACTA
1 GTCGATTAAGGAAGCAAAACCA
6896 GTCGATTTAAGGAAGCAAAACCA
1 GTCGA-TTAAGGAAGCAAAACCA
6919 -TCGA
1 GTCGA
6923 CCATAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.18
Consensus pattern (22 bp):
GTCGATTAAGGAAGCAAAACCA
Found at i:6929 original size:23 final size:23
Alignment explanation
Indices: 6880--6929 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6870 AATTGTCGAT
* **
6880 TAAGGAAGCAAAACTAGTCGATT
1 TAAGGAAGCAAAACCAGTCGACA
6903 TAAGGAAGCAAAACCA-TCGACCA
1 TAAGGAAGCAAAACCAGTCGA-CA
6926 TAAG
1 TAAG
6930 AGGCAATTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (23 bp):
TAAGGAAGCAAAACCAGTCGACA
Found at i:7932 original size:30 final size:29
Alignment explanation
Indices: 7887--7943 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
7877 TTAGGATTAG
7887 TTATCTATGTTTTAATTTTCAA-TTTCCT
1 TTATCTATGTTTTAATTTTCAAGTTTCCT
7915 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTATC-TATGT-TTTAATTTTCAAGTTTC
7944 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 5 0.19
30 12 0.46
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATCTATGTTTTAATTTTCAAGTTTCCT
Found at i:9003 original size:15 final size:15
Alignment explanation
Indices: 8983--9012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8973 GAATGGTAAG
8983 TGATTAAAGCTACTT
1 TGATTAAAGCTACTT
*
8998 TGATTATAGCTACTT
1 TGATTAAAGCTACTT
9013 AAGAATGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (15 bp):
TGATTAAAGCTACTT
Found at i:9479 original size:18 final size:19
Alignment explanation
Indices: 9445--9482 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9435 TCAAGACTTA
9445 TTGAAGACAATTTGAAGAT
1 TTGAAGACAATTTGAAGAT
*
9464 TTGAAGACCA-TTGAAGAT
1 TTGAAGACAATTTGAAGAT
9482 T
1 T
9483 AATTTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (19 bp):
TTGAAGACAATTTGAAGAT
Found at i:10916 original size:19 final size:18
Alignment explanation
Indices: 10892--10927 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10882 TCAAGACTTA
10892 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10911 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10928 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.