Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023708.1 Corchorus olitorius cultivar O-4 contig23741, 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: 39784
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3944 original size:27 final size:29
Alignment explanation
Indices: 3892--3955 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
3882 TGGCAAAACT
* * *
3892 GTAA-TTTAGTCAACCAAGGATAAAAT-G
1 GTAATTTTAGCCAACCAAGGAGAAAATAC
*
3919 GTAATTTTAGCCAACCAAGG-GCAAATAC
1 GTAATTTTAGCCAACCAAGGAGAAAATAC
3947 GTAATTTTA
1 GTAATTTTA
3956 ATATCCTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
GTAATTTTAGCCAACCAAGGAGAAAATAC
Found at i:4926 original size:35 final size:35
Alignment explanation
Indices: 4851--4933 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 35
4841 CCATGCTTGA
4851 GCGCTGGGCCATGGCTGGCCCGCACGCCAGGCCTGG
1 GCGCTGGGCCATGGCTGGCCCG-ACGCCAGGCCTGG
*
4887 GCGCTGGGCCATGTGCTGGCCCG-CGCCTGGCCTGG
1 GCGCTGGGCCATG-GCTGGCCCGACGCCAGGCCTGG
4922 GCGCTTGGGCCA
1 GCGC-TGGGCCA
4934 CGCCAGGCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 15 0.34
36 20 0.45
37 9 0.20
ACGTcount: A:0.06, C:0.37, G:0.42, T:0.14
Consensus pattern (35 bp):
GCGCTGGGCCATGGCTGGCCCGACGCCAGGCCTGG
Found at i:4991 original size:13 final size:13
Alignment explanation
Indices: 4973--4997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4963 CTCATCTTTT
4973 TTTTTTTTTTTCG
1 TTTTTTTTTTTCG
4986 TTTTTTTTTTTC
1 TTTTTTTTTTTC
4998 TTCTTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTCG
Found at i:5007 original size:12 final size:12
Alignment explanation
Indices: 4992--5018 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4982 TTCGTTTTTT
4992 TTTTTCTTCTTC
1 TTTTTCTTCTTC
5004 TTTTTCTTCTTC
1 TTTTTCTTCTTC
5016 TTT
1 TTT
5019 CCTTCCGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:5007 original size:15 final size:15
Alignment explanation
Indices: 4973--5017 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4963 CTCATCTTTT
* *
4973 TTTTTTTTTTTCGTTT
1 TTTTTTTTCTTC-TTC
4989 TTTTTTTTCTTCTTC
1 TTTTTTTTCTTCTTC
*
5004 TTTTTCTTCTTCTT
1 TTTTTTTTCTTCTT
5018 TCCTTCCGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTCTTCTTC
Found at i:6877 original size:21 final size:22
Alignment explanation
Indices: 6831--6877 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6821 TTCACTTTTG
* *
6831 AAATTAATATATTAATTTATCT
1 AAATTAATAAATTAATTTATCC
6853 AAATTAA-AAATTAA-TTATTCC
1 AAATTAATAAATTAATTTA-TCC
6874 AAAT
1 AAAT
6878 GAGATGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 12 0.55
22 7 0.32
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTAATAAATTAATTTATCC
Found at i:7085 original size:2 final size:2
Alignment explanation
Indices: 7078--7105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7068 AGCCATGAGC
7078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7106 GCCATCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7724 original size:40 final size:40
Alignment explanation
Indices: 7679--7764 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
7669 TGCCTGGCGT
* *
7679 GGCCCAAGCGTGTCAGGCCAAGCACGCTGGGCCAGCGCGC
1 GGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCAGCGCGC
* * *
7719 GGCCCAGGCGCGCCAGGCCAGGCGCGCTGGGCCAGCGCGC
1 GGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCAGCGCGC
7759 GGCCCA
1 GGCCCA
7765 GCTGGCTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.14, C:0.41, G:0.41, T:0.05
Consensus pattern (40 bp):
GGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCAGCGCGC
Found at i:14642 original size:2 final size:2
Alignment explanation
Indices: 14635--14675 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
14625 ATCCCTTCAT
14635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14676 AACACATGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14823 original size:2 final size:2
Alignment explanation
Indices: 14816--14847 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
14806 TATCTTCATA
*
14816 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14848 CTCAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17522 original size:1 final size:1
Alignment explanation
Indices: 17516--17540 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17506 CATGTAAGAC
17516 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17541 CTTGTTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22012 original size:24 final size:25
Alignment explanation
Indices: 21966--22016 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
21956 ATTGGAGTAT
*
21966 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
21991 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
22015 TT
1 TT
22017 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:25188 original size:30 final size:30
Alignment explanation
Indices: 25152--25210 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
25142 ATTTTATTAA
25152 TTTCCAAAACCTTCTTTTGGATTTCTTTAT
1 TTTCCAAAACCTTCTTTTGGATTTCTTTAT
* *
25182 TTTCCAAAATCTTCTTTTGGATTTGTTTA
1 TTTCCAAAACCTTCTTTTGGATTTCTTTA
25211 AGAAAAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTCCAAAACCTTCTTTTGGATTTCTTTAT
Found at i:29513 original size:21 final size:21
Alignment explanation
Indices: 29475--29514 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29465 GGGGCCCACC
* *
29475 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
29496 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
29515 GGTAGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:30590 original size:12 final size:12
Alignment explanation
Indices: 30551--30589 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
30541 GTTACTAACC
30551 TTTTTTTATTTA
1 TTTTTTTATTTA
*
30563 TTATTTTATTTA
1 TTTTTTTATTTA
*
30575 TTTATTTATTT-
1 TTTTTTTATTTA
30586 TTTT
1 TTTT
30590 AGAGTGACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:32972 original size:17 final size:19
Alignment explanation
Indices: 32946--32993 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
32936 AGAAGAAAAA
32946 TGAA-ATGGGTTTGG-G-T
1 TGAAGATGGGTTTGGAGAT
32962 TGAAGATGGGTTTTGGAGAAT
1 TGAAGATGGG-TTTGGAG-AT
32983 TGAAGATGGGT
1 TGAAGATGGGT
32994 GATGAGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 5 0.19
19 1 0.04
20 1 0.04
21 11 0.41
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (19 bp):
TGAAGATGGGTTTGGAGAT
Done.