Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018037.1 Corchorus olitorius cultivar O-4 contig18070, 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: 27178
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:710 original size:18 final size:19
Alignment explanation
Indices: 675--712 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
665 GAGGGAACGG
*
675 TATATATTCTAATTCAATT
1 TATATATTCTAATGCAATT
694 TATATATT-TAATGCAATT
1 TATATATTCTAATGCAATT
712 T
1 T
713 TTATTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (19 bp):
TATATATTCTAATGCAATT
Found at i:6858 original size:20 final size:21
Alignment explanation
Indices: 6833--6872 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6823 TGCCAAAAAA
6833 AAATCAC-AAAAAAGTTTAAT
1 AAATCACTAAAAAAGTTTAAT
*
6853 AAATCACTAAAAGAGTTTAA
1 AAATCACTAAAAAAGTTTAA
6873 GATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (21 bp):
AAATCACTAAAAAAGTTTAAT
Found at i:6923 original size:21 final size:21
Alignment explanation
Indices: 6898--6970 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
6888 CTTACAAGAT
6898 TACTAAAATTTTAATAAAGGC
1 TACTAAAATTTTAATAAAGGC
* * *
6919 TACTAAAAATTGTAATAAGGGT
1 TACT-AAAATTTTAATAAAGGC
* *
6941 TACTAAAACGTTTAGT-AAGGC
1 TACTAAAA-TTTTAATAAAGGC
6962 TACTTAAAA
1 TAC-TAAAA
6971 GCTTATTAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 14 0.34
22 27 0.66
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.32
Consensus pattern (21 bp):
TACTAAAATTTTAATAAAGGC
Found at i:6934 original size:22 final size:22
Alignment explanation
Indices: 6898--6948 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6888 CTTACAAGAT
*
6898 TACT-AAAATTTTAATAAAGGC
1 TACTAAAAATTGTAATAAAGGC
* *
6919 TACTAAAAATTGTAATAAGGGT
1 TACTAAAAATTGTAATAAAGGC
6941 TACTAAAA
1 TACTAAAA
6949 CGTTTAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
TACTAAAAATTGTAATAAAGGC
Found at i:7293 original size:20 final size:21
Alignment explanation
Indices: 7252--7295 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
7242 TTACTAAAAA
*
7252 AAAACTTCATAAGGTTATTAT
1 AAAACTTCATAAGGTTACTAT
7273 AAAA-TTCATAA-GTTAACTAT
1 AAAACTTCATAAGGTT-ACTAT
7293 AAA
1 AAA
7296 TCTTACAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAACTTCATAAGGTTACTAT
Found at i:7463 original size:85 final size:86
Alignment explanation
Indices: 7360--7538 Score: 297
Period size: 85 Copynumber: 2.1 Consensus size: 86
7350 AGATCACTAA
* *
7360 AAAACTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTAAAGTTTAATGA
1 AAAATTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTAAAGTTTAAAGA
7425 AAAATTTATAAACTTACCAA-
66 AAAATTTATAAACTTACCAAG
* *
7445 AAATTTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAAGA
1 AAAATTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTAAAGTTTAAAGA
* *
7510 AAACTTTATAAGCTTACCAAG
66 AAAATTTATAAACTTACCAAG
7531 AAAATTTA
1 AAAATTTA
7539 CAAGGTTTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
85 79 0.92
86 7 0.08
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (86 bp):
AAAATTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTAAAGTTTAAAGA
AAAATTTATAAACTTACCAAG
Found at i:7588 original size:21 final size:20
Alignment explanation
Indices: 7564--7616 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
7554 GGTTTACCAG
*
7564 TTACAATAAAAGTTAAATAGT
1 TTACAA-AAAAGCTAAATAGT
* *
7585 TTACTAAAAAGCTAAATAAGA
1 TTACAAAAAAGCTAAAT-AGT
7606 TTACCAAAAAA
1 TTA-CAAAAAA
7617 TTTTCAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.38
21 10 0.38
22 6 0.23
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.26
Consensus pattern (20 bp):
TTACAAAAAAGCTAAATAGT
Found at i:7953 original size:21 final size:21
Alignment explanation
Indices: 7929--8000 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
7919 TAAAATCCAC
* *
7929 AATAAGATTACTAAAAATCTT
1 AATAAGGTTACTAAAAAACTT
*
7950 AATAAGGTTAGGTAAAAACACTT
1 AATAAGGTTA-CTAAAAA-ACTT
*
7973 AATAAGGTGACTAAAAAACTT
1 AATAAGGTTACTAAAAAACTT
*
7994 TATAAGG
1 AATAAGG
8001 CCAAAAAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
21 19 0.44
22 12 0.28
23 12 0.28
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (21 bp):
AATAAGGTTACTAAAAAACTT
Found at i:9441 original size:4 final size:4
Alignment explanation
Indices: 9432--9473 Score: 66
Period size: 4 Copynumber: 10.2 Consensus size: 4
9422 CACCATATAA
*
9432 TATT TATT TATT TATT TATT TATT TAATT TATT CATT TATT T
1 TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT T
9474 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:11626 original size:21 final size:22
Alignment explanation
Indices: 11582--11626 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11572 GGTATTGTAC
11582 AAATTGAATTTTTCTAAATAAA
1 AAATTGAATTTTTCTAAATAAA
11604 AAATTGAATTTTTCTAAATAAA
1 AAATTGAATTTTTCTAAATAAA
11626 A
1 A
11627 TATTTCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATTGAATTTTTCTAAATAAA
Found at i:13640 original size:29 final size:29
Alignment explanation
Indices: 13567--13645 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
13557 GGCTAAATAT
*
13567 CCAAATTGGGCCTAAACCTTTCACGATCTC
1 CCAAATTGGGCCTAAACCTTTCAC-ATCGC
*
13597 CGCAAATTGAGCCTAAACCTTT-AC-TCGGC
1 C-CAAATTGGGCCTAAACCTTTCACATC-GC
13626 ACCAAATTGGGCCTAAACCT
1 -CCAAATTGGGCCTAAACCT
13646 ATTCGAGGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 2 0.05
29 18 0.42
30 4 0.09
31 19 0.44
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
CCAAATTGGGCCTAAACCTTTCACATCGC
Found at i:13954 original size:20 final size:21
Alignment explanation
Indices: 13926--13969 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
13916 ACTTCATTCC
*
13926 ATTCCGTTTCTT-TTTTTTTT
1 ATTCCGTTTCTTCTTCTTTTT
*
13946 ATTCTGTTTCTTCTTCTTTTT
1 ATTCCGTTTCTTCTTCTTTTT
13967 ATT
1 ATT
13970 TCTTTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.73
Consensus pattern (21 bp):
ATTCCGTTTCTTCTTCTTTTT
Found at i:13966 original size:27 final size:27
Alignment explanation
Indices: 13933--13991 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
13923 TCCATTCCGT
* *
13933 TTCTTTTT-TTT-TTATTCTGTTTCTTC
1 TTCTTTTTATTTCTT-TTCTCTTTCGTC
13959 TTCTTTTTATTTCTTTTCTCTTTCGTC
1 TTCTTTTTATTTCTTTTCTCTTTCGTC
13986 TTCTTT
1 TTCTTT
13992 CTCTTCCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 19 0.66
28 2 0.07
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (27 bp):
TTCTTTTTATTTCTTTTCTCTTTCGTC
Found at i:15647 original size:25 final size:26
Alignment explanation
Indices: 15596--15647 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
15586 TAGGACCATT
*
15596 ACTAAAATCTATGACTTTTTTTAGGG
1 ACTAAAATCTATGACTTTTATTAGGG
15622 ACTAAAATCTATGA-TTTTGATT-GGG
1 ACTAAAATCTATGACTTTT-ATTAGGG
15647 A
1 A
15648 ATTATAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (26 bp):
ACTAAAATCTATGACTTTTATTAGGG
Done.