Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000914.1 Kokia drynarioides strain JFW-HI SEQ_112055, 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: 5047
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2771 original size:6 final size:6
Alignment explanation
Indices: 2760--2811 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
2750 GGCCCAACAG
* * * *
2760 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
2806 AATTTA
1 AATTTA
2812 TTTAAATAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:2788 original size:17 final size:17
Alignment explanation
Indices: 2763--2805 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2753 CCAACAGAAT
2763 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
2780 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
2797 TTAAATTTA
1 TTAAATTTA
2806 AATTTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:2799 original size:23 final size:22
Alignment explanation
Indices: 2773--2818 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2763 TTAAATTTAT
*
2773 TTTAAAATTAAGTTTATTTTAAA
1 TTTAAAATTAAATTTA-TTTAAA
*
2796 TTTAAATTTAAATTTATTTAAA
1 TTTAAAATTAAATTTATTTAAA
2818 T
1 T
2819 AATATCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAAATTAAATTTATTTAAA
Found at i:2805 original size:12 final size:12
Alignment explanation
Indices: 2760--2811 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
2750 GGCCCAACAG
2760 AATTTAAATTT-
1 AATTTAAATTTA
* *
2771 ATTTTAAAATTA
1 AATTTAAATTTA
* *
2783 AGTTT-ATTTTA
1 AATTTAAATTTA
2794 AATTTAAATTTA
1 AATTTAAATTTA
2806 AATTTA
1 AATTTA
2812 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:3590 original size:3 final size:3
Alignment explanation
Indices: 3503--3574 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
3493 TTAATGACAT
3503 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3551 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3575 ATGATATCCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4555 original size:29 final size:29
Alignment explanation
Indices: 4506--4792 Score: 297
Period size: 29 Copynumber: 9.8 Consensus size: 29
4496 AGAGATCCCT
* *
4506 AAACTGTCCAAAAATTACATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* * * *
4536 GAGCTTCCAAAAATACCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
4565 AAACTTCAAAAAATTTCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
4594 AAACTTCCAAAAA-TCCTATTTTAACCCTA
1 AAACTTCCAAAAATTCC-ATTTTTACCCCA
* *
4623 AAAATTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
4653 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* ** *
4682 AAACTTCAAAAAATTCCATTTCGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
4711 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * * * *
4740 GAACCTCCAAAATTTCGATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
4770 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
4793 ACCATCGGAT
Statistics
Matches: 212, Mismatches: 40, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
28 2 0.01
29 154 0.73
30 50 0.24
31 6 0.03
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:4678 original size:88 final size:86
Alignment explanation
Indices: 4540--4783 Score: 308
Period size: 88 Copynumber: 2.8 Consensus size: 86
4530 ACCCCCGAGC
* * * *
4540 TTCCAAAAATACCATTTTTACCCCTAAACTTCAAAAAATTTCATTTTTACCCCTAAACTTCCAAA
1 TTCCAAAAATTCCATTTTTAACCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAA
*
4605 AATCCTATTTTAACCCTAAAAA
66 AATCC-ATTTCAACCCTAAAAA
*
4627 TTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAA
1 TTCCAAAAATTCCATTTTTAACCCT-AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAA
* *
4692 AAATTCCATTTCGACCCTAAAAC
65 AAA-TCCATTTCAACCCTAAAAA
* ** * * * * *
4715 TTCCAAAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCGATTTTTGACCCCGAAACTTTCAA
1 TTCCAAAAATTCCATTTTTAACCCTAAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAA
4780 AAAT
65 AAAT
4784 TACCATTTTA
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
87 43 0.31
88 91 0.66
89 3 0.02
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (86 bp):
TTCCAAAAATTCCATTTTTAACCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAA
AATCCATTTCAACCCTAAAAA
Found at i:4795 original size:117 final size:118
Alignment explanation
Indices: 4512--4792 Score: 338
Period size: 117 Copynumber: 2.4 Consensus size: 118
4502 CCCTAAACTG
* ** *
4512 TCCAAAAATTACATTTTT-ACCCCCGAGCTTCCAAAAA-TACCATTTTTACCCCTAAACTTCAAA
1 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTTACCCCTAAACTTCAAA
* ** * *
4575 AAATTTCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTAACCCTAAAAAT
66 AAATTCCATTTCGACCCCTAAACTTCCAAAAATCCTATTTTAACCCCAAAAAC
*
4628 TCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT-CCATTTTTACCCCTAAACTTCAAA
1 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTTACCCCTAAACTTCAAA
* ** *
4692 AAATTCCATTTCGA-CCCTAAAACTTCCAAAAATTCC-ATTTTTACCCCCGAACC
66 AAATTCCATTTCGACCCCT-AAACTTCCAAAAA-TCCTATTTTAACCCCAAAAAC
* * * * *
4745 TCCAAAATTTCGATTTTTGACCCCGAAACTTTCAAAAATTACCATTTT
1 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTT
4793 ACCATCGGAT
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
116 21 0.15
117 108 0.77
118 11 0.08
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (118 bp):
TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTTACCCCTAAACTTCAAA
AAATTCCATTTCGACCCCTAAACTTCCAAAAATCCTATTTTAACCCCAAAAAC
Done.