Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003301.1 Kokia drynarioides strain JFW-HI SEQ_115980, 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: 5133
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Found at i:1904 original size:13 final size:13
Alignment explanation
Indices: 1866--1909 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
1856 TTATGGGTGT
*
1866 TAATATATGATAAA
1 TAATATATTAT-AA
1880 TAATAGTATTATAA
1 TAATA-TATTATAA
1894 TAATATATTATAA
1 TAATATATTATAA
1907 TAA
1 TAA
1910 AAAAAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 12 0.43
15 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:4697 original size:16 final size:17
Alignment explanation
Indices: 4654--4697 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4644 ATATAATAAA
4654 TAAATTAAAA-AATATT
1 TAAATTAAAATAATATT
*
4670 TATATTAAAAATAAT-TT
1 TAAATT-AAAATAATATT
4687 TAAATTAAAAT
1 TAAATTAAAAT
4698 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTAAAATAATATT
Found at i:4704 original size:13 final size:13
Alignment explanation
Indices: 4682--4770 Score: 69
Period size: 13 Copynumber: 6.8 Consensus size: 13
4672 TATTAAAAAT
*
4682 AATTTTAAATTAA
1 AATTTAAAATTAA
4695 AATTTAAAATTTAA
1 AATTTAAAA-TTAA
4709 AATTTTAAAAAATT-A
1 AA-TTT--AAAATTAA
* *
4724 ACTTAAAAAATT-A
1 AATT-TAAAATTAA
4737 AA-TTAAAATTAA
1 AATTTAAAATTAA
*
4749 AAATTAAAATTAA
1 AATTTAAAATTAA
4762 AA-TTAAAAT
1 AATTTAAAAT
4771 CGAAGTTGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.09
12 11 0.17
13 28 0.44
14 8 0.12
15 5 0.08
16 2 0.03
17 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTTAAAATTAA
Found at i:4717 original size:8 final size:7
Alignment explanation
Indices: 4682--4770 Score: 57
Period size: 6 Copynumber: 13.4 Consensus size: 7
4672 TATTAAAAAT
*
4682 AATTTTA
1 AATTTAA
4689 AA-TTAA
1 AATTTAA
4695 AATTTAA
1 AATTTAA
4702 AATTTAA
1 AATTTAA
4709 AATTTTAAA
1 AA-TTT-AA
*
4718 AAATT-A
1 AATTTAA
* *
4724 ACTTAAA
1 AATTTAA
*
4731 AAATT-A
1 AATTTAA
4737 AA-TTAA
1 AATTTAA
4743 AA-TTAA
1 AATTTAA
*
4749 AAATTAA
1 AATTTAA
4756 AA-TTAA
1 AATTTAA
4762 AA-TTAA
1 AATTTAA
4768 AAT
1 AAT
4771 CGAAGTTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
5 2 0.03
6 32 0.48
7 24 0.36
8 5 0.07
9 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (7 bp):
AATTTAA
Found at i:4741 original size:18 final size:18
Alignment explanation
Indices: 4717--4769 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
4707 AAAATTTTAA
*
4717 AAAATTAACTTAAAAAATT
1 AAAATTAAATT-AAAAATT
4736 -AAATTAAAATTAAAAATT
1 AAAATT-AAATTAAAAATT
4754 AAAATTAAAATTAAAA
1 AAAATT-AAATTAAAA
4770 TCGAAGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTAAATTAAAAATT
Found at i:4747 original size:6 final size:6
Alignment explanation
Indices: 4730--4770 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
4720 ATTAACTTAA
4730 AAAATT -AAATT AAAATT AAAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT -AAAATT AAAATT AAAATT AAAAT
4771 CGAAGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:4887 original size:22 final size:22
Alignment explanation
Indices: 4862--4921 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
4852 AAGTTAAAAT
*
4862 TGAAATTCAAATTAATTTCAAA
1 TGAAATTCAAATTAAATTCAAA
*
4884 TGAACTTCAAATTAAATTCAAA
1 TGAAATTCAAATTAAATTCAAA
* *
4906 TGAAACTAAAATTAAA
1 TGAAATTCAAATTAAA
4922 ATTAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (22 bp):
TGAAATTCAAATTAAATTCAAA
Done.