Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001780.1 Kokia drynarioides strain JFW-HI SEQ_113506, 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: 13262
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:40 original size:4 final size:4
Alignment explanation
Indices: 20--98 Score: 63
Period size: 4 Copynumber: 19.5 Consensus size: 4
10 AACACATTAC
* * * *
20 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CTTT CCTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT
* *
68 CCTT CTTC CTTT CTTT CCTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CT
99 CGTTTATTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
3 6 0.10
4 44 0.73
5 10 0.17
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (4 bp):
CTTT
Found at i:52 original size:20 final size:20
Alignment explanation
Indices: 27--86 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
17 TACCTTTCTT
27 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
47 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
67 TCCTTCTTCCTTTCTTTCCT
1 TCCTTCTT-CTTTCTTTCCT
87 TTCTTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
20 28 0.72
21 11 0.28
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:54 original size:17 final size:17
Alignment explanation
Indices: 20--97 Score: 81
Period size: 17 Copynumber: 4.5 Consensus size: 17
10 AACACATTAC
20 CTTTCTTTCCT-T-CTT
1 CTTTCTTTCCTCTCCTT
35 CTTTCTTTCCTCTCCTTCTT
1 CTTTCTTTCCTCT-C--CTT
55 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTCTCCTT
* *
72 CTTCCTTT-CTTTCCTTT
1 CTTTCTTTCCTCTCC-TT
89 CTTTCTTTC
1 CTTTCTTTC
98 TCGTTTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
15 11 0.21
16 6 0.11
17 19 0.36
19 1 0.02
20 16 0.30
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTCTTTCCTCTCCTT
Found at i:98 original size:17 final size:19
Alignment explanation
Indices: 20--84 Score: 94
Period size: 20 Copynumber: 3.3 Consensus size: 19
10 AACACATTAC
*
20 CTTTCTTTCCTTCTTCTTT
1 CTTTCTCTCCTTCTTCTTT
39 CTTTCCTCTCCTTCTTCTTT
1 CTTT-CTCTCCTTCTTCTTT
59 CTTTCCTCTCCTTCTTCCTTT
1 CTTT-CTCTCCTTCTT-CTTT
80 CTTTC
1 CTTTC
85 CTTTCTTTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
19 4 0.09
20 31 0.72
21 8 0.19
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
CTTTCTCTCCTTCTTCTTT
Found at i:302 original size:27 final size:27
Alignment explanation
Indices: 271--325 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
261 ACACCCCTTA
271 GTGCCGCCACTT-GATATTCCTCCATTG
1 GTGCCGCCACTTCG-TATTCCTCCATTG
*
298 GTGCCGCCACTTCGTGTTCCTCCATTG
1 GTGCCGCCACTTCGTATTCCTCCATTG
325 G
1 G
326 GTGTCAGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.11, C:0.35, G:0.22, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTCGTATTCCTCCATTG
Found at i:1661 original size:22 final size:22
Alignment explanation
Indices: 1633--1677 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1623 TTATATTTAC
1633 TATATATAATATTGAATAAGCA
1 TATATATAATATTGAATAAGCA
* *
1655 TATATATATTCTTGAATAAGCA
1 TATATATAATATTGAATAAGCA
1677 T
1 T
1678 GTGCTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TATATATAATATTGAATAAGCA
Found at i:7769 original size:24 final size:25
Alignment explanation
Indices: 7742--7802 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
7732 TAATATATTA
* *
7742 CATATTATTTA-GATAATTTTTTTT
1 CATATTATTTATAATAAATTTTTTT
*
7766 CATAATTTTCTTATAATAAATTTTTTT
1 CAT-ATTAT-TTATAATAAATTTTTTT
*
7793 CATTTTATTT
1 CATATTATTT
7803 TTATTGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 3 0.10
25 6 0.21
26 6 0.21
27 14 0.48
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (25 bp):
CATATTATTTATAATAAATTTTTTT
Found at i:11771 original size:21 final size:21
Alignment explanation
Indices: 11747--11808 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
11737 AGTAATCTAT
11747 AGAATTTCAAAAGCAAACTGC
1 AGAATTTCAAAAGCAAACTGC
*
11768 AGAATTTCAAAAGCAAACTGT
1 AGAATTTCAAAAGCAAACTGC
* *
11789 AGATTTTCAAAAGAAAACTG
1 AGAATTTCAAAAGCAAACTG
11809 AGGCTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
AGAATTTCAAAAGCAAACTGC
Done.