Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002496.1 Kokia drynarioides strain JFW-HI SEQ_114652, 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: 25475
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1667 original size:23 final size:24
Alignment explanation
Indices: 1640--1694 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1630 ACCCAAACCC
*
1640 GTTGACCGAATCGGACCATTGACT
1 GTTGACCAAATCGGACCATTGACT
* * *
1664 -TTGACCAAATTGGATCGTTGACT
1 GTTGACCAAATCGGACCATTGACT
1687 GTTGACCA
1 GTTGACCA
1695 TTGACTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
GTTGACCAAATCGGACCATTGACT
Found at i:3643 original size:16 final size:15
Alignment explanation
Indices: 3622--3651 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3612 AAAAGCAAAA
3622 AAAATTTGTGTGAAAG
1 AAAATTTGT-TGAAAG
3638 AAAATTTGTTGAAA
1 AAAATTTGTTGAAA
3652 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAATTTGTTGAAAG
Found at i:4954 original size:32 final size:33
Alignment explanation
Indices: 4876--4965 Score: 128
Period size: 33 Copynumber: 2.8 Consensus size: 33
4866 AAGCAACCAT
*
4876 AAAGGCATTAATTTCAAGGAAGAAATTAGGCAA
1 AAAGGCATTAATTTCAAAGAAGAAATTAGGCAA
* * *
4909 AAAAGCATTAATTTCAAAGAAGATATTATGC-A
1 AAAGGCATTAATTTCAAAGAAGAAATTAGGCAA
*
4941 AAAGGCATTAATTTCAAAGACGAAA
1 AAAGGCATTAATTTCAAAGAAGAAA
4966 AGGGAACGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 23 0.46
33 27 0.54
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (33 bp):
AAAGGCATTAATTTCAAAGAAGAAATTAGGCAA
Found at i:6443 original size:28 final size:30
Alignment explanation
Indices: 6405--6489 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 30
6395 AAGCATCCAT
6405 AAAGGCATTAATTTCAAGGAAGAAATTA-A
1 AAAGGCATTAATTTCAAGGAAGAAATTACA
*
6434 AAA-GCATTAATTTCAAGGAAGATATTATGCA
1 AAAGGCATTAATTTCAAGGAAGAAATTA--CA
*
6465 AAAGGCATTAATTTCAAAGAAGAAA
1 AAAGGCATTAATTTCAAGGAAGAAA
6490 AGGGAACGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 23 0.47
29 3 0.06
31 4 0.08
32 19 0.39
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (30 bp):
AAAGGCATTAATTTCAAGGAAGAAATTACA
Found at i:7268 original size:15 final size:17
Alignment explanation
Indices: 7248--7284 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
7238 ACTTGTTACT
7248 TTTATA-TATT-CTAGA
1 TTTATACTATTACTAGA
7263 TTTATACTATTACTAGA
1 TTTATACTATTACTAGA
*
7280 ATTAT
1 TTTAT
7285 TAGAACTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTATACTATTACTAGA
Found at i:11345 original size:31 final size:31
Alignment explanation
Indices: 11309--11374 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
11299 TTATTTACTG
* * *
11309 AATTATTTTAAATTTTTCATTCAAATTATTA
1 AATTATTTAAAAATTTTCATTCAAATCATTA
*
11340 AATTATTTAAAAATTTTCATTTAAATCATTA
1 AATTATTTAAAAATTTTCATTCAAATCATTA
11371 AATT
1 AATT
11375 GTTAAGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (31 bp):
AATTATTTAAAAATTTTCATTCAAATCATTA
Found at i:14536 original size:28 final size:30
Alignment explanation
Indices: 14465--14536 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 30
14455 CTTCATAAAC
*
14465 TATATATCAATTATAATTTAATGTACAGTTG
1 TATATATAAATT-TAATTTAATGTACAGTTG
* *
14496 TATATATAAATTTAATTTTATGTA-A-TTT
1 TATATATAAATTTAATTTAATGTACAGTTG
14524 TATATATAAATTT
1 TATATATAAATTT
14537 TTGATTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.39
29 1 0.03
30 11 0.29
31 11 0.29
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (30 bp):
TATATATAAATTTAATTTAATGTACAGTTG
Found at i:14552 original size:30 final size:28
Alignment explanation
Indices: 14465--14554 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 28
14455 CTTCATAAAC
* * *
14465 TATATATCAATTATAATTTAATGTACAGTTG
1 TATATATAAATT-TAATTTGATGTA-A-TTT
*
14496 TATATATAAATTTAATTTTATGTAATTT
1 TATATATAAATTTAATTTGATGTAATTT
* *
14524 TATATATAAATTTTTGATTTGATTTAATTT
1 TATATATAAA--TTTAATTTGATGTAATTT
14554 T
1 T
14555 TGTAAATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 12 0.24
29 1 0.02
30 27 0.53
31 11 0.22
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (28 bp):
TATATATAAATTTAATTTGATGTAATTT
Found at i:14580 original size:39 final size:40
Alignment explanation
Indices: 14505--14580 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
14495 GTATATATAA
* *
14505 ATTTAATTTTATGTAATTTTATATATAAATTTTTGATTTG
1 ATTTAATTTTATGTAATATTATATATAAATTATTGATTTG
14545 ATTTAATTTT-TGTAA-ATTATCA-ATACAATTATTGAT
1 ATTTAATTTTATGTAATATTAT-ATATA-AATTATTGAT
14581 ATAACCAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 7 0.22
39 15 0.47
40 10 0.31
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.55
Consensus pattern (40 bp):
ATTTAATTTTATGTAATATTATATATAAATTATTGATTTG
Found at i:15624 original size:2 final size:2
Alignment explanation
Indices: 15617--15659 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
15607 TAATCAACCA
15617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15659 A
1 A
15660 AAGTAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.