Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007509.1 Kokia drynarioides strain JFW-HI SEQ_122133, 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: 35714
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:10717 original size:180 final size:178
Alignment explanation
Indices: 10421--10775 Score: 484
Period size: 180 Copynumber: 2.0 Consensus size: 178
10411 GATATTAGTC
10421 GAAGCTCAACCAAAAGCAATATGAATAAAAAGACCACTTTATAAGCCAAAACATGTGACATTTAA
1 GAAGCTCAACCAAAAGCAATATGAATAAAAAGACCACTTTATAAGCCAAAACATGTGACATTTAA
* * * * ** * *
10486 TACAAAGGGAATGGAAGAAGTCATATCAGCAGCATTAAAATGGAAAGAGATAAGAAGC-AA-AC-
66 CACAAAAGAAATGAAAGAAGGAATACCAGCAGCATTAAAAAGGAAAGAGATAAGAAGCAAACACA
*
10548 A-CAACTGCCTAATATCAAGGGAAACAAATAAAAAGGAGAAATTAGAT
131 ATCAACTGCCTAATACCAAGGGAAACAAATAAAAAGGAGAAATTAGAT
* *
10595 GAAGCTCAATCAAAAGCAATATGAATAAAATAATGAAGACCATTTTATAAGCCAAAACATGTGAC
1 GAAGCTCAACCAAAAGCAATATGAAT---A-AA--AAGACCACTTTATAAGCCAAAACATGTGAC
* *
10660 ATTTAACACAAAAGAAATGAAAGAAGGAATACCAGTAGCATTAAAAAGGAAAGAGATAAGAGGCA
60 ATTTAACACAAAAGAAATGAAAGAAGGAATACCAGCAGCATTAAAAAGGAAAGAGATAAGAAGCA
10725 AACACAACTGTCAACTGCCTAATACCAAGGGAAACAAATAAAAAGGAGAAA
125 AACACAA---TCAACTGCCTAATACCAAGGGAAACAAATAAAAAGGAGAAA
10776 ATCTAGTACA
Statistics
Matches: 155, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
174 25 0.16
177 1 0.01
178 2 0.01
180 83 0.54
181 2 0.01
182 2 0.01
183 1 0.01
187 39 0.25
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (178 bp):
GAAGCTCAACCAAAAGCAATATGAATAAAAAGACCACTTTATAAGCCAAAACATGTGACATTTAA
CACAAAAGAAATGAAAGAAGGAATACCAGCAGCATTAAAAAGGAAAGAGATAAGAAGCAAACACA
ATCAACTGCCTAATACCAAGGGAAACAAATAAAAAGGAGAAATTAGAT
Found at i:17996 original size:20 final size:22
Alignment explanation
Indices: 17963--18006 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
17953 TCACAAATTA
17963 TTTTAAAAATTA-TTATGTATT
1 TTTTAAAAATTATTTATGTATT
* *
17984 TTTTTAAAA-TATTTATTTATT
1 TTTTAAAAATTATTTATGTATT
18005 TT
1 TT
18007 AATATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAAAAATTATTTATGTATT
Found at i:18077 original size:17 final size:18
Alignment explanation
Indices: 18043--18080 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18033 TGACTTGTAC
**
18043 TAAATATTTTTTTGTATT
1 TAAATATTTTAATGTATT
18061 TAAATATTTTAAT-TATT
1 TAAATATTTTAATGTATT
18078 TAA
1 TAA
18081 GAGTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TAAATATTTTAATGTATT
Found at i:22329 original size:15 final size:16
Alignment explanation
Indices: 22302--22334 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22292 CTTTCTGTTT
22302 TTTCTACTCTTTCAAA
1 TTTCTACTCTTTCAAA
*
22318 TTTCTA-TCTTTCCAA
1 TTTCTACTCTTTCAAA
22333 TT
1 TT
22335 GTGTGTCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTCTACTCTTTCAAA
Found at i:26611 original size:23 final size:23
Alignment explanation
Indices: 26585--26654 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
26575 TTCGTTTAAC
*
26585 TTAATCGAACATGTTTACGAATA
1 TTAATCGAACATGTTCACGAATA
* * *
26608 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAATA
* *
26631 TACAATTGAACATGTTCACGAATA
1 T-TAATCGAACATGTTCACGAATA
26655 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAATA
Found at i:26773 original size:24 final size:24
Alignment explanation
Indices: 26741--26788 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26731 TCATCAATAA
* * *
26741 ATAAACGAATCAGTAAATGAGCTT
1 ATAAACGAACCAATAAACGAGCTT
26765 ATAAACGAACCAATAAACGAGCTT
1 ATAAACGAACCAATAAACGAGCTT
26789 GTTTGTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATAAACGAACCAATAAACGAGCTT
Done.