Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010455.1 Kokia drynarioides strain JFW-HI SEQ_125353, 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: 16792
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1932 original size:41 final size:41
Alignment explanation
Indices: 1860--2158 Score: 347
Period size: 41 Copynumber: 7.3 Consensus size: 41
1850 ACTTGACGTA
* *
1860 TAAATGGAACACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
*
1902 TAAAGGAAGACTCGTGTCTCGAGATAAGCAT-A-A-TATTAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTA-TAT
* * * *
1941 TAAAGGAAGACTCGTGACTCAAAATGAGCATGAAATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * *
1982 TAAAGGAGGACTCGTGAT-TCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCGTG-TCTCGAGATGAGCATGAGATTATAT
* * *
2023 TAAAGGAAAACTCGTGTCTCGGGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * * *
2064 TAAAGGAATACTCATGTCTCGGGGTAAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
*
2105 TAAAGGAAGACTCGTGAT-TCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCGTG-TCTCGAGATGAGCATGAGATTATA-T
2147 TAAAGGAAGACT
1 TAAAGGAAGACT
2159 TATGACTCGG
Statistics
Matches: 226, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.14
40 3 0.01
41 170 0.75
42 20 0.09
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
Found at i:4325 original size:52 final size:52
Alignment explanation
Indices: 4242--4427 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
4232 AAATGGTAAA
* *
4242 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* * *
4294 AGGTCCGATGACTATGTGTCATCTTGAGTATATGAATCCTTTACAAAATATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* * * * **
4346 AGGTCCGATGACTATGTGTCATCGTGAGTATATAAATCC-TAATGTATTAAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
*
4397 AGGTCCGATGACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
4428 TAAAATGAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 35 0.29
52 84 0.71
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:5098 original size:21 final size:24
Alignment explanation
Indices: 5058--5113 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 24
5048 TTGAATAGCA
*
5058 AGTATCGGTAGTTATGTGTTTAGT
1 AGTATCGGTAGTTATGTGTTTACT
5082 AGTATCGGTAG-T-T-TGTTTACT
1 AGTATCGGTAGTTATGTGTTTACT
*
5103 TGTATCGGTAG
1 AGTATCGGTAG
5114 AAGTTGCAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 17 0.57
22 1 0.03
23 1 0.03
24 11 0.37
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.45
Consensus pattern (24 bp):
AGTATCGGTAGTTATGTGTTTACT
Found at i:5380 original size:13 final size:13
Alignment explanation
Indices: 5348--5372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5338 AATTTATTTG
5348 AATAAAAAATAAA
1 AATAAAAAATAAA
5361 AATAAAAAATAA
1 AATAAAAAATAA
5373 TTATAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:8622 original size:25 final size:27
Alignment explanation
Indices: 8586--8642 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
8576 ATTTATTAGT
* *
8586 AAATATATTTATTT-TTAAAATTTATA
1 AAATATATTTATTTAATAAAATTTAAA
*
8612 AAATATA-TTATTTAATAAATTTTAAA
1 AAATATATTTATTTAATAAAATTTAAA
8638 AAATA
1 AAATA
8643 AACACATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATATATTTATTTAATAAAATTTAAA
Found at i:11648 original size:21 final size:21
Alignment explanation
Indices: 11624--11674 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
11614 AAATTTCAGC
* *
11624 AGCAATCTATAGATTTTCAAA
1 AGCAAACTACAGATTTTCAAA
*
11645 AGCAAACTGCAGATTTTCAAA
1 AGCAAACTACAGATTTTCAAA
11666 AGCAAACTA
1 AGCAAACTA
11675 AGGCATCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (21 bp):
AGCAAACTACAGATTTTCAAA
Found at i:15682 original size:16 final size:15
Alignment explanation
Indices: 15641--15687 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
15631 AGGCAACCCA
15641 TTTTTTA-ATTTTATT
1 TTTTTTATA-TTTATT
15656 TTTTTTATATTTATT
1 TTTTTTATATTTATT
15671 TTTCTATT-TATTTATT
1 TTT-T-TTATATTTATT
15687 T
1 T
15688 ATTATATGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 16 0.55
16 11 0.38
17 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTATATTTATT
Done.