Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014091.1 Kokia drynarioides strain JFW-HI SEQ_129122, 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: 14373
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 120 characters in sequence are not A, C, G, or T
Found at i:9055 original size:22 final size:21
Alignment explanation
Indices: 9030--9072 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
9020 AACCCTCTGT
9030 ATCGCGTCG-ATTTTCTCTTCTA
1 ATCGC-TCGTATTTT-TCTTCTA
*
9052 ATCGCTTGTATTTTTCTTCTA
1 ATCGCTCGTATTTTTCTTCTA
9073 TTTGTTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (21 bp):
ATCGCTCGTATTTTTCTTCTA
Found at i:13029 original size:96 final size:96
Alignment explanation
Indices: 12841--13032 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
12831 TTTTTACGAA
** *
12841 AAGGATATTCGATTATCTTGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
1 AAGGATATTCGATTATCTTGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATATTTCA
*
12906 AAACTGAAGATAAGGAAACATTACCTCGATT
66 AAACTGAAGATAAAGAAACATTACCTCGATT
* * *
12937 AAGGGTATTCGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGAACAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATA-TTT
* * *
13000 CGAAACTCGAA-ATATAAG-AATATTGCCTCGATT
64 CAAAACT-GAAGATA-AAGAAACATTACCTCGATT
13033 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 3 0.04
96 74 0.90
97 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATATTTCA
AAACTGAAGATAAAGAAACATTACCTCGATT
Found at i:13430 original size:30 final size:29
Alignment explanation
Indices: 13393--13773 Score: 373
Period size: 29 Copynumber: 12.9 Consensus size: 29
13383 GTAAAATAGT
13393 AATTTTTGGAAGTTTCGAGGTAAAAAATGG
1 AATTTTTGGAAGTTTCGAGGT-AAAAATGG
* * * *
13423 GATTTTTGGAAG-TTCAAAAGTAAAAATGA
1 AATTTTTGGAAGTTTC-GAGGTAAAAATGG
*
13452 AATTTTTGGAAGTTTCGAAGGTAAAAATGA
1 AATTTTTGGAAGTTTCG-AGGTAAAAATGG
* * *
13482 AATTTTTGGAAGTTTGGGGGTAAAAATGA
1 AATTTTTGGAAGTTTCGAGGTAAAAATGG
*
13511 AATTTTTGGAAG-TTCGGAGGTAAAAATAG
1 AATTTTTGGAAGTTTC-GAGGTAAAAATGG
*
13540 AATTTTTGGAAGTTTCG-GAGTCAAAATTGG
1 AATTTTTGGAAGTTTCGAG-GT-AAAAATGG
** * *
13570 GTTTTTTGGAAGTTTGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGAGGTAAAAATGG
*
13599 AATTTTTGGAAGTTTTGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGAGGT-AAAAATGG
* * *
13629 GATTTTTGGAAG-TTCGGGGGTAAAAATAG
1 AATTTTTGGAAGTTTC-GAGGTAAAAATGG
*
13658 AATTTTTGGAAGTTTCGAGGTCAAAAATGA
1 AATTTTTGGAAGTTTCGAGGT-AAAAATGG
* *
13688 AATTTTTAGAAG-TT-GAAGGGTAAAAACT-A
1 AATTTTTGGAAGTTTCG-A-GGTAAAAA-TGG
13717 AATTTTTGGAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCGAGG-TAAAAATGG
* *
13747 GATTTTTGGAAG-TTCGGGGGTAAAAAT
1 AATTTTTGGAAGTTTC-GAGGTAAAAAT
13774 TTAAATTTTT
Statistics
Matches: 295, Mismatches: 36, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.01
29 150 0.51
30 139 0.47
31 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAAGTTTCGAGGTAAAAATGG
Found at i:13446 original size:59 final size:57
Alignment explanation
Indices: 13393--13773 Score: 310
Period size: 59 Copynumber: 6.5 Consensus size: 57
13383 GTAAAATAGT
* **
13393 AATTTTTGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCAAAAGTAAAAATGA
1 AATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTC-GGAGTAAAAATGA
* * *
13452 AATTTTTGGAAGTTTCGAAGGTAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAATGA
1 AATTTTTGGAAGTTTCG-AGGTAAAAATGGAATTTTTGGAAG-TTCGGAGTAAAAATGA
* * *
13511 AATTTTTGGAAG-TTCGGAGGTAAAAATAGAATTTTTGGAAGTTTCGGAGTCAAAATTGG
1 AATTTTTGGAAGTTTC-GAGGTAAAAATGGAATTTTTGGAAG-TTCGGAGT-AAAAATGA
** * * ** *
13570 GTTTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTCGGA-GT-AAAAATGA
* * *
13629 GATTTTTGGAAG-TTCGGGGGTAAAAATAGAATTTTTGGAAGTTTC-GAGGTCAAAAATGA
1 AATTTTTGGAAGTTTC-GAGGTAAAAATGGAATTTTTGGAAG-TTCGGA-GT-AAAAATGA
* * *
13688 AATTTTTAGAAG-TT-GAAGGGTAAAAACT-AAATTTTTGGAAGTTTC-GAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCG-A-GGTAAAAA-TGGAATTTTTGGAAG-TTCGGA-G-TAAAAATGA
* *
13747 GATTTTTGGAAG-TTCGGGGGTAAAAAT
1 AATTTTTGGAAGTTTC-GAGGTAAAAAT
13774 TTAAATTTTT
Statistics
Matches: 275, Mismatches: 33, Indels: 29
0.82 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 39 0.14
59 222 0.81
60 12 0.04
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (57 bp):
AATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTCGGAGTAAAAATGA
Found at i:13501 original size:118 final size:117
Alignment explanation
Indices: 13379--13786 Score: 452
Period size: 118 Copynumber: 3.5 Consensus size: 117
13369 TCGGACATCC
* * * *
13379 GGGGGT-AAAATAGTAATTTTTGGAAGTTTC-GAGGTAAAAAATGGGATTTTTGGAAG-TTCAAA
1 GGGGGTAAAAAT-GAAATTTTTGGAAG-TTCGGAGGT-AAAAATAGAATTTTTGGAAGTTTC-GA
13441 AGT-AAAAATGAAATTTTTGGAAGTTTCGAAGGTAAAAATGAAATTTTTGGAAGTTT
62 AGTCAAAAATGAAATTTTTGGAAGTTT-GAAGGTAAAAATGAAATTTTTGGAAGTTT
*
13497 GGGGGTAAAAATGAAATTTTTGGAAGTTCGGAGGTAAAAATAGAATTTTTGGAAGTTTCGGAGTC
1 GGGGGTAAAAATGAAATTTTTGGAAGTTCGGAGGTAAAAATAGAATTTTTGGAAGTTTCGAAGTC
* *** ** *
13562 AAAATTGGGTTTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTT
66 AAAAATGAAATTTTTGGAAGTTTGAAGGTAAAAATGAAATTTTTGGAAGTTT
* * ** * *
13614 TGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTCGAGGT
1 GGGGGT-AAAAATGAAATTTTTGGAAGTTCGGAGGTAAAAATAGAATTTTTGGAAGTTTCGAAGT
*
13679 CAAAAATGAAATTTTTAGAAG-TTGAAGGGTAAAAACT-AAATTTTTGGAAGTTT
65 CAAAAATGAAATTTTTGGAAGTTTGAA-GGTAAAAA-TGAAATTTTTGGAAGTTT
* * ** *
13732 CGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATTTA-AATTTTTGGA
1 -GGGGGTAAAAATGAAATTTTTGGAAGTTCGGAGGTAAAAA--TAGAATTTTTGGA
13787 CAATTTAAGG
Statistics
Matches: 249, Mismatches: 31, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
117 57 0.23
118 172 0.69
119 18 0.07
120 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (117 bp):
GGGGGTAAAAATGAAATTTTTGGAAGTTCGGAGGTAAAAATAGAATTTTTGGAAGTTTCGAAGTC
AAAAATGAAATTTTTGGAAGTTTGAAGGTAAAAATGAAATTTTTGGAAGTTT
Found at i:14346 original size:13 final size:13
Alignment explanation
Indices: 14330--14354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14320 AAAAAAAACC
14330 AAAAACCTCTCCG
1 AAAAACCTCTCCG
14343 AAAAACCTCTCC
1 AAAAACCTCTCC
14355 CCCCTCTTTG
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:0.40, C:0.40, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAACCTCTCCG
Done.