Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001255.1 Kokia drynarioides strain JFW-HI SEQ_112626, 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: 2173
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Found at i:379 original size:23 final size:22
Alignment explanation
Indices: 257--642 Score: 125
Period size: 23 Copynumber: 16.7 Consensus size: 22
247 AAATGAAATT
* *
257 TAAATAAAAGTAAAATTTATAA
1 TAAATAAAATTGAAATTTATAA
*
279 TAAATAGAATATT-TAATTTATAA
1 TAAATA-AA-ATTGAAATTTATAA
* *
302 TAAATAAAATTTAAAAGTTGA-AA
1 TAAATAAAA-TTGAAA-TTTATAA
* *
325 TTGAAATAAATGAAATGAAAATTA-AA
1 -T-AAAT-AA--AATTGAAATTTATAA
351 TTTAAATAAAAGTTGAAATTTATAA
1 --TAAATAAAA-TTGAAATTTATAA
* *
376 TAAATAGAATTTATAATTTATAA
1 TAAATAAAATTGA-AATTTATAA
* *
399 TAAATAAATTTTGAAATTGA-AA
1 TAAATAAA-ATTGAAATTTATAA
421 TGAAATGAAAA-TGAAA-TT-TAA
1 T-AAAT-AAAATTGAAATTTATAA
* *
442 T---TAAAAGTTCAAATTTAAAA
1 TAAATAAAA-TTGAAATTTATAA
* *
462 TAAATAGAATTTATAATTTATAA
1 TAAATAAAATTGA-AATTTATAA
485 TAAAATAAAATTTGAAATTTGA-AA
1 T-AAATAAAA-TTGAAATTT-ATAA
* * *
509 TTGAAATGAAA-TGAAAATGA-AA
1 -T-AAATAAAATTGAAATTTATAA
* *
531 TTTAATTAAAAGTTTAAATTTATAA
1 --TAAATAAAA-TTGAAATTTATAA
* * *
556 TAAATAGATTTTATAATTTATAA
1 TAAATAAAATTGA-AATTTATAA
* *
579 TAAATAAATTTTGAAATTTGAAAA
1 TAAATAAA-ATTGAAATTT-ATAA
** *
603 TGAAATTTAATTAAAAGTTTA-AA
1 T-AAATAAAATTGAAA-TTTATAA
*
626 TGAAATGAAATTGAAAT
1 T-AAATAAAATTGAAAT
643 GAAGTGAAAA
Statistics
Matches: 278, Mismatches: 47, Indels: 78
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.01
17 1 0.00
18 4 0.01
19 2 0.01
20 3 0.01
21 5 0.02
22 38 0.14
23 119 0.43
24 54 0.19
25 30 0.11
26 10 0.04
27 6 0.02
28 2 0.01
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (22 bp):
TAAATAAAATTGAAATTTATAA
Found at i:456 original size:86 final size:88
Alignment explanation
Indices: 185--608 Score: 527
Period size: 94 Copynumber: 4.6 Consensus size: 88
175 ATATAAATAA
185 AATAAATAGAATTTATAATTTATAATAAATAAAATTTAAAAGTTGAAATTGAAATGAAATGAAAA
1 AATAAATAGAATTTATAATTTATAATAAATAAAATTT-----TTGAAATTGAAATGAAATGAAAA
250 TGAAATTTAAATAAAAG-TAAAATTTAT
61 TGAAATTTAAATAAAAGTTAAAATTTAT
277 AATAAATAGAATATT-TAATTTATAATAAATAAAATTTAAAAGTTGAAATTGAAATAAATGAAAT
1 AATAAATAGAAT-TTATAATTTATAATAAATAAAATTT-----TTGAAATTG----AAATGAAAT
* *
341 GAAAATTAAATTTAAATAAAAGTTGAAATTTAT
56 GAAAATGAAATTTAAATAAAAGTTAAAATTTAT
374 AATAAATAGAATTTATAATTTATAATAAAT-AAA-TTTTGAAATTGAAATGAAATGAAAATGAAA
1 AATAAATAGAATTTATAATTTATAATAAATAAAATTTTTGAAATTGAAATGAAATGAAAATGAAA
* * *
437 TTTAATTAAAAGTTCAAATTTAA
66 TTTAAATAAAAGTTAAAATTTAT
460 AATAAATAGAATTTATAATTTATAATAAAATAAAATTTGAAATTTGAAATTGAAATGAAATGAAA
1 AATAAATAGAATTTATAATTTATAAT-AAATAAAA-TT----TTTGAAATTGAAATGAAATGAAA
* *
525 ATGAAATTTAATTAAAAGTTTAAATTTAT
60 ATGAAATTTAAATAAAAGTTAAAATTTAT
*
554 AATAAATAGATTTTATAATTTATAATAAAT-AAA-TTTTGAAATTTGAAAATGAAAT
1 AATAAATAGAATTTATAATTTATAATAAATAAAATTTTTGAAA-TTG-AAATGAAAT
609 TTAATTAAAA
Statistics
Matches: 306, Mismatches: 9, Indels: 38
0.87 0.03 0.11
Matches are distributed among these distances:
86 71 0.23
87 7 0.02
88 12 0.04
90 11 0.04
92 51 0.17
93 6 0.02
94 75 0.25
95 2 0.01
96 35 0.11
97 36 0.12
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.36
Consensus pattern (88 bp):
AATAAATAGAATTTATAATTTATAATAAATAAAATTTTTGAAATTGAAATGAAATGAAAATGAAA
TTTAAATAAAAGTTAAAATTTAT
Found at i:618 original size:16 final size:16
Alignment explanation
Indices: 597--675 Score: 70
Period size: 16 Copynumber: 4.8 Consensus size: 16
587 TTTTGAAATT
597 TGAAAATGAAATTTAA
1 TGAAAATGAAATTTAA
* * **
613 TTAAAAGTTTAAATGAAA
1 TGAAAA--TGAAATTTAA
* *
631 TGAAATTGAAA-TGAA
1 TGAAAATGAAATTTAA
646 GTGAAAATGAAATTTAA
1 -TGAAAATGAAATTTAA
663 TGAAAATGAAATT
1 TGAAAATGAAATT
676 CAAATTCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
15 2 0.04
16 32 0.67
17 3 0.06
18 11 0.23
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.30
Consensus pattern (16 bp):
TGAAAATGAAATTTAA
Found at i:631 original size:5 final size:5
Alignment explanation
Indices: 623--674 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
613 TTAAAAGTTT
* * *
623 AAATG AAATG AAATTG AAATG AAGTG AAAATG AAATT TAATG AAAATG
1 AAATG AAATG AAA-TG AAATG AAATG -AAATG AAATG AAATG -AAATG
671 AAAT
1 AAAT
675 TCAAATTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 25 0.66
6 13 0.34
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (5 bp):
AAATG
Found at i:687 original size:50 final size:49
Alignment explanation
Indices: 597--695 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 49
587 TTTTGAAATT
* * * * *
597 TGAAAATGAAATTTAATTAAAAGTTTAAATGAAATGAAATTGAAATGAAG
1 TGAAAATGAAATTTAATGAAAAG-TGAAATCAAATCAAATTCAAATGAAG
647 TGAAAATGAAATTTAATGAAAA-TGAAATTCAAATTCAAATTCAAATGAA
1 TGAAAATGAAATTTAATGAAAAGTGAAA-TCAAA-TCAAATTCAAATGAA
696 AAACATAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 4 0.10
49 4 0.10
50 34 0.81
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (49 bp):
TGAAAATGAAATTTAATGAAAAGTGAAATCAAATCAAATTCAAATGAAG
Done.