Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006031.1 Kokia drynarioides strain JFW-HI SEQ_120484, 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: 39224
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:49 original size:23 final size:23
Alignment explanation
Indices: 1--50 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
*
1 ATATAAAAATATATTAATTATTA
1 ATATAAAAATATATTAATTATAA
*
24 ATATAAATATAATATTAA-TATAA
1 ATATAAAAAT-ATATTAATTATAA
47 ATAT
1 ATAT
51 TATTAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAAAAATATATTAATTATAA
Found at i:51 original size:12 final size:12
Alignment explanation
Indices: 11--91 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 12
1 ATATAAAAAT
*
11 ATATTAATTATTA
1 ATATTAA-TATAA
*
24 ATATAAATAT-A
1 ATATTAATATAA
35 ATATTAATATAA
1 ATATTAATATAA
47 ATATT-AT-TAA
1 ATATTAATATAA
*
57 TTACTTAATATATTA
1 ATA-TTAATATA--A
72 ATTACTTAATATAA
1 A-TA-TTAATATAA
*
86 AGATTA
1 ATATTA
92 TTAATTACTT
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
10 5 0.09
11 14 0.25
12 14 0.25
13 9 0.16
14 2 0.04
15 1 0.02
16 11 0.20
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (12 bp):
ATATTAATATAA
Found at i:57 original size:39 final size:41
Alignment explanation
Indices: 1--111 Score: 142
Period size: 39 Copynumber: 2.8 Consensus size: 41
1 ATATAAAAATATATTAATTA-TTAATATAAATATAA-TA-TTA
1 ATATAAAAAT-TATTAATTACTTAATAT-AATATAATTACTTA
*
41 ATATAAATATTATTAATTACTTAATAT-AT-TAATTACTTA
1 ATATAAAAATTATTAATTACTTAATATAATATAATTACTTA
*
80 ATATAAAGATTATTAATTACTTAATATTAATA
1 ATATAAAAATTATTAATTACTTAATA-TAATA
112 ACAAATAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
37 3 0.05
38 4 0.06
39 37 0.59
40 17 0.27
41 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (41 bp):
ATATAAAAATTATTAATTACTTAATATAATATAATTACTTA
Found at i:72 original size:16 final size:16
Alignment explanation
Indices: 46--84 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
36 TATTAATATA
46 AATATTATTAATTACTT
1 AATA-TATTAATTACTT
63 AATATATTAATTACTT
1 AATATATTAATTACTT
79 AATATA
1 AATATA
85 AAGATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATATTAATTACTT
Found at i:91 original size:16 final size:16
Alignment explanation
Indices: 55--96 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
45 AAATATTATT
*
55 AATTACTTAATATATT
1 AATTACTTAATATATA
71 AATTACTTAATATA-A
1 AATTACTTAATATATA
86 AGATTA-TTAAT
1 A-ATTACTTAAT
97 TACTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
AATTACTTAATATATA
Found at i:121 original size:39 final size:39
Alignment explanation
Indices: 1--125 Score: 132
Period size: 39 Copynumber: 3.2 Consensus size: 39
*
1 ATATAAAAATATATTAATTA-TTAATATAAATATA-ATATTA
1 ATATAAAAAT-TATTAATTACTTAATATTAATA-ACA-ATTA
* *
41 ATATAAATATTATTAATTACTTAATATATTAATTAC--TTA
1 ATATAAAAATTATTAATTACTT-A-ATATTAATAACAATTA
* *
80 ATATAAAGATTATTAATTACTTAATATTAATAACAAATA
1 ATATAAAAATTATTAATTACTTAATATTAATAACAATTA
119 ATATAAA
1 ATATAAA
126 TTAATAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
37 10 0.14
38 1 0.01
39 42 0.58
40 11 0.15
41 2 0.03
42 7 0.10
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATAAAAATTATTAATTACTTAATATTAATAACAATTA
Found at i:1569 original size:31 final size:29
Alignment explanation
Indices: 1504--1573 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
1494 CTCAGGTTGT
*
1504 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTGAAATGTAAC
***
1533 ATTTTAGTCACTTATGTTATCGCGTTGTAAC
1 ATTTTAGTCACTTATGTT-T-GAAATGTAAC
1564 ATTTTAGTCA
1 ATTTTAGTCA
1574 TTGAGCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
30 1 0.03
31 16 0.46
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTGAAATGTAAC
Found at i:31254 original size:22 final size:23
Alignment explanation
Indices: 31208--31255 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31198 GGTAATTTGA
31208 GGTAAAATATAATAAAAATGAAG
1 GGTAAAATATAATAAAAATGAAG
31231 GGTAAAATATAATAAAAATG-AG
1 GGTAAAATATAATAAAAATGAAG
31253 GGT
1 GGT
31256 TTAAGTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (23 bp):
GGTAAAATATAATAAAAATGAAG
Found at i:34473 original size:41 final size:41
Alignment explanation
Indices: 34395--34524 Score: 161
Period size: 41 Copynumber: 3.1 Consensus size: 41
34385 GAGTCATAAA
* * *
34395 TCTTCCTTTAACCAAATTCTCATTCTCAACTCGAGACATGAG
1 TCTTCC-TTAATCAAAATCTCATTCTCATCTCGAGACATGAG
* *
34437 TCTTCCTTAATCAAAATCTCATTCTCATTTCAAGACATGAG
1 TCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAG
* * * * *
34478 TCTTCCTTATTTATAATTTCATTCTCATCTCGAGACATAAG
1 TCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAG
34519 TCTTCC
1 TCTTCC
34525 ATTTATACAA
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 70 0.92
42 6 0.08
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (41 bp):
TCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAG
Found at i:34537 original size:41 final size:40
Alignment explanation
Indices: 34383--34538 Score: 143
Period size: 41 Copynumber: 3.8 Consensus size: 40
34373 TTATGCTCTT
* * *
34383 TCGAGTCATAAATCTTCCTTTA-ACCAAATTCTCATTCTCAAC
1 TCGAGACATAAGTCTTCCTTTATA-C-AATT-TCATTCTCATC
* * * * *
34425 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATAAGTCTTCCTTTAT-ACAATTTCATTCTCATC
* * * *
34466 TCAAGACATGAGTCTTCCTTATTTATAATTTCATTCTCATC
1 TCGAGACATAAGTCTTCCTT-TATACAATTTCATTCTCATC
34507 TCGAGACATAAGTCTTCCATTTATACAATTTC
1 TCGAGACATAAGTCTTCC-TTTATACAATTTC
34539 TCATGATTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
41 67 0.73
42 24 0.26
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.38
Consensus pattern (40 bp):
TCGAGACATAAGTCTTCCTTTATACAATTTCATTCTCATC
Found at i:35397 original size:20 final size:21
Alignment explanation
Indices: 35362--35400 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35352 ACTTTCATCA
*
35362 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATTT
35383 TTAACCTTT-ATTAAACAT
1 TTAACCTTTAATTAAACAT
35401 ATTAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATTT
Found at i:38423 original size:21 final size:22
Alignment explanation
Indices: 38394--38435 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
38384 AATATTTTAA
* *
38394 AAATTAATTTTTAT-ACTTTTT
1 AAATAAATTTTAATAACTTTTT
38415 AAATAAATTTTAATAACTTTT
1 AAATAAATTTTAATAACTTTT
38436 ATACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATAAATTTTAATAACTTTTT
Done.