Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009443.1 Kokia drynarioides strain JFW-HI SEQ_124150, 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: 6157
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:336 original size:48 final size:47
Alignment explanation
Indices: 309--517 Score: 319
Period size: 48 Copynumber: 4.3 Consensus size: 47
299 AAAAAAGTTT
*
309 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAATATG
1 CATTTAACAAACAAAACAGTTAATAATGCAGATTA-TAAACAAAGATG
* *
357 CATTTTAACAAACAAAACAATTAATAATGCAGATTACTAAATAAAGATG
1 CA-TTTAACAAACAAAACAGTTAATAATGCAGATTA-TAAACAAAGATG
406 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATG
1 CATTTAACAAACAAAACAGTTAATAATGCAGATTA-TAAACAAAGATG
* *
454 CATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAAAGATG
1 CATTTAACAAACAAAACAGTTAATAATGCAGATTA-TAAACAAAGATG
*
502 CATTTAACAAAAAAAA
1 CATTTAACAAACAAAA
518 AACACTTAAT
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
48 106 0.70
49 45 0.30
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (47 bp):
CATTTAACAAACAAAACAGTTAATAATGCAGATTATAAACAAAGATG
Found at i:413 original size:97 final size:96
Alignment explanation
Indices: 309--517 Score: 355
Period size: 96 Copynumber: 2.2 Consensus size: 96
299 AAAAAAGTTT
*
309 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAATATGCATTTTAACAAACAAAA
1 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATGCA-TTTAACAAACAAAA
*
374 CAATTAATAATGCAGATTACTAAATAAAGATG
65 CAATTAATAATGCAGATTACTAAACAAAGATG
406 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAAC
1 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAAC
* * *
471 ACTTAATGATGCAGATTATTAAACAAAGATG
66 AATTAATAATGCAGATTACTAAACAAAGATG
*
502 CATTTAACAAAAAAAA
1 CATTTAACAAACAAAA
518 AACACTTAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 57 0.54
97 49 0.46
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (96 bp):
CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAAC
AATTAATAATGCAGATTACTAAACAAAGATG
Found at i:542 original size:48 final size:47
Alignment explanation
Indices: 309--544 Score: 246
Period size: 48 Copynumber: 4.9 Consensus size: 47
299 AAAAAAGTTT
* * *
309 CATTTAACAAACAAAACAGTTAAT-AATGCAGATTACTAAACAAATATG
1 CATTTAACAAACAAAACACTTAATGAA-GCA-ATTAATAAACAAAGATG
* * *
357 CATTTTAACAAACAAAACAATTAAT-AATGCAGATTACTAAATAAAGATG
1 CA-TTTAACAAACAAAACACTTAATGAA-GCA-ATTAATAAACAAAGATG
* *
406 CATTTAACAAACAAAACAGTTAAT-AATGCAGATTACTAAACAAAGATG
1 CATTTAACAAACAAAACACTTAATGAA-GCA-ATTAATAAACAAAGATG
* *
454 CATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAAAGATG
1 CATTTAACAAACAAAACACTTAATGAAGCA-ATTAATAAACAAAGATG
* *
502 CATTTAACAAAAAAAAAACACTTAATGAAGC-ATAAATAAACAA
1 CATTTAAC--AAACAAAACACTTAATGAAGCAATTAATAAACAA
545 CTTTATTTAT
Statistics
Matches: 172, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
48 107 0.62
49 46 0.27
50 19 0.11
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (47 bp):
CATTTAACAAACAAAACACTTAATGAAGCAATTAATAAACAAAGATG
Found at i:542 original size:96 final size:96
Alignment explanation
Indices: 309--544 Score: 289
Period size: 96 Copynumber: 2.4 Consensus size: 96
299 AAAAAAGTTT
* * * * *
309 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAATATGCATTTTAACAAACAAAA
1 CATTTAACAAAAAAAACACTTAATAATGCA-ATAAATAAACAAAGATGCATTTTAACAAACAAAA
*
374 CAATTAATAATGCAGATTACTAAATAAAGATG
65 CAATTAATAATGCAGATTACTAAACAAAGATG
* * * *
406 CATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGATGCA-TTTAACAAACAAAA
1 CATTTAACAAAAAAAACACTTAATAATGCA-ATAAATAAACAAAGATGCATTTTAACAAACAAAA
* * *
470 CACTTAATGATGCAGATTATTAAACAAAGATG
65 CAATTAATAATGCAGATTACTAAACAAAGATG
502 CATTTAACAAAAAAAAAACACTTAATGAA-GC-ATAAATAAACAA
1 CATTTAAC--AAAAAAAACACTTAAT-AATGCAATAAATAAACAA
545 CTTTATTTAT
Statistics
Matches: 127, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
96 60 0.47
97 49 0.39
98 16 0.13
99 2 0.02
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (96 bp):
CATTTAACAAAAAAAACACTTAATAATGCAATAAATAAACAAAGATGCATTTTAACAAACAAAAC
AATTAATAATGCAGATTACTAAACAAAGATG
Found at i:5259 original size:24 final size:24
Alignment explanation
Indices: 5218--5273 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
5208 TTGCCATGAA
5218 TTTTTTTTCCTAAATTG-TCTTTC
1 TTTTTTTTCCTAAATTGTTCTTTC
* * *
5241 TTTTTTTTTCTCAATTTGTTTTTTC
1 TTTTTTTTCCT-AAATTGTTCTTTC
*
5266 TTTGTTTT
1 TTTTTTTT
5274 ACTTCTGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 10 0.37
24 5 0.19
25 12 0.44
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.73
Consensus pattern (24 bp):
TTTTTTTTCCTAAATTGTTCTTTC
Found at i:5989 original size:80 final size:79
Alignment explanation
Indices: 5850--6007 Score: 262
Period size: 80 Copynumber: 2.0 Consensus size: 79
5840 TACAAACACT
* * *
5850 AATTTCTTTTTAACTCTTGTAGGGAAGCTAATGAGTCATGTCTCTTTAATAGGATCTGATGTAGT
1 AATTTCTTTTTAACTCTTGTAGGAAAGCTAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGC
5915 TAAAAAGGCATGGC
66 TAAAAAGGCATGGC
*
5929 AATTTCGTTTTTAACTCTTGTAGGAAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAG
1 AATTTC-TTTTTAACTCTTGTAGGAAAGCTAATGAGTCATGTCTCTTCAATAGGATCTGATGTAG
*
5994 CTGAAAAGGCATGG
65 CTAAAAAGGCATGG
6008 TATTTCTCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 6 0.08
80 67 0.92
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (79 bp):
AATTTCTTTTTAACTCTTGTAGGAAAGCTAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGC
TAAAAAGGCATGGC
Done.