Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006195.1 Kokia drynarioides strain JFW-HI SEQ_120764, 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: 37315
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:318 original size:28 final size:26
Alignment explanation
Indices: 265--319 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
255 TTGATAAAAA
* *
265 ATAATTTTTAACAAAAAACTATTAAT
1 ATAATTTTAAACAAAAAACTAGTAAT
291 ATAATTTTAAACAAAAAAACCTAGTAAT
1 ATAATTTTAAAC-AAAAAA-CTAGTAAT
319 A
1 A
320 ATGTCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.44
27 6 0.24
28 8 0.32
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATTTTAAACAAAAAACTAGTAAT
Found at i:15600 original size:1 final size:1
Alignment explanation
Indices: 15594--15619 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
15584 ATTTTAAAAG
15594 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
15620 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17344 original size:19 final size:19
Alignment explanation
Indices: 17323--17358 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17313 ATTCGATATT
17323 TTTTAAA-TAAAATTTTAA
1 TTTTAAATTAAAATTTTAA
*
17341 TTTTAAATTTAAATTTTA
1 TTTTAAATTAAAATTTTA
17359 TTGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAATTAAAATTTTAA
Found at i:21148 original size:29 final size:30
Alignment explanation
Indices: 21115--21183 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
21105 GAGTAATTTA
* *
21115 ATACATGAATTTTGATT-TGGTGCAATTAT
1 ATACATGAACTTGGATTGTGGTGCAATTAT
* * *
21144 GTACATGTAACTTGGATTGTGGTTCAATTGT
1 ATACATG-AACTTGGATTGTGGTGCAATTAT
21175 ATACATGAA
1 ATACATGAA
21184 ACTTTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 6 0.19
30 10 0.31
31 16 0.50
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (30 bp):
ATACATGAACTTGGATTGTGGTGCAATTAT
Found at i:27771 original size:29 final size:26
Alignment explanation
Indices: 27732--27791 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
27722 GACTCTCTTT
* *
27732 AAAAAAAAATGATTAAATTTAGCTAAAA
1 AAAAAAAAATGATCAAA-TT-GATAAAA
27760 AAAAAAATAATGATCAAATTGATAAAA
1 AAAAAAA-AATGATCAAATTGATAAAA
27787 AAAAA
1 AAAAA
27792 TGTAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.38
28 9 0.31
29 9 0.31
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (26 bp):
AAAAAAAAATGATCAAATTGATAAAA
Found at i:27793 original size:22 final size:23
Alignment explanation
Indices: 27760--27806 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
27750 TTAGCTAAAA
*
27760 AAAAAAATAATGATCAA-ATTGAT
1 AAAAAAATAATG-TAAATATTGAT
27783 AAAAAAA-AATGTAAATATTGAT
1 AAAAAAATAATGTAAATATTGAT
27805 AA
1 AA
27807 TTAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
23 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAAAAATAATGTAAATATTGAT
Found at i:28145 original size:16 final size:17
Alignment explanation
Indices: 28124--28158 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28114 CAAAAGCATA
*
28124 TTATTT-AACAATATTT
1 TTATTTCAAAAATATTT
28140 TTATTTCAAAAATATTT
1 TTATTTCAAAAATATTT
28157 TT
1 TT
28159 TTTTTATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTCAAAAATATTT
Found at i:29630 original size:55 final size:55
Alignment explanation
Indices: 29506--29636 Score: 176
Period size: 55 Copynumber: 2.4 Consensus size: 55
29496 GTTTTTCAGG
* *
29506 CCCAATATGAGAACAATTGCTAAGGTCAAGGACTAAGACAAAAAAAAAAGTTCAAAT
1 CCCAATATG-GAACAATTGCCAAGGTCAAAGACTAAGAC-AAAAAAAAAGTTCAAAT
* *
29563 CCCAATAT-GAACAATTGCCAAGGTCAAAGACTAAGAC-AAAAAAAAGTTTAAGT
1 CCCAATATGGAACAATTGCCAAGGTCAAAGACTAAGACAAAAAAAAAGTTCAAAT
*
29616 TCCAATATGGGAACAATTGCC
1 CCCAATAT-GGAACAATTGCC
29637 TAGTTCAGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
53 21 0.31
55 38 0.57
57 8 0.12
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (55 bp):
CCCAATATGGAACAATTGCCAAGGTCAAAGACTAAGACAAAAAAAAAGTTCAAAT
Found at i:34395 original size:52 final size:52
Alignment explanation
Indices: 34316--34501 Score: 241
Period size: 52 Copynumber: 3.6 Consensus size: 52
34306 AATGAAAAAG
* * *
34316 GGTCCGATGATTAAGTGTCATCGTGAGTACATTAATCCTTCACGGATTATAA
1 GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCACGGATTATAA
*
34368 GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCACGAATTATAA
1 GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCACGGATTATAA
* * * **
34420 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATTCCTTTACGGAACA-AGA
1 GGTCCGATGACTAAGTGTCATCATGAGTACATGAA-TCCTTCACGGATTATA-A
*
34473 GGTCCGATGACTATA-TGTCATTATGAGTA
1 GGTCCGATGACTA-AGTGTCATCATGAGTA
34502 TTAAATGAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
52 82 0.69
53 36 0.30
54 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCACGGATTATAA
Done.