Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013075.1 Kokia drynarioides strain JFW-HI SEQ_128093, 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: 540471
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 504 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:515909 original size:56 final size:60
Alignment explanation
Indices: 515847--515970 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 60
515837 AGTAGTCACT
* * * *
515847 CAACTATTACTA-A-ATTTTTTTTG-TCA-CTCAATTATGAAAAGTTACAACA-TGTCA-C
1 CAACTATTAATATATATATTTTTTGCTCACCT-AACTATGAAAAGTTACAAAATTGTCATC
515902 CGAACTATTAATATATATATTTTTTGCTCACCTAACTATGAAAAGTTACAAAATTGTCATC
1 C-AACTATTAATATATATATTTTTTGCTCACCTAACTATGAAAAGTTACAAAATTGTCATC
515963 CAACTATT
1 CAACTATT
515971 CAATTTTATC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
55 1 0.02
56 10 0.17
57 1 0.02
58 9 0.16
59 21 0.36
60 14 0.24
61 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (60 bp):
CAACTATTAATATATATATTTTTTGCTCACCTAACTATGAAAAGTTACAAAATTGTCATC
Found at i:517291 original size:23 final size:23
Alignment explanation
Indices: 517265--517434 Score: 143
Period size: 23 Copynumber: 7.3 Consensus size: 23
517255 TGCTAGGCAA
517265 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
517288 CAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
517311 CATAGAGCAC-CGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* * *
517333 AACAGAAAGCACGA-GACGTGCTGAA-
1 --CAGAGAGCAC-ACAAAGTGCT-AAT
*
517358 CAGAGAGCACACACAGTGCTGAA-
1 CAGAGAGCACACAAAGTGCT-AAT
* *
517381 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* * *
517404 CAGAAAGCACACACAA-TTCTAAA
1 CAGAGAGCACACA-AAGTGCTAAT
517427 CAGAGAGC
1 CAGAGAGC
517435 GCGCTAGTGT
Statistics
Matches: 126, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
22 15 0.12
23 93 0.74
24 9 0.07
25 7 0.06
26 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:517354 original size:70 final size:69
Alignment explanation
Indices: 517280--517413 Score: 170
Period size: 70 Copynumber: 1.9 Consensus size: 69
517270 AGCACACAAA
*
517280 GTGCT-AATCAGAGAGCACACGA-AGTGCT-AATCATAGAGCAC-CGA-AGTGCTAATAACAGAA
1 GTGCTGAA-CAGAGAGCACAC-ACAGTGCTGAA-CAGAGAGCACAC-ACAGTGCT-A-AACAGAA
517340 AGCACGAGAC
60 AGCACGAGAC
517350 GTGCTGAACAGAGAGCACACACAGTGCTGAACAGAGAGCACACACAGTGCTAAACAGAAAGCAC
1 GTGCTGAACAGAGAGCACACACAGTGCTGAACAGAGAGCACACACAGTGCTAAACAGAAAGCAC
517414 ACACAATTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
69 13 0.22
70 34 0.59
71 11 0.19
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (69 bp):
GTGCTGAACAGAGAGCACACACAGTGCTGAACAGAGAGCACACACAGTGCTAAACAGAAAGCACG
AGAC
Found at i:519855 original size:29 final size:30
Alignment explanation
Indices: 519799--519877 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
519789 ATTTTAAAAT
* * *
519799 TATACATGAACTTTGATTTAATGTGTAATTG
1 TATACATGAATTTTAATTTAA-GTGTAATTA
*
519830 TATACATGAATTTTAATTTGA-TGTAATTA
1 TATACATGAATTTTAATTTAAGTGTAATTA
* *
519859 TACACGTGAAATTTTAATT
1 TATACATG-AATTTTAATT
519878 ATAATTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.32
30 10 0.24
31 18 0.44
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAAGTGTAATTA
Found at i:520477 original size:11 final size:11
Alignment explanation
Indices: 520461--520485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
520451 TATTTTCGAC
520461 TTTTTAATATT
1 TTTTTAATATT
520472 TTTTTAATATT
1 TTTTTAATATT
520483 TTT
1 TTT
520486 CATCTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:530584 original size:43 final size:43
Alignment explanation
Indices: 530523--530608 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
530513 AAGGCCACTC
530523 ACACCACAAATGCATCTCCCAAGAATCTAAACCGAGAATACTT
1 ACACCACAAATGCATCTCCCAAGAATCTAAACCGAGAATACTT
530566 ACACCACAAATGCATCTCCCAAGAATCTAAACCGAGAATACTT
1 ACACCACAAATGCATCTCCCAAGAATCTAAACCGAGAATACTT
530609 TCCAACCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (43 bp):
ACACCACAAATGCATCTCCCAAGAATCTAAACCGAGAATACTT
Found at i:536096 original size:18 final size:20
Alignment explanation
Indices: 536058--536097 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
536048 ATAGAAATTT
*
536058 TTTTTATTTAAGTTCTTAAA
1 TTTTTATTTAAATTCTTAAA
536078 TTTTT-TTTAAATT-TTAAA
1 TTTTTATTTAAATTCTTAAA
536096 TT
1 TT
536098 AGTAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTTATTTAAATTCTTAAA
Done.