Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013932.1 Kokia drynarioides strain JFW-HI SEQ_128962, 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: 56637
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:37061 original size:10 final size:10
Alignment explanation
Indices: 37048--37081 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
37038 TATGATTTTT
37048 TAATAATTTA
1 TAATAATTTA
37058 TAATAAATTTA
1 TAAT-AATTTA
37069 T-ATAATTTA
1 TAATAATTTA
37078 TAAT
1 TAAT
37082 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.32
10 8 0.36
11 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATAATTTA
Found at i:39530 original size:24 final size:23
Alignment explanation
Indices: 39498--39550 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
39488 AAAACTCAAT
*
39498 TAAACATTAATTTATTTGAAAAAA
1 TAAAAATTAATTTATTT-AAAAAA
* *
39522 TAAAAATTATTTTATTTAAAATA
1 TAAAAATTAATTTATTTAAAAAA
39545 TAAAAA
1 TAAAAA
39551 ATATTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAATTAATTTATTTAAAAAA
Found at i:39551 original size:24 final size:23
Alignment explanation
Indices: 39498--39565 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
39488 AAAACTCAAT
* * *
39498 TAAACATTAATTTATTTGAAAAAA
1 TAAAAATTATTTTATTT-AAAATA
39522 TAAAAATTATTTTATTTAAAATA
1 TAAAAATTATTTTATTTAAAATA
* *
39545 TAAAAAATATTATA-TTAAAAT
1 TAAAAATTATTTTATTTAAAAT
39566 TATTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.18
23 17 0.44
24 15 0.38
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TAAAAATTATTTTATTTAAAATA
Found at i:43306 original size:56 final size:56
Alignment explanation
Indices: 43246--43398 Score: 166
Period size: 56 Copynumber: 2.7 Consensus size: 56
43236 ATTAACATCC
* * * *
43246 AAACAACAAAAATAACAACCAAAATAGTAGCAAAAATAACAGT-AAAACAACATTAA
1 AAACAACAAAAATAGCAACAAAAATAGCAGCAAAAATAACAGTAAAAACAACA-AAA
* * * * *
43302 AAACAACAAAAATGGCAGCAAAAATAGCAG-TAAAACAACATTAAAAACAACAAAA
1 AAACAACAAAAATAGCAACAAAAATAGCAGCAAAAATAACAGTAAAAACAACAAAA
* * *
43357 ATAATAACAAAAATAGCAACAAAAACAACAGCAAAAATAACA
1 A-AACAACAAAAATAGCAACAAAAATAGCAGCAAAAATAACA
43399 CGAAAATAAC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
55 12 0.15
56 58 0.74
57 8 0.10
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.10
Consensus pattern (56 bp):
AAACAACAAAAATAGCAACAAAAATAGCAGCAAAAATAACAGTAAAAACAACAAAA
Found at i:43365 original size:12 final size:12
Alignment explanation
Indices: 43347--43421 Score: 80
Period size: 12 Copynumber: 6.2 Consensus size: 12
43337 CAACATTAAA
43347 AACAACAAAAAT
1 AACAACAAAAAT
*
43359 AATAACAAAAAT
1 AACAACAAAAAT
* *
43371 AGCAACAAAAAC
1 AACAACAAAAAT
*
43383 AACAGCAAAAAT
1 AACAACAAAAAT
*
43395 AAC-ACGAAAAT
1 AACAACAAAAAT
43406 AACAATCAAACAAT
1 AACAA-CAAA-AAT
43420 AA
1 AA
43422 AAAACAACTC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.18
12 33 0.66
13 3 0.06
14 5 0.10
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:43372 original size:44 final size:44
Alignment explanation
Indices: 43246--43374 Score: 179
Period size: 44 Copynumber: 2.9 Consensus size: 44
43236 ATTAACATCC
* * *
43246 AAACAACA-AAAATAACAACCAAAATAGTAGCAAAAATAACAGTA
1 AAACAACATTAAA-AACAACAAAAATAGTAGCAAAAATAGCAGTA
* *
43290 AAACAACATTAAAAACAACAAAAATGGCAGCAAAAATAGCAGTA
1 AAACAACATTAAAAACAACAAAAATAGTAGCAAAAATAGCAGTA
* *
43334 AAACAACATTAAAAACAACAAAAATAATAACAAAAATAGCA
1 AAACAACATTAAAAACAACAAAAATAGTAGCAAAAATAGCA
43375 ACAAAAACAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
44 72 0.96
45 3 0.04
ACGTcount: A:0.66, C:0.16, G:0.07, T:0.12
Consensus pattern (44 bp):
AAACAACATTAAAAACAACAAAAATAGTAGCAAAAATAGCAGTA
Found at i:43391 original size:24 final size:24
Alignment explanation
Indices: 43317--43395 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
43307 ACAAAAATGG
**
43317 CAGCAAAAATAGC-AGTAAAACAA
1 CAGCAAAAATAGCAACAAAAACAA
** *
43340 CA-TTAAAA-A-CAACAAAAATAA
1 CAGCAAAAATAGCAACAAAAACAA
* *
43361 TAACAAAAATAGCAACAAAAACAA
1 CAGCAAAAATAGCAACAAAAACAA
43385 CAGCAAAAATA
1 CAGCAAAAATA
43396 ACACGAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.02
21 9 0.22
22 8 0.20
23 3 0.07
24 20 0.49
ACGTcount: A:0.67, C:0.16, G:0.06, T:0.10
Consensus pattern (24 bp):
CAGCAAAAATAGCAACAAAAACAA
Found at i:55831 original size:26 final size:25
Alignment explanation
Indices: 55780--55847 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
55770 ATACGGAACA
* *
55780 AACAGAGAGCACATAAGTGCTGGGC
1 AACAGAGAACACACAAGTGCTGGGC
55805 AACAGAGAACACACACAGTGCTGGGC
1 AACAGAGAACACACA-AGTGCTGGGC
*
55831 AACAGAGTACACA-AAGT
1 AACAGAGAACACACAAGT
55848 ACTAATTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 3 0.08
25 14 0.36
26 22 0.56
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.10
Consensus pattern (25 bp):
AACAGAGAACACACAAGTGCTGGGC
Found at i:55951 original size:23 final size:23
Alignment explanation
Indices: 55807--55955 Score: 111
Period size: 23 Copynumber: 6.3 Consensus size: 23
55797 TGCTGGGCAA
* ***
55807 CAGAGAACACACACAGTGCTGGG
1 CAGAGAGCACACACAGTGCTAAT
* * * *
55830 CAACAGAGTACACAAAGTACTAAT
1 C-AGAGAGCACACACAGTGCTAAT
* * *
55854 TAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* *
55877 CAAAAAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* * *
55900 AACAAAGAGCACGAGAC-GTGCTAAA
1 --CAGAGAGCAC-ACACAGTGCTAAT
55925 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
55948 CAGAGAGC
1 CAGAGAGC
55956 GCGCTAGTGT
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
22 3 0.03
23 63 0.64
24 14 0.14
25 16 0.16
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACACAGTGCTAAT
Done.