Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003392.1 Kokia drynarioides strain JFW-HI SEQ_116131, 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: 37274
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:299 original size:3 final size:3
Alignment explanation
Indices: 291--318 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
281 TGTATTTTTT
291 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
319 AACCTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:15838 original size:17 final size:17
Alignment explanation
Indices: 15818--15850 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15808 TTAAAAATTA
15818 TAAA-GATATAAATTATT
1 TAAATGATA-AAATTATT
15835 TAAATGATAAAATTAT
1 TAAATGATAAAATTAT
15851 ATTTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TAAATGATAAAATTATT
Found at i:28828 original size:42 final size:41
Alignment explanation
Indices: 28753--29084 Score: 152
Period size: 42 Copynumber: 7.9 Consensus size: 41
28743 ATTTATGGGA
*
28753 AAACGCCGCTATTGC-TTACCTTTAGCGGCGTTTTTCCCAT
1 AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCCAT
* * *
28793 AAACGCCGCTAATGCTATTACCTTTAGTGGTGTTTTTCCTAT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCCAT
** * * * *
28835 AAACGCCGCTAATGCTCTTATTTTTTTGCGGC-ATTTTCTCAC
1 AAACGCCGCTAATGCT-TTA-CCTTTAGCGGCGTTTTTCCCAT
* * * * * * *
28877 AAACGCCACTAGTGCTCTTCCCTTTTGCGGC-ATTTTCTCAC
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCCAT
* * * * *
28918 AAACGCCGCTAATGTTCTTACTTTTTGCGGCATTAGCGCCATTTTCTCAT
1 AAACGCCGCTAATGCT-TTACCTTTAGC-G-----GCG--TTTTTCCCAT
* * * *
28968 AAACGCCGCTAATACTCTTATCTTTTGCGACGTTTTTCCCAT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCCAT
* * * * * ** *
29010 AAACGCAGCT-ATGGGTTTACCTTTTGCGGCATTTAT-GAAA
1 AAACGCCGCTAAT-GCTTTACCTTTAGCGGCGTTTTTCCCAT
* * * *
29050 AAACGCCACTATTGCTTTACTTTTTGCGGCGTTTT
1 AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTT
29085 CGGTCCAAAC
Statistics
Matches: 229, Mismatches: 49, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
40 41 0.18
41 61 0.27
42 83 0.36
43 6 0.03
44 2 0.01
47 2 0.01
49 1 0.00
50 33 0.14
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (41 bp):
AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCCAT
Found at i:28901 original size:84 final size:82
Alignment explanation
Indices: 28753--28951 Score: 188
Period size: 84 Copynumber: 2.4 Consensus size: 82
28743 ATTTATGGGA
* * * * * *
28753 AAACGCCGCTATTG--CTTACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGCTATTACCT
1 AAACGCCGCTAATGCTCTTACTTTTTGCGGC-ATTTTCCCACAAACGCCACTAATGCTATTACCT
* ** *
28816 TTAGTGGTGTTTT-TCCTAT
65 TTAGCGGCATTTTCT-C-AC
* * * * *
28835 AAACGCCGCTAATGCTCTTATTTTTTTGCGGCATTTTCTCACAAACGCCACTAGTGCTCTTCCCT
1 AAACGCCGCTAATGCTCTTA-CTTTTTGCGGCATTTTCCCACAAACGCCACTAATGCTATTACCT
*
28900 TTTGCGGCATTTTCTCAC
65 TTAGCGGCATTTTCTCAC
*
28918 AAACGCCGCTAATGTTCTTACTTTTTGCGGCATT
1 AAACGCCGCTAATGCTCTTACTTTTTGCGGCATT
28952 AGCGCCATTT
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
82 26 0.27
83 20 0.21
84 40 0.42
85 9 0.09
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCTTACTTTTTGCGGCATTTTCCCACAAACGCCACTAATGCTATTACCTT
TAGCGGCATTTTCTCAC
Found at i:28914 original size:41 final size:41
Alignment explanation
Indices: 28767--28951 Score: 156
Period size: 41 Copynumber: 4.4 Consensus size: 41
28757 GCCGCTATTG
* * * * *
28767 CTTACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGCT
1 CTTACCTTTTGCGGC-ATTTTCTCACAAACGCCACTAATGCT
* * * ** * *
28809 ATTACCTTTAGTGGTGTTTT-TCCTATAAACGCCGCTAATGCT
1 CTTACCTTTTGCGGCATTTTCT-C-ACAAACGCCACTAATGCT
** *
28851 CTTATTTTTTTGCGGCATTTTCTCACAAACGCCACTAGTGCT
1 CTTA-CCTTTTGCGGCATTTTCTCACAAACGCCACTAATGCT
* * *
28893 CTTCCCTTTTGCGGCATTTTCTCACAAACGCCGCTAATGTT
1 CTTACCTTTTGCGGCATTTTCTCACAAACGCCACTAATGCT
*
28934 CTTACTTTTTGCGGCATT
1 CTTACCTTTTGCGGCATT
28952 AGCGCCATTT
Statistics
Matches: 116, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
41 53 0.46
42 51 0.44
43 11 0.09
44 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (41 bp):
CTTACCTTTTGCGGCATTTTCTCACAAACGCCACTAATGCT
Found at i:29982 original size:24 final size:24
Alignment explanation
Indices: 29943--29998 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
29933 TTTATAAGTG
29943 AAATATTT-TAAATACACATACAA
1 AAATATTTATAAATACACATACAA
29966 AAATATTTATAAATACACATACAA
1 AAATATTTATAAATACACATACAA
29990 AAATATTTA
1 AAATATTTA
29999 CTACACTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATATTTATAAATACACATACAA
Found at i:31874 original size:21 final size:21
Alignment explanation
Indices: 31857--31898 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31847 AACTTCTATT
31857 GATACAAGTGACAGTTCTACC
1 GATACAAGTGACAGTTCTACC
**
31878 GATACAAGTGACTCTTCTACC
1 GATACAAGTGACAGTTCTACC
31899 AAAACAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (21 bp):
GATACAAGTGACAGTTCTACC
Found at i:31905 original size:21 final size:21
Alignment explanation
Indices: 31860--31905 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
31850 TTCTATTGAT
* * *
31860 ACAAGTGACAGTTCTACCGAT
1 ACAAGTGACACTTCTACCAAA
*
31881 ACAAGTGACTCTTCTACCAAA
1 ACAAGTGACACTTCTACCAAA
31902 ACAA
1 ACAA
31906 ATCTTACTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (21 bp):
ACAAGTGACACTTCTACCAAA
Found at i:34625 original size:80 final size:79
Alignment explanation
Indices: 34492--34677 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 79
34482 TAAGTGACTA
* * * * *
34492 AACTGGCAGTGATATTGTAAACACTGCAATACTATTACTTAATTGGAAGTGACACTGTAAACACT
1 AACTGGCAGTGACACTGTAAACACAGCAATACTACTACTAAATTGGAAGTGACACTG-AAACACT
34557 ACAATATTACCACTG
65 ACAATATTACCACTG
* * *
34572 AACTGGCAGTGACACTGTAAACACAGCGATATTACTACTAAACTT-GCAGTGACACTGAAACACT
1 AACTGGCAGTGACACTGTAAACACAGCAATACTACTACTAAA-TTGGAAGTGACACTGAAACACT
* * *
34636 GCAATGTTACTACTG
65 ACAATATTACCACTG
* * * *
34651 AACTAGCTGTAACACTATAAACACAGC
1 AACTGGCAGTGACACTGTAAACACAGC
34678 TAGACTACCA
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 42 0.47
80 46 0.51
81 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (79 bp):
AACTGGCAGTGACACTGTAAACACAGCAATACTACTACTAAATTGGAAGTGACACTGAAACACTA
CAATATTACCACTG
Found at i:34666 original size:39 final size:40
Alignment explanation
Indices: 34492--34674 Score: 179
Period size: 40 Copynumber: 4.6 Consensus size: 40
34482 TAAGTGACTA
* * * * * *
34492 AACTGGCAGTGATATTGTAAACACTGCAATACTATTACTT
1 AACTAGCAGTGACACTGTAAACACTGCAATATTACTACTG
* * * * *
34532 AATTGGAAGTGACACTGTAAACACTACAATATTACCACTG
1 AACTAGCAGTGACACTGTAAACACTGCAATATTACTACTG
* * * *
34572 AACTGGCAGTGACACTGTAAACACAGCGATATTACTACTA
1 AACTAGCAGTGACACTGTAAACACTGCAATATTACTACTG
* *
34612 AACTTGCAGTGACACTG-AAACACTGCAATGTTACTACTG
1 AACTAGCAGTGACACTGTAAACACTGCAATATTACTACTG
* * *
34651 AACTAGCTGTAACACTATAAACAC
1 AACTAGCAGTGACACTGTAAACAC
34675 AGCTAGACTA
Statistics
Matches: 117, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
39 31 0.26
40 86 0.74
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (40 bp):
AACTAGCAGTGACACTGTAAACACTGCAATATTACTACTG
Found at i:35969 original size:38 final size:38
Alignment explanation
Indices: 35895--35970 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
35885 CCTAAGGCAT
* * *
35895 ATGTGGGGGTTTAGGTGTTAAAACTGAATAATTAAAGC
1 ATGTGGGGGTTTAGGTGTTAAAACCGAACAAGTAAAGC
*
35933 ATGTGTGGGG-TTAGGTGTTAAAGCCGAACAAGTAAAGC
1 ATGTG-GGGGTTTAGGTGTTAAAACCGAACAAGTAAAGC
35971 TAGTAAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.28
Consensus pattern (38 bp):
ATGTGGGGGTTTAGGTGTTAAAACCGAACAAGTAAAGC
Done.