Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013400.1 Kokia drynarioides strain JFW-HI SEQ_128425, 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: 31506
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3246 original size:43 final size:43
Alignment explanation
Indices: 3192--3332 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 43
3182 TTTATTAATG
* * *
3192 TTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGATTATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
* * *
3235 TTAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
* * *
3278 TTAGCGGCATTTGTGTGAAAAGTGCCGCTAAAGATCATGTT-T
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
*
3320 TATAGCGGTGTTT
1 T-TAGCGGCGTTT
3333 TTTCTAATAA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.02
43 81 0.98
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
Found at i:3367 original size:15 final size:15
Alignment explanation
Indices: 3349--3384 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3339 ATAAGCGCCG
3349 TTATTTTTAGCGGCA
1 TTATTTTTAGCGGCA
*
3364 TTATCTTTAGCGGCA
1 TTATTTTTAGCGGCA
3379 TT-TTTT
1 TTATTTT
3385 GCAGCGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (15 bp):
TTATTTTTAGCGGCA
Found at i:6373 original size:24 final size:25
Alignment explanation
Indices: 6346--6399 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
6336 AAATTCTTTC
* *
6346 AATTATTTTATTT-T-AATATTTAAT
1 AATTATTTAATTTATAAATA-TTAAA
6370 AATTATTTAATTTATAAATATTAAA
1 AATTATTTAATTTATAAATATTAAA
6395 AATTA
1 AATTA
6400 AAAAATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 12 0.46
25 10 0.38
26 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTATTTAATTTATAAATATTAAA
Found at i:18606 original size:10 final size:10
Alignment explanation
Indices: 18591--18635 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
18581 ATTCATGGAA
18591 TTTGTATTGT
1 TTTGTATTGT
18601 TTTGTATT-T
1 TTTGTATTGT
*
18610 TTT-TTTTG-
1 TTTGTATTGT
*
18618 GTTGTATTGT
1 TTTGTATTGT
18628 TTTGTATT
1 TTTGTATT
18636 TTAAGCACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
8 5 0.18
9 8 0.29
10 15 0.54
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.73
Consensus pattern (10 bp):
TTTGTATTGT
Found at i:20865 original size:23 final size:23
Alignment explanation
Indices: 20815--20869 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
20805 ACGTGGCATT
* *
20815 CAGTCAGCAGCTTCTAAAAGATC
1 CAGTCAGCAGCTTCCAAAAGATA
* *
20838 CAGTCAGCAGCTTCCAGAAGGTA
1 CAGTCAGCAGCTTCCAAAAGATA
*
20861 TAGTCAGCA
1 CAGTCAGCA
20870 AGGATGGACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (23 bp):
CAGTCAGCAGCTTCCAAAAGATA
Found at i:21600 original size:17 final size:17
Alignment explanation
Indices: 21578--21611 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21568 AGGCTGATAC
*
21578 TTAAATTGAGTTTCTTT
1 TTAAATTAAGTTTCTTT
*
21595 TTAAATTAATTTTCTTT
1 TTAAATTAAGTTTCTTT
21612 AAATTCTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
TTAAATTAAGTTTCTTT
Found at i:27708 original size:27 final size:27
Alignment explanation
Indices: 27643--27710 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
27633 CAAGAACCTT
*
27643 AAACCTTTAACCTCAAACATCAAATCC
1 AAACCTTAAACCTCAAACATCAAATCC
** * * *
27670 AAACCCCAAACCTTAAATATCAAATCG
1 AAACCTTAAACCTCAAACATCAAATCC
*
27697 AAACCTTGAACCTC
1 AAACCTTAAACCTC
27711 GAGATTCGAG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.21
Consensus pattern (27 bp):
AAACCTTAAACCTCAAACATCAAATCC
Found at i:28742 original size:19 final size:21
Alignment explanation
Indices: 28705--28753 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
28695 GGTCACATGA
28705 CCGTGTGTTTCAAACACACGC
1 CCGTGTGTTTCAAACACACGC
28726 CCGTGTGTTTCAAACACACGC
1 CCGTGTGTTTCAAACACACGC
28747 CCGTGTG
1 CCGTGTG
28754 CCTACTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.24
Consensus pattern (21 bp):
CCGTGTGTTTCAAACACACGC
Found at i:29834 original size:37 final size:37
Alignment explanation
Indices: 29758--29900 Score: 144
Period size: 37 Copynumber: 3.7 Consensus size: 37
29748 CCGATAATAT
*
29758 CGACACAAAGGTCTGCTAGGCACATAGCCCGATCT-CAC
1 CGACACAAA-GCCTGCTAGGCACATAGCCCGAT-TACAC
*
29796 CGGCACAAAGCCTGCTAGGCACATAGCCCGATTACAC
1 CGACACAAAGCCTGCTAGGCACATAGCCCGATTACAC
* * *
29833 CGACACCAACACGAAGTCTGCTAGGCACATAGCCTGATTACAT
1 CG--A-C-ACA--AAGCCTGCTAGGCACATAGCCCGATTACAC
* *
29876 CGAAACGAAGCCTGCTAGGCACATA
1 CGACACAAAGCCTGCTAGGCACATA
29901 ACCCAATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
36 1 0.01
37 44 0.49
38 8 0.09
39 2 0.02
40 1 0.01
41 4 0.04
43 29 0.33
ACGTcount: A:0.31, C:0.32, G:0.21, T:0.15
Consensus pattern (37 bp):
CGACACAAAGCCTGCTAGGCACATAGCCCGATTACAC
Done.