Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002562.1 Kokia drynarioides strain JFW-HI SEQ_114759, 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: 17166
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:4844 original size:31 final size:31
Alignment explanation
Indices: 4782--4844 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
4772 ATGAAATGAT
* *
4782 AGAAAAAATAAATAAAAATCATATTTCTAAA
1 AGAAAAAATAAATAAAAATCAAAATTCTAAA
* *
4813 AGAAGAAATATATAAAATATCAAAATT-TAAA
1 AGAAAAAATAAATAAAA-ATCAAAATTCTAAA
4844 A
1 A
4845 TTTGGACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (31 bp):
AGAAAAAATAAATAAAAATCAAAATTCTAAA
Found at i:6220 original size:19 final size:19
Alignment explanation
Indices: 6196--6255 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
6186 AGAAAAGAAG
6196 AACAAATAAACTAAATTGA
1 AACAAATAAACTAAATTGA
* ***
6215 AACAAAT-CA-TTGGTT--
1 AACAAATAAACTAAATTGA
6230 AACAAATAAACTAAATTGA
1 AACAAATAAACTAAATTGA
6249 AACAAAT
1 AACAAAT
6256 CATTGGTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
15 7 0.24
16 1 0.03
17 6 0.21
18 1 0.03
19 14 0.48
ACGTcount: A:0.58, C:0.12, G:0.07, T:0.23
Consensus pattern (19 bp):
AACAAATAAACTAAATTGA
Found at i:6234 original size:34 final size:34
Alignment explanation
Indices: 6196--6264 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
6186 AGAAAAGAAG
6196 AACAAATAAACTAAATTGAAACAAATCATTGGTT
1 AACAAATAAACTAAATTGAAACAAATCATTGGTT
6230 AACAAATAAACTAAATTGAAACAAATCATTGGTT
1 AACAAATAAACTAAATTGAAACAAATCATTGGTT
6264 A
1 A
6265 TTTAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.26
Consensus pattern (34 bp):
AACAAATAAACTAAATTGAAACAAATCATTGGTT
Found at i:10059 original size:21 final size:22
Alignment explanation
Indices: 10017--10067 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
10007 ATGATTTGAT
*
10017 AAAAAATAAAAATTTAAGAACTAA
1 AAAAAATAAAAA--TAAAAACTAA
10041 AAAAAATAAAAA-AAAAACTAA
1 AAAAAATAAAAATAAAAACTAA
*
10062 ATAAAA
1 AAAAAA
10068 GTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
24 12 0.48
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAAATAAAAATAAAAACTAA
Found at i:12812 original size:30 final size:29
Alignment explanation
Indices: 12776--12979 Score: 171
Period size: 30 Copynumber: 6.9 Consensus size: 29
12766 CCTTGGAGGT
12776 CCCTAAACTATCCAAAAATTACATTTTTAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
*
12806 CCCTAAACTTTCAAAAAATT-CATTTTTGAC
1 CCCTAAAC-TTCCAAAAATTACATTTTT-AC
* * *
12836 CTCGAAACTTCTAAAAATTACATTTTTA-
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * * *
12864 CCTTAAACTTTCTAAAATTCCATTTTTAAC
1 CCCTAAACTTCCAAAAATTACATTTTT-AC
* * *
12894 CCCAAAACATCCAAAAAATACATTTTTA-
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* *
12922 CCCTCGAACTTCCAAAAATTCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTACATTTTT-AC
* * * *
12953 CTCAAAACTTGCAAAATTTACCATTTT
1 CCCTAAACTTCCAAAAATTA-CATTTT
12980 GCCCTCGAGT
Statistics
Matches: 136, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
28 23 0.17
29 39 0.29
30 65 0.48
31 9 0.07
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:12911 original size:59 final size:59
Alignment explanation
Indices: 12780--12979 Score: 233
Period size: 59 Copynumber: 3.4 Consensus size: 59
12770 GGAGGTCCCT
* *
12780 AAACTATCCAAAAATTACATTTTTACCCCTAAACTTTCAAAAAATT-CATTTTTGACCTCG
1 AAAC-ATCCAAAAATTACATTTTTACCCTTAAACTTTC-AAAAATTCCATTTTTGACCTCA
* * * * *
12840 AAACTTCTAAAAATTACATTTTTA-CCTTAAACTTTCTAAAATTCCATTTTTAACCCCA
1 AAACATCCAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTCCATTTTTGACCTCA
* ** *
12898 AAACATCCAAAAAATACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCA
1 AAACATCCAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTCCATTTTTGACCTCA
* * *
12957 AAACTTGCAAAATTTACCATTTT
1 AAACATCCAAAAATTA-CATTTT
12980 GCCCTCGAGT
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
57 6 0.05
58 43 0.37
59 58 0.50
60 10 0.09
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACATCCAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTCCATTTTTGACCTCA
Found at i:13944 original size:16 final size:16
Alignment explanation
Indices: 13919--13962 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
13909 GACCTACATG
*
13919 TTTTTCAAAACGGCTT
1 TTTTTAAAAACGGCTT
13935 TTTTTAAAAACGGCTT
1 TTTTTAAAAACGGCTT
13951 TTTTTAAAAACG
1 TTTTTAAAAACG
13963 TTTTGTGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTTTAAAAACGGCTT
Done.