Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012397.1 Kokia drynarioides strain JFW-HI SEQ_127401, 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: 3524
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1894 original size:72 final size:72
Alignment explanation
Indices: 1793--1958 Score: 230
Period size: 72 Copynumber: 2.3 Consensus size: 72
1783 CGAAGTACTT
* *
1793 AACAGAAGCACATA-AGTGCTGGGGAAACAGAAGCACATA-AGTGCTGGGGAAACAGAAGCACAC
1 AACAGAAGCACACACAGTGCT-GGGAAACAGAAGCACACACAGTGCT-GGGAAACAGAAGCACAC
1856 AC-GATGCTG
64 ACAG-TGCTG
* * *
1865 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTGGGTAACAGCAGCACACAC
1 AACAGAAGCACACACAGTGCTGGGAAACAGAAGCACACACAGTGCTGGGAAACAGAAGCACACAC
1930 AGTGCTG
66 AGTGCTG
*
1937 AACAAAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
1959 AATAGTAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
72 72 0.85
73 13 0.15
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (72 bp):
AACAGAAGCACACACAGTGCTGGGAAACAGAAGCACACACAGTGCTGGGAAACAGAAGCACACAC
AGTGCTG
Found at i:1911 original size:47 final size:49
Alignment explanation
Indices: 1792--1958 Score: 179
Period size: 47 Copynumber: 3.5 Consensus size: 49
1782 CCGAAGTACT
* *
1792 TAACAGAAGCACATA-AGTGCTGGGGAAACAGAAGCACATA-AGTGCTGGGG
1 TAACAGAAGCACACACAGTGCT--GGAAACAGAAGCACACACAGTGCT-GGG
*
1842 AAACAGAAGCACACAC-GATGCT-G-AACAGAAGCACACACAGTGCTGGG
1 TAACAGAAGCACACACAG-TGCTGGAAACAGAAGCACACACAGTGCTGGG
* *
1889 TAACAGAAGCACACACAGTGCTGGGTAACAGCAGCACACACAGTGCT--G
1 TAACAGAAGCACACACAGTGCT-GGAAACAGAAGCACACACAGTGCTGGG
*
1937 -AACAAAAGCACACACAGTGCTG
1 TAACAGAAGCACACACAGTGCTG
1959 AATAGTAAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
46 1 0.01
47 55 0.53
48 9 0.09
49 1 0.01
50 34 0.33
51 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (49 bp):
TAACAGAAGCACACACAGTGCTGGAAACAGAAGCACACACAGTGCTGGG
Found at i:1928 original size:27 final size:25
Alignment explanation
Indices: 1792--1958 Score: 190
Period size: 25 Copynumber: 6.9 Consensus size: 25
1782 CCGAAGTACT
*
1792 TAACAGAAGCACATA-AGTGCTGGGG
1 TAACAGAAGCACACACAGTGCT-GGG
* *
1817 AAACAGAAGCACATA-AGTGCTGGGG
1 TAACAGAAGCACACACAGTGCT-GGG
*
1842 AAACAGAAGCACACAC-GATGCT--G
1 TAACAGAAGCACACACAG-TGCTGGG
1865 -AACAGAAGCACACACAGTGCTGGG
1 TAACAGAAGCACACACAGTGCTGGG
1889 TAACAGAAGCACACACAGTGCTGGG
1 TAACAGAAGCACACACAGTGCTGGG
*
1914 TAACAGCAGCACACACAGTGCT--G
1 TAACAGAAGCACACACAGTGCTGGG
*
1937 -AACAAAAGCACACACAGTGCTG
1 TAACAGAAGCACACACAGTGCTG
1959 AATAGTAAAT
Statistics
Matches: 130, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
22 38 0.29
23 3 0.02
24 1 0.01
25 84 0.65
26 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (25 bp):
TAACAGAAGCACACACAGTGCTGGG
Found at i:2069 original size:24 final size:26
Alignment explanation
Indices: 2031--2078 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
2021 TCAACATGGG
2031 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
2057 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
2079 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:2645 original size:22 final size:22
Alignment explanation
Indices: 2617--2735 Score: 150
Period size: 22 Copynumber: 5.1 Consensus size: 22
2607 GTGCTGGGGA
2617 AACAGAAGCACACAC-GATGCTG
1 AACAGAAGCACACACAG-TGCTG
2639 AACAGAAGCACACACAAGTGCTGGG
1 AACAGAAGCACACAC-AGTGCT--G
2664 TAACAGAAGCACACACAGTGCTGGG
1 -AACAGAAGCACACACAGTGCT--G
*
2689 TAACAGCAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
2712 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
2734 AA
1 AA
2736 TAGTAAATGC
Statistics
Matches: 90, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
22 38 0.42
23 5 0.06
24 1 0.01
25 31 0.34
26 15 0.17
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.10
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:2689 original size:25 final size:24
Alignment explanation
Indices: 2596--2733 Score: 162
Period size: 25 Copynumber: 5.8 Consensus size: 24
2586 NNNNNNNNNN
*
2596 GAAGCACATA-AGTGCTGGGGAAACA
1 GAAGCACACACAGTGCT-GGG-AACA
2621 GAAGCACACAC-GATGCT--GAACA
1 GAAGCACACACAG-TGCTGGGAACA
2643 GAAGCACACACAAGTGCTGGGTAACA
1 GAAGCACACAC-AGTGCTGGG-AACA
2669 GAAGCACACACAGTGCTGGGTAACA
1 GAAGCACACACAGTGCTGGG-AACA
*
2694 GCAGCACACACAGTGCT--GAACA
1 GAAGCACACACAGTGCTGGGAACA
2716 GAAGCACACACAGTGCTG
1 GAAGCACACACAGTGCTG
2734 AATAGTAAAT
Statistics
Matches: 102, Mismatches: 3, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
22 35 0.34
23 6 0.06
24 1 0.01
25 41 0.40
26 19 0.19
ACGTcount: A:0.38, C:0.25, G:0.27, T:0.11
Consensus pattern (24 bp):
GAAGCACACACAGTGCTGGGAACA
Found at i:2715 original size:73 final size:72
Alignment explanation
Indices: 2596--2733 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 72
2586 NNNNNNNNNN
*
2596 GAAGCACATAAGTGCTGGGGAAACAGAAGCACACACGATGCTGAACAGAAGCACACACAAGTGCT
1 GAAGCACACAAGTGCTGGGGAAACAGAAGCACACACGATGCTGAACAGAAGCACACAC-AGTGCT
2661 GGGTAACA
65 GGGTAACA
* *
2669 GAAGCACACACAGTGCT-GGGTAACAGCAGCACACAC-AGTGCTGAACAGAAGCACACACAGTGC
1 GAAGCACACA-AGTGCTGGGGAAACAGAAGCACACACGA-TGCTGAACAGAAGCACACACAGTGC
2732 TG
64 TG
2734 AATAGTAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
72 8 0.13
73 46 0.77
74 6 0.10
ACGTcount: A:0.38, C:0.25, G:0.27, T:0.11
Consensus pattern (72 bp):
GAAGCACACAAGTGCTGGGGAAACAGAAGCACACACGATGCTGAACAGAAGCACACACAGTGCTG
GGTAACA
Found at i:2844 original size:24 final size:26
Alignment explanation
Indices: 2806--2853 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
2796 TCTACATGGG
2806 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
2832 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
2854 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.