Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011215.1 Kokia drynarioides strain JFW-HI SEQ_126193, 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: 9053
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:2075 original size:16 final size:17
Alignment explanation
Indices: 2054--2096 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2044 ATATTAATAA
2054 AAATAATATTAT-TTTT
1 AAATAATATTATATTTT
*
2070 AAATAA-ATAAATATTTT
1 AAATAATAT-TATATTTT
2087 AAATAATATT
1 AAATAATATT
2097 TTAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 8 0.36
17 10 0.45
18 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATAATATTATATTTT
Found at i:2737 original size:10 final size:10
Alignment explanation
Indices: 2718--2786 Score: 52
Period size: 10 Copynumber: 7.1 Consensus size: 10
2708 ATCATGTCTA
2718 ATAA-TTTTT
1 ATAATTTTTT
2727 ATAATTTTTT
1 ATAATTTTTT
* * *
2737 ACAATATTTA
1 ATAATTTTTT
* * *
2747 ACAATTTCTA
1 ATAATTTTTT
*
2757 ATAATTTTTA
1 ATAATTTTTT
*
2767 ATAATTTTAT
1 ATAATTTTTT
2777 -TAATTTTTT
1 ATAATTTTTT
2786 A
1 A
2787 CAAATTTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
9 12 0.25
10 36 0.75
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:7887 original size:29 final size:29
Alignment explanation
Indices: 7855--7988 Score: 82
Period size: 28 Copynumber: 4.6 Consensus size: 29
7845 CAAAAATAGG
7855 ATTTTTAGCAA-CTCGAGGG-TAAAATGGTA
1 ATTTTT-GCAAGCTCG-GGGATAAAATGGTA
* *
7884 A-TTTTGGAAGTTCGGGGATAAAATGGTA
1 ATTTTTGCAAGCTCGGGGATAAAATGGTA
* * * *
7912 ATTTTTGGAAGATTCGGGGTTAAAAATGG-G
1 ATTTTTGCAAG-CTCGGGGAT-AAAATGGTA
* * *
7942 ATTTTTGGAAG-TCCGGGGGTAAGATGGTA
1 ATTTTTGCAAGCT-CGGGGATAAAATGGTA
*
7971 A-TTTTGGAAGCTTCGGGG
1 ATTTTTGCAAGC-TCGGGG
7989 TCAAAAAATG
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
27 6 0.07
28 34 0.38
29 22 0.25
30 20 0.22
31 7 0.08
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.32
Consensus pattern (29 bp):
ATTTTTGCAAGCTCGGGGATAAAATGGTA
Found at i:7930 original size:30 final size:30
Alignment explanation
Indices: 7871--8191 Score: 208
Period size: 28 Copynumber: 10.8 Consensus size: 30
7861 AGCAACTCGA
7871 GGGTAAAATGGTAA-TTTTGGAAG-TTCGG
1 GGGTAAAATGGTAATTTTTGGAAGATTCGG
*
7899 GGATAAAATGGTAATTTTTGGAAGATTCGG
1 GGGTAAAATGGTAATTTTTGGAAGATTCGG
* * *
7929 GGTTAAAAATGG-GATTTTTGGAAG-TCCGG
1 GGGT-AAAATGGTAATTTTTGGAAGATTCGG
* *
7958 GGGTAAGATGGTAA-TTTTGGAAGCTTC-G
1 GGGTAAAATGGTAATTTTTGGAAGATTCGG
* *
7986 GGGTCAAAAAATGG-GATTTTTGGGA-ATTCGG
1 GGGT---AAAATGGTAATTTTTGGAAGATTCGG
* * *
8017 GGGTAAAACGATAA-TTTTGGAAGCTTCGG
1 GGGTAAAATGGTAATTTTTGGAAGATTCGG
* *
8046 GGTTAAAAAT-G-AGATTTTTGGAA-ATTTGCTTCG
1 GGGT-AAAATGGTA-ATTTTTGGAAGA-TT-C--GG
* *
8079 GGGTCAAAAATGG-GATTTTTGGGA-ATTCGG
1 GGGT--AAAATGGTAATTTTTGGAAGATTCGG
* * * *
8109 GGGTAAAACGATATTTTTTGGAAGCTTC-G
1 GGGTAAAATGGTAATTTTTGGAAGATTCGG
* *
8138 GGGTCAAAAATGG-GATTTTTGGGA-ATTCGG
1 GGGT--AAAATGGTAATTTTTGGAAGATTCGG
8168 GGGTAAAATGGTAATTTTTGGAAG
1 GGGTAAAATGGTAATTTTTGGAAG
8192 GTTCAGGGAC
Statistics
Matches: 225, Mismatches: 40, Indels: 54
0.71 0.13 0.17
Matches are distributed among these distances:
28 58 0.26
29 54 0.24
30 58 0.26
31 31 0.14
32 1 0.00
33 6 0.03
34 16 0.07
35 1 0.00
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.32
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTGGAAGATTCGG
Found at i:7947 original size:87 final size:87
Alignment explanation
Indices: 7846--8024 Score: 220
Period size: 87 Copynumber: 2.0 Consensus size: 87
7836 GTTCGAAATC
*
7846 AAAAATAGGATTTTTAGCAACT-CGAGGGTAAAATGGTAATTTTGGAAG-TTCGGGG-ATAAAAT
1 AAAAATAGGATTTTT-GCAACTCCGAGGGTAAAATGGTAATTTTGGAAGCTTCGGGGCAAAAAAT
*
7908 GGTAATTTTTGGAAGATTCGGGGTT
65 GG-AATTTTTGGAA-ATTCGGGGGT
* * * * *
7933 AAAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTAATTTTGGAAGCTTCGGGGTCAAAAAAT
1 AAAAATAGGATTTTTGCAACTCCGAGGGTAAAATGGTAATTTTGGAAGCTTCGGGG-CAAAAAAT
* *
7998 GGGATTTTTGGGAATTCGGGGGT
65 GGAATTTTTGGAAATTCGGGGGT
8021 AAAA
1 AAAA
8025 CGATAATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
86 4 0.05
87 38 0.48
88 20 0.25
89 9 0.11
90 8 0.10
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (87 bp):
AAAAATAGGATTTTTGCAACTCCGAGGGTAAAATGGTAATTTTGGAAGCTTCGGGGCAAAAAATG
GAATTTTTGGAAATTCGGGGGT
Found at i:7948 original size:59 final size:58
Alignment explanation
Indices: 7875--8068 Score: 264
Period size: 59 Copynumber: 3.3 Consensus size: 58
7865 ACTCGAGGGT
* * * *
7875 AAAATGGTAATTTTGGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGATTCGGGGTTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAA-TTTTGGAAGCTTCGGGGTTA
* * *
7934 AAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTAATTTTGGAAGCTTCGGGGTCAA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGAAGCTTCGGGGT-TA
* *
7993 AAAATGGGATTTTTGGGAA-TTCGGGGGTAAAACGATAATTTTGGAAGCTTCGGGGTTA
1 AAAATGGGATTTTT-GGAAGTTCGGGGGTAAAATGGTAATTTTGGAAGCTTCGGGGTTA
*
8051 AAAATGAGATTTTTGGAA
1 AAAATGGGATTTTTGGAA
8069 ATTTGCTTCG
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
57 4 0.03
58 31 0.26
59 81 0.68
60 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (58 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGAAGCTTCGGGGTTA
Found at i:8034 original size:29 final size:29
Alignment explanation
Indices: 7885--8188 Score: 113
Period size: 29 Copynumber: 10.2 Consensus size: 29
7875 AAAATGGTAA
* *
7885 TTTT-GGAAGTTCGGGGAT-AAAATGGTAAT
1 TTTTGGGAACTTCGGGGGTAAAAAT-G-AAT
* * *
7914 TTTT-GGAAGATTCGGGGTTAAAAATGGGAT
1 TTTTGGGAA-CTTCGGGGGTAAAAAT-GAAT
* * *
7944 TTTT-GGAAGTCCGGGGGT-AAGATGGTAA-
1 TTTTGGGAACTTCGGGGGTAAAAAT-G-AAT
*
7972 TTTT-GGAAGCTTC-GGGGTCAAAAAATGGGAT
1 TTTTGGGAA-CTTCGGGGGT--AAAAAT-GAAT
8003 TTTTGGGAA-TTCGGGGGTAAAACGAT-AA-
1 TTTTGGGAACTTCGGGGGTAAAA--ATGAAT
*
8031 TTTT-GGAAGCTTCGGGGTTAAAAATGAGAT
1 TTTTGGGAA-CTTCGGGGGTAAAAATGA-AT
* *
8061 TTTTGGAAATTTGCTTC-GGGGTCAAAAATGGGAT
1 TTTTGGGAA----CTTCGGGGGT-AAAAAT-GAAT
*
8095 TTTTGGGAA-TTCGGGGGT-AAAACGATAT
1 TTTTGGGAACTTCGGGGGTAAAAATGA-AT
* *
8123 TTTTTGGAAGCTTC-GGGGTCAAAAATGGGAT
1 TTTTGGGAA-CTTCGGGGGT-AAAAAT-GAAT
8154 TTTTGGGAA-TTCGGGGGT-AAAATGGTAAT
1 TTTTGGGAACTTCGGGGGTAAAAAT-G-AAT
8183 TTTTGG
1 TTTTGG
8189 AAGGTTCAGG
Statistics
Matches: 218, Mismatches: 25, Indels: 64
0.71 0.08 0.21
Matches are distributed among these distances:
27 7 0.03
28 45 0.21
29 55 0.25
30 39 0.18
31 41 0.19
32 5 0.02
33 4 0.02
34 21 0.10
35 1 0.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (29 bp):
TTTTGGGAACTTCGGGGGTAAAAATGAAT
Found at i:8080 original size:34 final size:34
Alignment explanation
Indices: 8039--8105 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
8029 AATTTTGGAA
*
8039 GCTTCGGGGTTAAAAATGAGATTTTTGGAAATTT
1 GCTTCGGGGTCAAAAATGAGATTTTTGGAAATTT
* *
8073 GCTTCGGGGTCAAAAATGGGATTTTTGGGAATT
1 GCTTCGGGGTCAAAAATGAGATTTTTGGAAATT
8106 CGGGGGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (34 bp):
GCTTCGGGGTCAAAAATGAGATTTTTGGAAATTT
Found at i:8106 original size:92 final size:94
Alignment explanation
Indices: 7980--8164 Score: 320
Period size: 93 Copynumber: 2.0 Consensus size: 94
7970 AATTTTGGAA
7980 GCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATA-ATTTTGGAAGCTTC
1 GCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATATATTTTGGAAGCTTC
*
8044 GGGGTTAAAAATGAGATTTTTGGAAATTT
66 GGGGTCAAAAATGAGATTTTTGGAAATTT
*
8073 GCTTCGGGGTC-AAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATATTTTTTGGAAGCTTC
1 GCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATATATTTTGGAAGCTTC
* *
8137 GGGGTCAAAAATGGGATTTTTGGGAATT
66 GGGGTCAAAAATGAGATTTTTGGAAATT
8165 CGGGGGTAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 38 0.44
93 49 0.56
ACGTcount: A:0.28, C:0.08, G:0.31, T:0.32
Consensus pattern (94 bp):
GCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATATATTTTGGAAGCTTC
GGGGTCAAAAATGAGATTTTTGGAAATTT
Found at i:8157 original size:59 final size:59
Alignment explanation
Indices: 8073--8191 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
8063 TTGGAAATTT
*
8073 GCTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATATTTTTTGGAA
1 GCTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATAATTTTTGGAA
* *
8132 GCTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAATGGTAATTTTTGGAA
1 GCTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATAATTTTTGGAA
8191 G
1 G
8192 GTTCAGGGAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.27, C:0.08, G:0.34, T:0.32
Consensus pattern (59 bp):
GCTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGATAATTTTTGGAA
Done.