Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005414.1 Kokia drynarioides strain JFW-HI SEQ_119433, 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: 5319
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:665 original size:30 final size:30
Alignment explanation
Indices: 631--707 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
621 AAAGTTTGAG
*
631 GGGTTAAAATGTAATTTTCAAAAAGTCTAA
1 GGGTTAAAATGCAATTTTCAAAAAGTCTAA
* * * *
661 GGGTT-AAATGCAATTTTTAGAAAGTTTGA
1 GGGTTAAAATGCAATTTTCAAAAAGTCTAA
690 GGGTTAAAAT-CAAATTTT
1 GGGTTAAAATGC-AATTTT
708 TGGAAAGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGCAATTTTCAAAAAGTCTAA
Found at i:737 original size:60 final size:59
Alignment explanation
Indices: 672--830 Score: 176
Period size: 59 Copynumber: 2.7 Consensus size: 59
662 GGTTAAATGC
* *
672 AATTTTTAGAAAGTTTGAGGGTTAAAATCAAATTTTTGGAAAGTTTGAGGGTCAAAATTG
1 AATTTTTAGAAAGTTCGAGGGTCAAAATCAAATTTTTGGAAAGTTT-AGGGTCAAAATTG
* * ** * * * *
732 AATTTTTAGAAAGTCCGTGGGTCAAAATTGAA-TTGTCGAGAAGTTTAAGGTCAAATTTG
1 AATTTTTAGAAAGTTCGAGGGTCAAAATCAAATTTTTGGA-AAGTTTAGGGTCAAAATTG
* * *
791 AATTTTTTGGAAGTTCGAGGGTCAAATTCAAATTTTTGGA
1 AATTTTTAGAAAGTTCGAGGGTCAAAATCAAATTTTTGGA
831 TAAAATAGGG
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
59 41 0.53
60 37 0.47
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.36
Consensus pattern (59 bp):
AATTTTTAGAAAGTTCGAGGGTCAAAATCAAATTTTTGGAAAGTTTAGGGTCAAAATTG
Found at i:754 original size:30 final size:30
Alignment explanation
Indices: 600--816 Score: 156
Period size: 30 Copynumber: 7.3 Consensus size: 30
590 AAGGAAAATG
* * *
600 GGGTCAAAATAGAAATTTTGGAAAGTTTGA
1 GGGTCAAAATTGAATTTTTAGAAAGTTTGA
* * * * *
630 GGGGTTAAAA-TGTAATTTTCAAAAAGTCTAA
1 -GGGTCAAAATTG-AATTTTTAGAAAGTTTGA
*
661 GGGT-TAAA-TGCAATTTTTAGAAAGTTTGA
1 GGGTCAAAATTG-AATTTTTAGAAAGTTTGA
* ** *
690 GGGTTAAAATCAAATTTTTGGAAAGTTTGA
1 GGGTCAAAATTGAATTTTTAGAAAGTTTGA
** *
720 GGGTCAAAATTGAATTTTTAGAAAGTCCGT
1 GGGTCAAAATTGAATTTTTAGAAAGTTTGA
* *
750 GGGTCAAAATTGAA-TTGTCGAGAAGTTT-A
1 GGGTCAAAATTGAATTTTTAGA-AAGTTTGA
* * * * *
779 AGGTCAAATTTGAATTTTTTGGAAGTTCGA
1 GGGTCAAAATTGAATTTTTAGAAAGTTTGA
809 GGGTCAAA
1 GGGTCAAA
817 TTCAAATTTT
Statistics
Matches: 143, Mismatches: 37, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
29 45 0.31
30 78 0.55
31 20 0.14
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATTGAATTTTTAGAAAGTTTGA
Found at i:2557 original size:46 final size:46
Alignment explanation
Indices: 2456--2751 Score: 396
Period size: 46 Copynumber: 6.4 Consensus size: 46
2446 GCTTCTATGA
* * * *
2456 GATGGTAGCTTCAATCTGCCCCTCTTTATTGTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTCTTGACT-TAGGGGTAAAAGATTG
* *
2503 GATTGTGGCTTCAATCTACCCCTCTTGACTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
* * * *
2549 AATGGTGGCTTTAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
* * * * *
2595 GATGGTGGCTTCAATCTTCCTCTCTTGACTCAGGGATAAAAGATCG
1 GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
* ** *
2641 GATGGTGACTTCAATCTGTCTCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
*
2687 G-TGGTAGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
2732 GATGGTGGCTTCAATCTACC
1 GATGGTGGCTTCAATCTACC
2752 TCATGATCTG
Statistics
Matches: 216, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
45 40 0.19
46 151 0.70
47 25 0.12
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (46 bp):
GATGGTGGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
Found at i:2739 original size:137 final size:139
Alignment explanation
Indices: 2456--2753 Score: 402
Period size: 137 Copynumber: 2.2 Consensus size: 139
2446 GCTTCTATGA
* * * * * * * * * *
2456 GATGGTAGCTTCAATCTGCCCCTCTTTATTGTAGGGGTAAAAGATTGGATTGTGGCTTCAATCTA
1 GATGGTGGCTTCAATCTACCTCTCTTGACTGCAGGGATAAAAGATCGGATGGTGACTTCAATCTA
* * * *
2521 CCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTGGCTTTAATTTGCCCCTCTTGACTTAGGGGT
66 CCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTAGCTTCAATCTACCCCTCTTGACTTAGGGGT
2586 AAAAGATTG
131 AAAAGATTG
* *
2595 GATGGTGGCTTCAATCTTCCTCTCTTGACT-CAGGGATAAAAGATCGGATGGTGACTTCAATCTG
1 GATGGTGGCTTCAATCTACCTCTCTTGACTGCAGGGATAAAAGATCGGATGGTGACTTCAATCTA
* * * *
2659 TCTCTCTTGACTTAGGGGTAAAAGATTG-GTGGTAGCTTCAATCTACCCCTCTTGACTTAGGGGT
66 CCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTAGCTTCAATCTACCCCTCTTGACTTAGGGGT
2723 AAAAGATTG
131 AAAAGATTG
2732 GATGGTGGCTTCAATCTACCTC
1 GATGGTGGCTTCAATCTACCTC
2754 ATGATCTGGG
Statistics
Matches: 139, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
137 61 0.44
138 53 0.38
139 25 0.18
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (139 bp):
GATGGTGGCTTCAATCTACCTCTCTTGACTGCAGGGATAAAAGATCGGATGGTGACTTCAATCTA
CCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTAGCTTCAATCTACCCCTCTTGACTTAGGGGT
AAAAGATTG
Found at i:2835 original size:38 final size:39
Alignment explanation
Indices: 2718--3284 Score: 508
Period size: 38 Copynumber: 14.4 Consensus size: 39
2708 TCTTGACTTA
* * *
2718 GGGGTAAAAGATTGGATGGTGGCTTCAATCTACCTCATGATC
1 GGGGTAAGAGATTGGAT-GT--CTTCAATCTGCCCCATGATC
* * *
2760 TGGGTAAAAGATTGAATGATGTCTTCAATCTGTCCCATGATC
1 GGGGTAAGAGATTG---GATGTCTTCAATCTGCCCCATGATC
2802 GGGGTAAGAGATTGGATGT-TTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
* * * * *
2840 GGTGTAAGAGATTGGACGGCTACAATCTGTCCCATGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
* *
2879 GGGGTAAGAGATTGTATGATGTCTTCAATCTGTCCCATGATT
1 GGGGTAAGAGATTG---GATGTCTTCAATCTGCCCCATGATC
* * * * * *
2921 TGGGTAAAAGATCGGATG-CTTTAATCTACCCCGTGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
* * **
2959 GAGGTAAGAGATTGGTGTGTCTTCAATCTGCCTTATGATC
1 GGGGTAAGAGATTGG-ATGTCTTCAATCTGCCCCATGATC
* *
2999 GGGGTAAGAGATTCGAT-ACTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
*
3037 GGGGTAAGAGATTGG-TGTGGCTTCAATCTGCCCTCCTGAT-
1 GGGGTAAGAGATTGGATGT--CTTCAATCTGCCC-CATGATC
* * * *
3077 -TGGTAAAAGATTGGATG-CTTCAATCTACCCTATGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
* ** *
3114 GGGGTAAGAGATT-GATGTGTCTTCAATCTACCCTTTGATT
1 GGGGTAAGAGATTGGA--TGTCTTCAATCTGCCCCATGATC
* * * *
3154 AGGGTAAAAGATTGGATG-CTTCAATCTGCGCCATTATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
* * * *
3192 AGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTC-TGATT
1 GGGGTAAGAGATTGG-ATGTCTTCAATCTGCCC-CATGATC
* *
3232 AGGGTAAAAGATTGGATG-CTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
3270 GGGGTAAGAGATTGG
1 GGGGTAAGAGATTGG
3285 TGTGTAGCTT
Statistics
Matches: 428, Mismatches: 73, Indels: 52
0.77 0.13 0.09
Matches are distributed among these distances:
36 4 0.01
37 16 0.04
38 159 0.37
39 62 0.14
40 100 0.23
41 8 0.02
42 74 0.17
44 2 0.00
45 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (39 bp):
GGGGTAAGAGATTGGATGTCTTCAATCTGCCCCATGATC
Found at i:3004 original size:78 final size:78
Alignment explanation
Indices: 2718--3289 Score: 620
Period size: 78 Copynumber: 7.3 Consensus size: 78
2708 TCTTGACTTA
* * * *
2718 GGGGTAAAAGATTGGATGGTGGCTTCAATCTACCTCATGATCTGGGTAAAAGATTGAATGATGTC
1 GGGGTAAGAGATTGG-T-GTGTCTTCAATCTGCCTCATGATCAGGGTAAAAGATTG---GATG-C
*
2783 TTCAATCTGTCCCATGATC
60 TTCAATCTGCCCCATGATC
* * * * *
2802 GGGGTAAGAGATTGG-ATGT-TTCAATCTGCCCCATGATC-GGTGTAAGAGATTGGACGGCTACA
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCTCATGATCAGG-GTAAAAGATTGGA-TGCTTCA
*
2864 ATCTGTCCCATGATC
64 ATCTGCCCCATGATC
* ** * *
2879 GGGGTAAGAGATTGTATGATGTCTTCAATCTGTCC-CATGATTTGGGTAAAAGATCGGATGCTTT
1 GGGGTAAGAGATTG-GTG-TGTCTTCAATCTG-CCTCATGATCAGGGTAAAAGATTGGATGCTTC
* *
2943 AATCTACCCCGTGATC
63 AATCTGCCCCATGATC
* * * * * *
2959 GAGGTAAGAGATTGGTGTGTCTTCAATCTGCCTTATGATCGGGGTAAGAGATTCGATACTTCAAT
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCTCATGATCAGGGTAAAAGATTGGATGCTTCAAT
3024 CTGCCCCATGATC
66 CTGCCCCATGATC
* * *
3037 GGGGTAAGAGATTGGTGTGGCTTCAATCTGCCCTCCTGAT--TGGTAAAAGATTGGATGCTTCAA
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTG-CCTCATGATCAGGGTAAAAGATTGGATGCTTCAA
* *
3100 TCTACCCTATGATC
65 TCTGCCCCATGATC
* * * *
3114 GGGGTAAGAGATTGATGTGTCTTCAATCTACC-CTTTGATTAGGGTAAAAGATTGGATGCTTCAA
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCTC-ATGATCAGGGTAAAAGATTGGATGCTTCAA
* *
3178 TCTGCGCCATTATC
65 TCTGCCCCATGATC
* * *
3192 AGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTC-TGATTAGGGTAAAAGATTGGATGCTTCAA
1 GGGGTAAGAGATTGGTGTGTCTTCAATCT-GCCTCATGATCAGGGTAAAAGATTGGATGCTTCAA
3256 TCTGCCCCATGATC
65 TCTGCCCCATGATC
3270 GGGGTAAGAGATTGGTGTGT
1 GGGGTAAGAGATTGGTGTGT
3290 AGCTTCGCTT
Statistics
Matches: 417, Mismatches: 56, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
75 1 0.00
76 6 0.01
77 95 0.23
78 196 0.47
79 13 0.03
80 60 0.14
81 28 0.07
82 4 0.01
84 14 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (78 bp):
GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCTCATGATCAGGGTAAAAGATTGGATGCTTCAAT
CTGCCCCATGATC
Found at i:3216 original size:233 final size:233
Alignment explanation
Indices: 2719--3289 Score: 690
Period size: 233 Copynumber: 2.4 Consensus size: 233
2709 CTTGACTTAG
* * * *
2719 GGGTAAAAGATTGGATGGTGGCTTCAATCTACCTCATGATCTGGGTAAAAGATTGAATGATGTCT
1 GGGTAAGAGATTGG-T-GTGTCTTCAATCTACCTTATGATCAGGGTAAAAGATTG-AT-A---CT
* *
2784 TCAATCTGTCCCATGATCGGGGTAAGAGATTGGATGT-TTCAATCTGCCCCATGATCGGTGTAAG
59 TCAATCTGCCCCATGATCGGGGTAAGAGATTGG-TGTGTTCAATCTGCCCCATGATCGGTGTAAA
* *
2848 AGATTGGACGGCTACAATCTGTCCCATGATCGGGGTAAGAGATTGTATGATGTCTTCAATCTGTC
123 AGATTGGACGGCTACAATCTGACCCATGATCGGGGTAAGAGATTGTATGATGTCTTCAATCTGAC
* * *
2913 CCATGATTTGGGTAAAAGATCGGATGCTTTAATCTACCCCGTGATC
188 CCATGATTAGGGTAAAAGATCGGATGCTTCAATCTACCCCATGATC
* * *
2959 GAGGTAAGAGATTGGTGTGTCTTCAATCTGCCTTATGATCGGGGTAAGAGATTCGATACTTCAAT
1 G-GGTAAGAGATTGGTGTGTCTTCAATCTACCTTATGATCAGGGTAAAAGATT-GATACTTCAAT
* *
3024 CTGCCCCATGATCGGGGTAAGAGATTGGTGTGGCTTCAATCTGCCCTCCTGAT-TG-GTAAAAGA
64 CTGCCCCATGATCGGGGTAAGAGATTGGTGT-G-TTCAATCTGCCC-CATGATCGGTGTAAAAGA
* *
3087 TTGGA-TGCTTCAATCT-ACCCTATGATCGGGGTAAGAGATTG-ATG-TGTCTTCAATCT-ACCC
126 TTGGACGGCTACAATCTGACCC-ATGATCGGGGTAAGAGATTGTATGATGTCTTCAATCTGACCC
* * * * *
3147 TTTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCGCCATTATC
190 -ATGATTAGGGTAAAAGATCGGATGCTTCAATCTACCCCATGATC
* * * *
3192 AGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGATGCTTCAAT
1 -GGGTAAGAGATTGGTGTGTCTTCAATCTACCTTATGATCAGGGTAAAAGATT-GATACTTCAAT
3257 CTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
64 CTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
3290 AGCTTCGCTT
Statistics
Matches: 292, Mismatches: 30, Indels: 27
0.84 0.09 0.08
Matches are distributed among these distances:
231 1 0.00
232 4 0.01
233 134 0.46
234 10 0.03
235 63 0.22
236 12 0.04
237 13 0.04
238 6 0.02
239 34 0.12
240 3 0.01
241 12 0.04
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (233 bp):
GGGTAAGAGATTGGTGTGTCTTCAATCTACCTTATGATCAGGGTAAAAGATTGATACTTCAATCT
GCCCCATGATCGGGGTAAGAGATTGGTGTGTTCAATCTGCCCCATGATCGGTGTAAAAGATTGGA
CGGCTACAATCTGACCCATGATCGGGGTAAGAGATTGTATGATGTCTTCAATCTGACCCATGATT
AGGGTAAAAGATCGGATGCTTCAATCTACCCCATGATC
Done.