Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004960.1 Kokia drynarioides strain JFW-HI SEQ_118687, 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: 26445
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:4510 original size:199 final size:197
Alignment explanation
Indices: 3981--4551 Score: 710
Period size: 193 Copynumber: 2.9 Consensus size: 197
3971 CAAGTAGCAC
* * *
3981 ATCTCAATCT-CTGTAAGGTTACAGTGGAATGGAGTGAAGCTACTACA-CTAGATCCTATATCCT
1 ATCTCAATGTCCT-TAAGGTTACAGTGGAATGGAGTGAAGCTTC-ACATC-AAATCCTATATCCT
* * *
4044 TGAAGTTGCAATGGATCAGATTAAAATAAGTAACGGATCTCAATCTCCTTGAGGTTACAATGGAA
63 TGAAGTTACAGTGGATCAGATTAAAATAAGTAACGGATCTCAATATCCTTGAGGTTACAATGGAA
* *
4109 TGAAGTGAAGTTACAACGCCAAATCCTATACTCCTAAAGTTGTAA-TGGGTCAGATTAAAACAAC
128 TGGAGTGAAGTTACAACGCCAAATCCTATAC-CCTAAAGTTG-AAGTGGGTCAGATAAAAACAAC
*
4173 AAAGCAG
191 AAAGAAG
* *
4180 ATCTCAATGTCCTTAAGGTTACAGTGGAACGGAGTGAAGCTT----T-AAATCCTATATCCTTAA
1 ATCTCAATGTCCTTAAGGTTACAGTGGAATGGAGTGAAGCTTCACATCAAATCCTATATCCTTGA
* * * * * *
4240 AATTACAGTGGATCGGATTAAAATAAGTAACGAATCTCAATCATCC-TAAGGTTATAGTGGAATG
66 AGTTACAGTGGATCAGATTAAAATAAGTAACGGATCTCAAT-ATCCTTGAGGTTACAATGGAATG
* * * ** *
4304 GAGTGAAGTTACAATGCCAAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATAAAAATTATAAA
130 GAGTGAAGTTACAACGCCAAATCCTATACCC-TAAAGTTGAAGTGGGTCAGATAAAAACAACAAA
4369 GAAG
194 GAAG
* * * *
4373 ATCTCAGTGTCTTTAAGGTTATAGTGGAATGGAGTGAAGCTTCAACATCAAATCCTATATCCCTG
1 ATCTCAATGTCCTTAAGGTTACAGTGGAATGGAGTGAAGCTTC-ACATCAAATCCTATATCCTTG
* *
4438 AAGTTACAGTGGATCAGATTAAAATCAGTAACGGATCTCAATGTCCTTGAGGTTACAATGGAATG
65 AAGTTACAGTGGATCAGATTAAAATAAGTAACGGATCTCAATATCCTTGAGGTTACAATGGAATG
* * *
4503 GAGTGAAGTTATAACACCAAATCCTATACCCCTAAAGTTGAAGTAGGTC
130 GAGTGAAGTTACAACGCCAAATCCTATA-CCCTAAAGTTGAAGTGGGTC
4552 GGATTAAAGT
Statistics
Matches: 316, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
192 3 0.01
193 159 0.50
194 3 0.01
198 4 0.01
199 142 0.45
200 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (197 bp):
ATCTCAATGTCCTTAAGGTTACAGTGGAATGGAGTGAAGCTTCACATCAAATCCTATATCCTTGA
AGTTACAGTGGATCAGATTAAAATAAGTAACGGATCTCAATATCCTTGAGGTTACAATGGAATGG
AGTGAAGTTACAACGCCAAATCCTATACCCTAAAGTTGAAGTGGGTCAGATAAAAACAACAAAGA
AG
Found at i:4541 original size:99 final size:99
Alignment explanation
Indices: 3925--4559 Score: 531
Period size: 99 Copynumber: 6.5 Consensus size: 99
3915 GGACTAGTGA
* * * * * * * * **
3925 AACACTAAATCCTAT-CTTCCTGAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCACATCTCAAT
1 AACACCAAATCCTATAC-CCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACGGATCTCAAT
* *
3989 CT-CTGTAAGGTTACAGTGGAATGGAGTGAAGCTAC
65 GTCCT-TAAGGTTACAGTGGAATGGAGTGAAGTTAC
* * * * * * * *
4024 TACACTAGATCCTATATCCTTGAAGTTGCAATGGATCAGATTAAAATAAGTAACGGATCTCAATC
1 AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACGGATCTCAATG
* * *
4089 TCCTTGAGGTTACAATGGAATGAAGTGAAGTTAC
66 TCCTTAAGGTTACAGTGGAATGGAGTGAAGTTAC
* * * * * * ** *
4123 AACGCCAAATCCTATACTCCTAAAGTTGTAATGGGTCAGATTAAAACAACAAAGCAGATCTCAAT
1 AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAA-CGGATCTCAAT
*
4188 GTCCTTAAGGTTACAGTGGAACGGAGTGAAGCTT--
65 GTCCTTAAGGTTACAGTGGAATGGAGTGAAG-TTAC
* * * * * * *
4222 -----TAAATCCTATATCCTTAAAATTACAGTGGATCGGATTAAAATAAGTAACGAATCTCAATC
1 AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACGGATCTCAAT-
* *
4282 ATCC-TAAGGTTATAGTGGAATGGAGTGAAGTTAC
65 GTCCTTAAGGTTACAGTGGAATGGAGTGAAGTTAC
** * * * * * * *
4316 AATGCCAAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATAAAAATTA-TAAAGAAGATCTCAG
1 AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACG--GATCTCAA
* *
4380 TGTCTTTAAGGTTATAGTGGAATGGAGTGAAGCTT-C
64 TGTCCTTAAGGTTACAGTGGAATGGAGTGAAG-TTAC
* * * * *
4416 AACATCAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTAAAATCAGTAACGGATCTCAATG
1 AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACGGATCTCAATG
* * *
4481 TCCTTGAGGTTACAATGGAATGGAGTGAAGTTAT
66 TCCTTAAGGTTACAGTGGAATGGAGTGAAGTTAC
* *
4515 AACACCAAATCCTATACCCCTAAAGTTGAAGTAGG-TCGGATTAAA
1 AACACCAAATCCTATACCCCTAAAGTTGCAGT-GGATCAGATTAAA
4560 GTTACAAAAG
Statistics
Matches: 427, Mismatches: 90, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
92 2 0.00
93 33 0.08
94 38 0.09
98 6 0.01
99 226 0.53
100 114 0.27
101 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (99 bp):
AACACCAAATCCTATACCCCTAAAGTTGCAGTGGATCAGATTAAAATAAGTAACGGATCTCAATG
TCCTTAAGGTTACAGTGGAATGGAGTGAAGTTAC
Found at i:4627 original size:50 final size:50
Alignment explanation
Indices: 4566--5028 Score: 330
Period size: 50 Copynumber: 9.3 Consensus size: 50
4556 TAAAGTTACA
* * * * *
4566 AAAGCTGTAGAGAGGCATATTGAAGTTGCAAAAGCGAATCTTATTCCCTT
1 AAAGATGTAGAGAGGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * * * * ** * * * * *
4616 AAAGCTATAGAG-GGGAGAATTAAAACCACAAAGGTGAATATTATATCCCG
1 AAAGATGTAGAGAGGCAG-ATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * * * * * *
4666 AAAGATATAAAGGGGCAGGTTAAAGCTGCAAAAGCGAATTTTATACCCCC
1 AAAGATGTAGAGAGGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * *
4716 AAAGATGTA-AAAGGGTAGATTGAAG-TCGCAAAGGCGAATCTTATACCCCT
1 AAAGATGTAGAGA-GGCAGATTGAAGCT-GCAAAAGCGAATCTTATACCCCT
* * * * * * *
4766 AAAGCTATAGAGGGGTAAATTGAAGCTACAAAAGCGAACCTTATACCCCT
1 AAAGATGTAGAGAGGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * * * *
4816 AAAGATGTA-AAAGGACAGATTAAAG-TCGCAAAGGCAAATCTTATATCCCT
1 AAAGATGTAGAGAGG-CAGATTGAAGCT-GCAAAAGCGAATCTTATACCCCT
* *
4866 AAAGCTGTAGA-AGGGCAGATTGAAGCTGCAAAATCGAATCTTATACCCCT
1 AAAGATGTAGAGA-GGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * **
4916 AAAGATGTAAAGGGGCAGATTGAAGCTAAAAAAGCGAATCTTATACCCCT
1 AAAGATGTAGAGAGGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
* * * * * *
4966 AAAGATGTA-AAAGGGCAGATTGAAGCCG-TAAAGATGAATCTTATACTCTT
1 AAAGATGTAGAGA-GGCAGATTGAAGCTGCAAAAG-CGAATCTTATACCCCT
*
5016 AAAGCTGTAGAGA
1 AAAGATGTAGAGA
5029 AGTGGATATG
Statistics
Matches: 320, Mismatches: 78, Indels: 29
0.75 0.18 0.07
Matches are distributed among these distances:
49 14 0.04
50 294 0.92
51 12 0.04
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (50 bp):
AAAGATGTAGAGAGGCAGATTGAAGCTGCAAAAGCGAATCTTATACCCCT
Found at i:4798 original size:100 final size:100
Alignment explanation
Indices: 4566--4991 Score: 401
Period size: 100 Copynumber: 4.3 Consensus size: 100
4556 TAAAGTTACA
* * * * * * * *
4566 AAAGCTGTAG-AGAGGCATATTGAAGTTGCAAAAGCGAATCTTATTCCCTTAAAGCTAT-AGAGG
1 AAAGCTATAGAAG-GGCAAATTGAAGCTGCAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGG
* * ** * * * * *
4629 GGAGAATTAAAACCACAAAGGTGAATATTATATCCCG
65 GCAG-ATTGAAGTCGCAAAGGCGAATCTTATACCCCT
* ** * * *
4666 AAAGATATA-AAGGGGCAGGTTAAAGCTGCAAAAGCGAATTTTATACCCCCAAAGATGTAAAAGG
1 AAAGCTATAGAA-GGGCAAATTGAAGCTGCAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGG
*
4730 GTAGATTGAAGTCGCAAAGGCGAATCTTATACCCCT
65 GCAGATTGAAGTCGCAAAGGCGAATCTTATACCCCT
* * * * *
4766 AAAGCTATAGAGGGGTAAATTGAAGCTACAAAAGCGAACCTTATACCCCTAAAGATGTAAAAGGA
1 AAAGCTATAGAAGGGCAAATTGAAGCTGCAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGG
* * *
4831 CAGATTAAAGTCGCAAAGGCAAATCTTATATCCCT
66 CAGATTGAAGTCGCAAAGGCGAATCTTATACCCCT
* * * *
4866 AAAGCTGTAGAAGGGCAGATTGAAGCTGCAAAATCGAATCTTATACCCCTAAAGATGTAAAGGGG
1 AAAGCTATAGAAGGGCAAATTGAAGCTGCAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGG
** *
4931 CAGATTGAAG-CTAAAAAAGCGAATCTTATACCCCT
66 CAGATTGAAGTC-GCAAAGGCGAATCTTATACCCCT
* * * *
4966 AAAGATGTAAAAGGGCAGATTGAAGC
1 AAAGCTATAGAAGGGCAAATTGAAGC
4992 CGTAAAGATG
Statistics
Matches: 267, Mismatches: 54, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
99 1 0.00
100 257 0.96
101 9 0.03
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (100 bp):
AAAGCTATAGAAGGGCAAATTGAAGCTGCAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGG
CAGATTGAAGTCGCAAAGGCGAATCTTATACCCCT
Found at i:5006 original size:150 final size:147
Alignment explanation
Indices: 4566--5026 Score: 485
Period size: 150 Copynumber: 3.1 Consensus size: 147
4556 TAAAGTTACA
* * *
4566 AAAGCTGTAG-AGAGGCATATTGAAGTTGCAAAAGCGAATCTTATTCCCTTAAAGCTATAGAGGG
1 AAAGCTGTAGAAG-GGCAGATTGAAG-TGCAAAAGCGAATCTTATACCCCTAAAGCTATAGAGGG
* * * * * * * * * * * *
4630 GAGAATTAAAACCACAAAGGTGAATATTATATCCCGAAAGATATAAAGGGGCAGGTTAAAGCTGC
64 GAG-ATTGAAGCTACAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGGCAGATTAAAGCCGC
* *
4695 AAA-AGCGAATTTTATACCCCC
128 AAAGA-CGAATCTTATA-CCCT
* * * *
4716 AAAGATGTAAAAGGGTAGATTGAAGTCGCAAAGGCGAATCTTATACCCCTAAAGCTATAGAGGGG
1 AAAGCTGTAGAAGGGCAGATTGAAGT-GCAAAAGCGAATCTTATACCCCTAAAGCTATAGAGGGG
* * * *
4781 TAAATTGAAGCTACAAAAGCGAACCTTATACCCCTAAAGATGTAAAAGGACAGATTAAAGTCGCA
65 -AGATTGAAGCTACAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGGCAGATTAAAGCCGCA
* *
4846 AAGGCAAATCTTATATCCCT
129 AAGACGAATCTTATA-CCCT
* * * *
4866 AAAGCTGTAGAAGGGCAGATTGAAGCTGCAAAATCGAATCTTATACCCCTAAAGATGTAAAGGGG
1 AAAGCTGTAGAAGGGCAGATTGAAG-TGCAAAAGCGAATCTTATACCCCTAAAGCTATAGAGGGG
* * *
4931 CAGATTGAAGCTAAAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGGCAGATTGAAGCCGTA
65 -AGATTGAAGCTACAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGGCAGATTAAAGCCGCA
* *
4996 AAGATGAATCTTATACTCTT
129 AAGACGAATCTTATAC-CCT
5016 AAAGCTGTAGA
1 AAAGCTGTAGA
5027 GAAGTGGATA
Statistics
Matches: 257, Mismatches: 48, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
149 2 0.01
150 251 0.98
151 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (147 bp):
AAAGCTGTAGAAGGGCAGATTGAAGTGCAAAAGCGAATCTTATACCCCTAAAGCTATAGAGGGGA
GATTGAAGCTACAAAAGCGAATCTTATACCCCTAAAGATGTAAAAGGGCAGATTAAAGCCGCAAA
GACGAATCTTATACCCT
Found at i:6682 original size:29 final size:27
Alignment explanation
Indices: 6648--6716 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
6638 TGCTTTTCCC
*
6648 TTTTAAAATTTTCCCTTTTATTCTATTT
1 TTTTTAAATTTT-CCTTTTATTCTATTT
* *
6676 TTTTTAAATTAAGTCCTTTTATTTTATTT
1 TTTTTAAATT--TTCCTTTTATTCTATTT
*
6705 TTCTTAAATTTT
1 TTTTTAAATTTT
6717 AATATTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 9 0.26
29 23 0.68
30 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTTAAATTTTCCTTTTATTCTATTT
Found at i:15591 original size:23 final size:20
Alignment explanation
Indices: 15564--15607 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 20
15554 TTTGAAAATT
15564 TCAAATAAAATAATAAAATCAAA
1 TCAAAT-AAA-AATAAAA-CAAA
15587 TCAAATAAAAATAAAACAAA
1 TCAAATAAAAATAAAACAAA
15607 T
1 T
15608 TCCAACTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 3 0.14
23 6 0.29
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (20 bp):
TCAAATAAAAATAAAACAAA
Found at i:17824 original size:43 final size:43
Alignment explanation
Indices: 17763--17911 Score: 203
Period size: 43 Copynumber: 3.5 Consensus size: 43
17753 AACTTGATAT
17763 TTAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
1 TTAAA-GGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* * * *
17807 TAAAAGGAATATTCATGTCTCGGGTTGAGCATGAAAATTTATA
1 TTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* * * *
17850 TTGAAGGAAGACTCATGTCTCAGGATGAGAATGAG-A-TTATA
1 TTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
17891 TTAAAGGAAGACTCATGTCTC
1 TTAAAGGAAGACTCATGTCTC
17912 AAAATGAGCG
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 25 0.27
42 1 0.01
43 62 0.67
44 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (43 bp):
TTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
Found at i:17998 original size:40 final size:40
Alignment explanation
Indices: 17938--18037 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
17928 TTGTTTTTTA
* *
17938 AAAAGGAAGACTTATGACTCGATAGAGCATTAGAGTGATT
1 AAAAGGAAGACTTATAACTCGATAGAGCATAAGAGTGATT
* * * * *
17978 AAAAGGAATACTTGTAACTCGGTAGAGCATAATATTGATT
1 AAAAGGAAGACTTATAACTCGATAGAGCATAAGAGTGATT
18018 AAAAGGAAGACTTATGAACT
1 AAAAGGAAGACTTAT-AACT
18038 TATGAAGTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (40 bp):
AAAAGGAAGACTTATAACTCGATAGAGCATAAGAGTGATT
Found at i:24788 original size:16 final size:17
Alignment explanation
Indices: 24767--24800 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24757 ATAAATATAT
24767 TTCTTTT-TCTTTTCTA
1 TTCTTTTCTCTTTTCTA
*
24783 TTCTTTTCTTTTTTCTA
1 TTCTTTTCTCTTTTCTA
24800 T
1 T
24801 GCGACTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTTCTCTTTTCTA
Done.