Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010665.1 Kokia drynarioides strain JFW-HI SEQ_125610, 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: 4657
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:253 original size:19 final size:19
Alignment explanation
Indices: 229--272 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
219 AATTTCCATT
229 TATTTATTTA-ATATTATAA
1 TATTTATTTATATATTAT-A
*
248 TATTTA-TTATTTATTATA
1 TATTTATTTATATATTATA
266 TATTTAT
1 TATTTAT
273 GGTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATTTATATATTATA
Found at i:1796 original size:8 final size:9
Alignment explanation
Indices: 1768--1815 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
1758 ATTTCAAAAA
*
1768 AAAAAAGAC
1 AAAAAAGAG
**
1777 AAAAAATTG
1 AAAAAAGAG
1786 AAAAAAG-G
1 AAAAAAGAG
1794 AAAAAAGAG
1 AAAAAAGAG
1803 -AAAAAGAG
1 AAAAAAGAG
1811 AAAAA
1 AAAAA
1816 GAAAAGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 16 0.48
9 17 0.52
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:1813 original size:17 final size:17
Alignment explanation
Indices: 1768--1815 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1758 ATTTCAAAAA
*
1768 AAAAAAGACAAAAAATTG
1 AAAAAAGAGAAAAAA-TG
1786 AAAAAAG-GAAAAAA-G
1 AAAAAAGAGAAAAAATG
1801 AGAAAAAGAGAAAAA
1 A-AAAAAGAGAAAAA
1816 GAAAAGGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 6 0.22
17 12 0.44
18 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (17 bp):
AAAAAAGAGAAAAAATG
Found at i:1820 original size:6 final size:6
Alignment explanation
Indices: 1804--1848 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
1794 AAAAAAGAGA
*
1804 AAAAGAG AAAAAG AAAAGG AAAAAG AAGAAAAG AAAAAG AAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG AAAAAG
1849 GAGAGGTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 23 0.68
7 6 0.18
8 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1827 original size:21 final size:21
Alignment explanation
Indices: 1796--1853 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
1786 AAAAAAGGAA
1796 AAAAGAGAAAAAGAGA-AAAAG
1 AAAA-AGAAAAAGAGAGAAAAG
*
1817 AAAAGGAAAAAGA-AGAAAAG
1 AAAAAGAAAAAGAGAGAAAAG
1837 AAAAAGAAAAAGGAGAG
1 AAAAAGAAAAA-GAGAG
1854 GTCGAGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 23 0.72
21 6 0.19
22 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAGAGAGAAAAG
Found at i:2947 original size:50 final size:50
Alignment explanation
Indices: 2772--2946 Score: 242
Period size: 50 Copynumber: 3.5 Consensus size: 50
2762 CTTTTACCCT
*
2772 TAAAGCTGTAGAGGTGCAGATTGAAACTGCAATAGCAAATCTCATACACC
1 TAAAGCTGTAGAGGTGCAGATTGAAACTGTAATAGCAAATCTCATACACC
* * * *
2822 TAAAGCTATAGAGGTGCAGATTGAAACCGTAATGGCAAATCTGATACACC
1 TAAAGCTGTAGAGGTGCAGATTGAAACTGTAATAGCAAATCTCATACACC
* * * * *
2872 TAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATAGCAAATCTCATTCACT
1 TAAAGCTGTAGAGGTGCAGATTGAAACTGTAATAGCAAATCTCATACACC
* *
2922 TAAAGCTGTAGAGGAGAAGATTGAA
1 TAAAGCTGTAGAGGTGCAGATTGAA
2947 GTCACAAGGA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (50 bp):
TAAAGCTGTAGAGGTGCAGATTGAAACTGTAATAGCAAATCTCATACACC
Found at i:3143 original size:80 final size:80
Alignment explanation
Indices: 3003--3495 Score: 677
Period size: 80 Copynumber: 6.2 Consensus size: 80
2993 TTACAACCTT
* * *
3003 CAATCTATTACCCTAACCAGAGGGCAAGATTGAAA-ACCATCTGATTTTTTACCTCGATCATGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATT-AAAGACCATCTGATCTTTTACCCCGATCATGGG
3067 GCAGATTGAAGAAATC
65 GCAGATTGAAGAAATC
* * * * * *
3083 TAATCTTTTACCCTAACCAAAAGGCAAGATTAAAGACCATCTGATATTTTACCCCCATCATGGGA
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGG
*
3148 AAGATTGAAGAAATC
66 CAGATTGAAGAAATC
* * * *
3163 CAATATTTTATCCTAACTAGAGGGCAAGATTAAAGATCATCTGATCTTTTACCCCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGG
*
3228 TAGATTGAAGAAATC
66 CAGATTGAAGAAATC
* * *
3243 CAAT-TTTTACCCTAATCAGAGGGTAAGATTGAAGACCAT-TCGATCTTTTACCCCGATCATGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCT-GATCTTTTACCCCGATCATGGG
*
3306 ACAGATTGAAGAAATC
65 GCAGATTGAAGAAATC
* *
3322 CAATCTTTTACCCTAACCAGAGGGAAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGG
* *
3387 CAAATTGAAGAAATT
66 CAGATTGAAGAAATC
* * * ** *
3402 CAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCCTAATCATAGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGG
*
3467 TAGATTGAAGAAATC
66 CAGATTGAAGAAATC
3482 CAATCTTTTACCCT
1 CAATCTTTTACCCT
3496 GACAATGGGG
Statistics
Matches: 365, Mismatches: 44, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
78 1 0.00
79 72 0.20
80 291 0.80
81 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (80 bp):
CAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGG
CAGATTGAAGAAATC
Found at i:3429 original size:239 final size:240
Alignment explanation
Indices: 3003--3495 Score: 731
Period size: 239 Copynumber: 2.1 Consensus size: 240
2993 TTACAACCTT
* * * *
3003 CAATCTATTACCCTAACCAGAGGGCAAGATTGAAAACCATCTGATTTTTTACCTCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCTGATCTTTTACCCCGATCATGGGA
* *
3068 CAGATTGAAGAAATCTAATCTTTTACCCTAACCAAAAGGCAAGATTAAAGACCATCTGATATTTT
66 CAGATTGAAGAAATCCAATCTTTTACCCTAACCAAAAGGAAAGATTAAAGACCATCTGATATTTT
* *
3133 ACCCCCATCATGGGAAAGATTGAAGAAATCCAATATTTTATCCTAACTAGAGGGCAAGATTAAAG
131 ACCCCCATCATGGGAAAGATTGAAGAAATCCAATATTTTACCCTAACTAAAGGGCAAGATTAAAG
* * * *
3198 ATCATCTGATCTTTTACCCCGATCATGGGGTAGATTGAAGAAATC
196 ACCATCCGATCTTTTACCCCAATCATAGGGTAGATTGAAGAAATC
* * *
3243 CAAT-TTTTACCCTAATCAGAGGGTAAGATTGAAGACCAT-TCGATCTTTTACCCCGATCATGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCT-GATCTTTTACCCCGATCATGGG
* * * *
3306 ACAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGAAAGATTGAAGACCATCTGATCTTT
65 ACAGATTGAAGAAATCCAATCTTTTACCCTAACCAAAAGGAAAGATTAAAGACCATCTGATATTT
* * * *
3371 TACCCCGATCATGGGGCAA-ATTGAAGAAATTCAATCTTTTACCCTAACTAAAGGGCAAGATTAA
130 TACCCCCATCAT-GGGAAAGATTGAAGAAATCCAATATTTTACCCTAACTAAAGGGCAAGATTAA
*
3435 AGACCATCCGATCTTTTACCCTAATCATAGGGTAGATTGAAGAAATC
194 AGACCATCCGATCTTTTACCCCAATCATAGGGTAGATTGAAGAAATC
3482 CAATCTTTTACCCT
1 CAATCTTTTACCCT
3496 GACAATGGGG
Statistics
Matches: 226, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
238 1 0.00
239 207 0.92
240 18 0.08
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (240 bp):
CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCTGATCTTTTACCCCGATCATGGGA
CAGATTGAAGAAATCCAATCTTTTACCCTAACCAAAAGGAAAGATTAAAGACCATCTGATATTTT
ACCCCCATCATGGGAAAGATTGAAGAAATCCAATATTTTACCCTAACTAAAGGGCAAGATTAAAG
ACCATCCGATCTTTTACCCCAATCATAGGGTAGATTGAAGAAATC
Found at i:3507 original size:39 final size:40
Alignment explanation
Indices: 3059--3612 Score: 330
Period size: 39 Copynumber: 13.9 Consensus size: 40
3049 TTTTACCTCG
* *
3059 ATCATGGGGCAGATTGAAGA-AATCTAATCTTTTACCCTA
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* ** ** * * ** * **
3098 ACCAAAAGGCAAGATTAAAGACCATCTGATATTTTACCCCC
1 ATC-ATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
** * *
3139 ATCATGGGAAAGATTGAAGA-AATCCAATATTTTATCCTA
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* * ** **
3178 A-C-TAGAGGGCAAGATTAAAGATC-ATCTGATCTTTTACCCCG
1 ATCAT-G-GGG-TAGATTGAAGA-CAATCCAATCTTTTACCCTA
3219 ATCATGGGGTAGATTGAAGA-AATCCAAT-TTTTACCCTA
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* * * **
3257 ATCA-GAGGGTAAGATTGAAGACCATTCGATCTTTTACCCCG
1 ATCATG-GGGT-AGATTGAAGACAATCCAATCTTTTACCCTA
**
3298 ATCATGGGACAGATTGAAGA-AATCCAATCTTTTACCCTA
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* * * ** **
3337 ACCA-GAGGGAAAGATTGAAGACCATCTGATCTTTTACCCCG
1 ATCATG-GGG-TAGATTGAAGACAATCCAATCTTTTACCCTA
* * *
3378 ATCATGGGGCAAATTGAAGA-AATTCAATCTTTTACCCTA
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* * ** * * *
3417 ACTAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCCTA
1 A-TCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* *
3458 ATCATAGGGTAGATTGAAGA-AATCCAATCTTTTACCCTG
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
**
3497 A-CAATGGGGTAGAGCGAAG-CAATCCAATCTTTTACCCTA
1 ATC-ATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* * * * * * **
3536 ACCA-GAGGGCAAATTGAAGACCATCCGATCTCTTACCCCG
1 ATCATG-GGGTAGATTGAAGACAATCCAATCTTTTACCCTA
* *
3576 ACCATGGGGTAGATTGAA-ATAATCCAATCTTTTACCC
1 ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCC
3613 CTAAAACTAT
Statistics
Matches: 386, Mismatches: 102, Indels: 54
0.71 0.19 0.10
Matches are distributed among these distances:
37 2 0.01
38 21 0.05
39 140 0.36
40 134 0.35
41 84 0.22
42 4 0.01
43 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (40 bp):
ATCATGGGGTAGATTGAAGACAATCCAATCTTTTACCCTA
Found at i:3601 original size:79 final size:78
Alignment explanation
Indices: 3440--3612 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 78
3430 ATTAAAGACC
* * * * * * *
3440 ATCCGATCTTTTACCCTAATCATAGGGTAGATTGAAGAAATCCAATCTTTTACCCTGACAATGGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGAAATCCAATCTCTTACCCCGACAATGGG
*
3505 GTAGAGCGAAGCA
66 GTAGAGCGAAACA
* * *
3518 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGA-AATCCAATCTCTTACCCCGACAATGG
** *
3583 GGTAGATTGAAATA
65 GGTAGAGCGAAACA
3597 ATCCAATCTTTTACCC
1 ATCCAATCTTTTACCC
3613 CTAAAACTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 33 0.41
79 47 0.59
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (78 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGAAATCCAATCTCTTACCCCGACAATGGG
GTAGAGCGAAACA
Done.