Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003238.1 Kokia drynarioides strain JFW-HI SEQ_115886, 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: 9421
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1806 original size:98 final size:97
Alignment explanation
Indices: 1619--1808 Score: 242
Period size: 98 Copynumber: 1.9 Consensus size: 97
1609 TCTTTGCGAA
* *
1619 AAGGATATTTGATTATCTCGATTTGAAGAAAAAATTGCACCTAGTGAGTTAAGACGCAATATTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAATTGCAACTAGTGAGTTAAGACGCAATATTTC
** * *
1684 GGAATCGAAGATAAGGAAACATTGCCTCAATT
66 AAAACCGAAGATAAAGAAACATTGCCTCAATT
* *
1716 AAGGATATTCGATTATTTCGATTTGAAGAAAAAAATTGCAACTAGTGAGTTAAGGCGCAA-ATTT
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAAATTGCAACTAGTGAGTTAAGACGCAATA-TT
*
1780 TCAAAACCCGAA-ATGAAAG-AATATTGCCT
64 TCAAAA-CCGAAGAT-AAAGAAACATTGCCT
1809 TGATATTAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
97 27 0.34
98 46 0.57
99 7 0.09
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAAATTGCAACTAGTGAGTTAAGACGCAATATTTC
AAAACCGAAGATAAAGAAACATTGCCTCAATT
Found at i:2139 original size:29 final size:28
Alignment explanation
Indices: 2086--2507 Score: 427
Period size: 29 Copynumber: 14.4 Consensus size: 28
2076 CTCGAGGGTG
* * *
2086 AAATGGTAATTTTGGGAAAATTTGGGGTTAA
1 AAATGG-AATTTTTGG-AAGTTCGGGG-TAA
* *
2117 AAATGGAATTTTTGGAAGTTTGGGGGTTA
1 AAATGGAATTTTTGGAAG-TTCGGGGTAA
**
2146 AAATGGAATTTTTGGAAGTTTTTGGGTCAA
1 AAATGGAATTTTTGGAAG-TTCGGGGT-AA
*
2176 AAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTCG-GGGTAA
* *
2205 AAATGGGGATTTTTTGAAGTTCGAGGGTAA
1 AAAT-GGAATTTTTGGAAGTTCG-GGGTAA
*
2235 AAATAGG-ATTTTTGGAAGTTCAGGGGTCA
1 AAAT-GGAATTTTTGGAAGTTC-GGGGTAA
*
2264 AAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTCG-GGGTAA
*
2293 AAATGGGATTTTTGGAAGTTCGGGGGTCAA
1 AAATGGAATTTTTGGAAGTTC-GGGGT-AA
*
2323 AAATGGGATTTTTGGAAGTTCGGGAGTAA
1 AAATGGAATTTTTGGAAGTTCGGG-GTAA
2352 AAAT-GAGATTTTTGGAAGTTCGGGGTCAA
1 AAATGGA-ATTTTTGGAAGTTCGGGGT-AA
* *
2381 AAAT-GAGATTTTTGAAAGTTCGAGCGTAA
1 AAATGGA-ATTTTTGGAAGTTCG-GGGTAA
* *
2410 AAACGGAATTTTTGAAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTC-GGGGTAA
* *
2439 AAATAGAATTTTTGAAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTCG-GGGTAA
*
2468 AAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTC-GGGGTAA
*
2497 AAATGGGATTT
1 AAATGGAATTT
2508 CTAGATAGTT
Statistics
Matches: 349, Mismatches: 25, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.02
29 236 0.68
30 100 0.29
31 6 0.02
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (28 bp):
AAATGGAATTTTTGGAAGTTCGGGGTAA
Found at i:2302 original size:58 final size:58
Alignment explanation
Indices: 2114--2507 Score: 531
Period size: 58 Copynumber: 6.7 Consensus size: 58
2104 AATTTGGGGT
* * * * ***
2114 TAAAAATGGAATTTTTGGAAGTTTGGGGGTTAAAATGGAATTTTTGGAAGTTTTTGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGAGGG
* *
2172 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGGGATTTTTTGAAGTTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GGGATTTTTGGAAGTTCGAGGG
* * *
2232 TAAAAATAGGATTTTTGGAAGTTCAGGGGTCAAAATGGGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGAGGG
2290 TAAAAATGGGATTTTTGGAAGTTCGGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGAG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGT-AAAAATGGGATTTTTGGAAGTTCGAGG-G
* * * *
2349 TAAAAATGAGATTTTTGGAAGTTC-GGGGTCAAAAATGAGATTTTTGAAAGTTCGAGCG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGT-AAAAATGGGATTTTTGGAAGTTCGAGGG
* * * * * *
2407 TAAAAACGGAATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGTTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGAGGG
2465 TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTT
1 TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTT
2508 CTAGATAGTT
Statistics
Matches: 296, Mismatches: 34, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
58 163 0.55
59 115 0.39
60 18 0.06
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (58 bp):
TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGAGGG
Found at i:3238 original size:78 final size:78
Alignment explanation
Indices: 3145--3380 Score: 366
Period size: 78 Copynumber: 3.0 Consensus size: 78
3135 CCCGTCGCAA
*
3145 GTCCATAGCCACGCGCCGTTGTGCGCTTCTGCCAAGGCAACGTCCGACCGTCCACGCGCCCCACA
1 GTCCGTAGCCACGCGCCGTTGTGCGCTTCTGCCAAGGCAACGTCCGACCGTCCACGCGCCCCACA
*
3210 TCTCTAGTCACCG
66 TCTCTGGTCACCG
* *
3223 GTCCGTAGCCACGCGCCGTTGTGTGCTT-TCGCCAAGGCAACGCCCGACCGTCCACGCGCCCCAC
1 GTCCGTAGCCACGCGCCGTTGTGCGCTTCT-GCCAAGGCAACGTCCGACCGTCCACGCGCCCCAC
*
3287 ATCTCCGGTCACCG
65 ATCTCTGGTCACCG
* * * * *
3301 GTCCGTAGCCATGCGCCGTTGTGCGCTTCCGCCAAGGCAACATCCAACCGTCCACGCGCCTCACA
1 GTCCGTAGCCACGCGCCGTTGTGCGCTTCTGCCAAGGCAACGTCCGACCGTCCACGCGCCCCACA
3366 TCTCTGGTCACCG
66 TCTCTGGTCACCG
3379 GT
1 GT
3381 AAGTTCAAAA
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
77 1 0.01
78 142 0.99
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (78 bp):
GTCCGTAGCCACGCGCCGTTGTGCGCTTCTGCCAAGGCAACGTCCGACCGTCCACGCGCCCCACA
TCTCTGGTCACCG
Done.