Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013918.1 Kokia drynarioides strain JFW-HI SEQ_128948, 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: 10717
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2284 original size:97 final size:96
Alignment explanation
Indices: 2109--2301 Score: 232
Period size: 97 Copynumber: 2.0 Consensus size: 96
2099 AATTTGGGAA
* * ** *
2109 AAGGGTGTTCGATTATCTCAATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACATTTCA
1 AAGGGTATTCGATTATCTCAATTTGAGAAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCA
*
2174 GAATCGAAGAT-AAAGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* *
2205 AAGGGTATTCGATTATTTCGATTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTT
1 AAGGGTATTCGATTATCTCAATTTG-AGAAAAAATTGCACCTAGTAAGTTAAGGCACAACA-TTT
*
2269 C-GAAACTCGAA-ATAAAAGAATATTACCTCGATT
64 CAG-AA-TCGAAGATAAAAGAACATTACCTCGATT
2302 TTAAAGTCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
96 24 0.29
97 50 0.60
98 9 0.11
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (96 bp):
AAGGGTATTCGATTATCTCAATTTGAGAAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:2733 original size:60 final size:59
Alignment explanation
Indices: 2594--2860 Score: 290
Period size: 59 Copynumber: 4.5 Consensus size: 59
2584 TTAGACATTC
* * * * * *
2594 GGGGTAAAAAGGGTAA-TTTTGGGAGTTTTGAGGTC-GAAAATGGAGATTTTGGAAGTTCG
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGATCAAAAAATGGA-TTTTTGGAAGTTCG
* ** *
2653 AGGACAAAAATGGAATTTTTGGAAGTTTCGAGATC-AAAAACGAGATTTTTGGAAGTTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGATCAAAAAATG-GATTTTTGGAAG-TTCG
*
2713 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGATCAAAAAATGGATTTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGATCAAAAAATGGA-TTTTTGGAAGTTCG
** * * *
2773 GGGGTAAAAATTCAATTTTTGGAAGTTTTGAGGTC-AAAAATGGAATTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGATCAAAAAATGG-ATTTTTGGAAGTTCG
*
2832 GGGGTAAAAATGCAATTTTTGGATAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
2861 AGGGACCTCT
Statistics
Matches: 179, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
58 2 0.01
59 82 0.46
60 79 0.44
61 16 0.09
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGATCAAAAAATGGATTTTTGGAAGTTCG
Found at i:2831 original size:29 final size:30
Alignment explanation
Indices: 2610--2860 Score: 248
Period size: 30 Copynumber: 8.4 Consensus size: 30
2600 AAAAGGGTAA
* * *
2610 TTTTGGGAGTTTTGAGGTCGAAAATGGAGA-
1 TTTTGGAAGTTTCGAGGTCAAAAATGGA-AT
*
2640 TTTTGGAAG-TTCGAGGACAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
2669 TTTTGGAAGTTTCGAGATCAAAAA-CGAGAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGA-AT
*
2699 TTTTGGAAGTTTCGGGGGT-AAAAATGGAAT
1 TTTTGGAAGTTTC-GAGGTCAAAAATGGAAT
*
2729 TTTTGGAAGTTTCG-GGATCAAAAAATGGATT
1 TTTTGGAAGTTTCGAGG-TC-AAAAATGGAAT
* **
2760 TTTTGGAAG-TTCGGGGGT-AAAAATTCAAT
1 TTTTGGAAGTTTC-GAGGTCAAAAATGGAAT
*
2789 TTTTGGAAGTTTTGAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* * *
2819 TTTTGGAAGTTTGGGGGT-AAAAATGCAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
2848 TTTTGGATAGTTT
1 TTTTGGA-AGTTT
2861 AGGGACCTCT
Statistics
Matches: 187, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.02
29 66 0.35
30 90 0.48
31 26 0.14
32 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (30 bp):
TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
Found at i:4452 original size:16 final size:16
Alignment explanation
Indices: 4424--4457 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4414 CATTTTGATG
4424 TTATTTTTGTGCCATT
1 TTATTTTTGTGCCATT
4440 TTATTATTT-TGCCATT
1 TTATT-TTTGTGCCATT
4456 TT
1 TT
4458 TTTGTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.65
Consensus pattern (16 bp):
TTATTTTTGTGCCATT
Found at i:8664 original size:24 final size:24
Alignment explanation
Indices: 8637--8684 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
8627 ATAGAAACTT
8637 CGAAGAATGAGGCCTGACGCGCTA
1 CGAAGAATGAGGCCTGACGCGCTA
8661 CGAAGAATGAGGCCTGACGCGCTA
1 CGAAGAATGAGGCCTGACGCGCTA
8685 TCTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.33, T:0.12
Consensus pattern (24 bp):
CGAAGAATGAGGCCTGACGCGCTA
Done.