Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014444.1 Kokia drynarioides strain JFW-HI SEQ_129483, 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: 5435
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.32
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:4203 original size:59 final size:59
Alignment explanation
Indices: 4118--4530 Score: 321
Period size: 59 Copynumber: 7.1 Consensus size: 59
4108 ATCGGGGGAC
* ** *
4118 AAAATGGTAATTTTGGGAAAGTTCAAGGTTAAAAATGAAATTTT-AATCA-TCCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGAAATTTTGAAT-AGTTCGAGGGT
* * * * * *
4176 AAAATGGTAATTTTTGGATAGAATCAAGATCAAAAATGGAATTTTTG-ATAGTTTGGGGGT
1 AAAATGGTAATTTTTGGA-AAAATCAAGGTTAAAAAT-GAAATTTTGAATAGTTCGAGGGT
** * ** * *
4236 AAAAAAGT-ATTTTGGGAGGAAT-AAGGGTTAAAAATGAAATTTTGGAA-AGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAA-GGTTAAAAATGAAATTTT-GAATAGTTCGAGGGT
* * * * * *
4294 AAAATGTTAATTTTTGGAAAAATGAAGGTAAAAAATGGAAATTTTGGA-AGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAAT-GAAATTTTGAATAGTTCGAGGGT
* * * * *
4353 AAAATGGTAA--ATTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGA-AGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGAAATTTTGA-ATAGTTCGAGGGT
* * *
4410 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATTG-AATTTTGGA-AGGTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAA-TGAAATTTTGAATAGTTCGAGGGT
* * * * * *
4468 AAAATGGTAATTTTTGGAAAAATCGATGTAAAAAATGGAATTTAGGAAT-GTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGAAATTT-TGAATAGTTCGAGGGT
4527 AAAA
1 AAAA
4531 ATGTTATTTT
Statistics
Matches: 292, Mismatches: 46, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
56 7 0.02
57 51 0.17
58 95 0.33
59 106 0.36
60 33 0.11
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGAAATTTTGAATAGTTCGAGGGT
Found at i:4354 original size:30 final size:30
Alignment explanation
Indices: 4260--4356 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
4250 GGAGGAATAA
*
4260 GGGTTAAAAAT-GAAATTTTGGAAAGTTTGG
1 GGGTAAAAAATGGAAATTTTGG-AAGTTTGG
* * *** *
4290 GGGT--AAAATGTTAATTTTTGGAAAAATGA
1 GGGTAAAAAATG-GAAATTTTGGAAGTTTGG
*
4319 AGGTAAAAAATGGAAATTTTGGAAGTTTGG
1 GGGTAAAAAATGGAAATTTTGGAAGTTTGG
4349 GGGTAAAA
1 GGGTAAAA
4357 TGGTAAATTG
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 5 0.10
29 7 0.14
30 31 0.63
31 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (30 bp):
GGGTAAAAAATGGAAATTTTGGAAGTTTGG
Found at i:4405 original size:29 final size:29
Alignment explanation
Indices: 4302--4510 Score: 139
Period size: 29 Copynumber: 7.2 Consensus size: 29
4292 GTAAAATGTT
4302 AATTTTTGGAAAAAT-GAAGGTAAAAAATGG
1 AATTTTTGGAAAAATCG-AGGT-AAAAATGG
* *** * *
4332 AAATTTTGGAAGTTTGGGGGT-AAAATGG
1 AATTTTTGGAAAAATCGAGGTAAAAATGG
*
4360 TAA--ATTGGAAAAATCGAGGTCAAAAATGG
1 -AATTTTTGGAAAAATCGAGGT-AAAAATGG
* **
4389 AATTTTTAG-AAGTTCGAGGGT-AAAATGG
1 AATTTTTGGAAAAATCGA-GGTAAAAATGG
*
4417 TAATTTTTGGAAAAATCGAGGTTAAAAATTG
1 -AATTTTTGGAAAAATCGAGG-TAAAAATGG
**
4448 AA-TTTTGG-AAGGTCGAGGGT-AAAATGG
1 AATTTTTGGAAAAATCGA-GGTAAAAATGG
*
4475 TAATTTTTGGAAAAATCGATGTAAAAAATGG
1 -AATTTTTGGAAAAATCGAGGT-AAAAATGG
4506 AATTT
1 AATTT
4511 AGGAATGTTC
Statistics
Matches: 137, Mismatches: 25, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
27 17 0.12
28 25 0.18
29 41 0.30
30 40 0.29
31 14 0.10
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (29 bp):
AATTTTTGGAAAAATCGAGGTAAAAATGG
Found at i:4488 original size:58 final size:58
Alignment explanation
Indices: 4109--4530 Score: 374
Period size: 58 Copynumber: 7.2 Consensus size: 58
4099 TTTTTGGGTA
* * ** * *
4109 TCGGGGGACAAAATGGTAATTTTGGGAAAGTTCAAGGTTAAAAATGAAATTTT--AA-T
1 TCGGGGG-TAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAGT
* * * * * *
4165 CATCCGAGGGTAAAATGGTAATTTTTGGATAGAATCAAGATCAAAAATGGAATTTTTGATAGT
1 --T-CGGGGGTAAAATGGTAATTTTTGGA-AAAATCGAGGTTAAAAATGGAATTTTGGA-AGT
* ** * ** * *
4228 TTGGGGGTAAAAAAGT-ATTTTGGGAGGAAT-AAGGGTTAAAAATGAAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTTAAAAATGGAATTTTGG-AAGT
* * *
4286 TTGGGGGTAAAATGTTAATTTTTGGAAAAAT-GAAGGTAAAAAATGGAAATTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCG-AGGTTAAAAATGG-AATTTTGGAAGT
* * * *
4345 TTGGGGGTAAAATGGTAA--ATTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAA-TTTTGGAAGT
* * *
4402 TCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATTGAATTTTGGAAGG
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAGT
* * * *
4460 TCGAGGGTAAAATGGTAATTTTTGGAAAAATCGATGTAAAAAATGGAATTTAGGAATGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAA-GT
4519 TCGGGGGTAAAA
1 TCGGGGGTAAAA
4531 ATGTTATTTT
Statistics
Matches: 303, Mismatches: 45, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
56 2 0.01
57 49 0.16
58 115 0.38
59 113 0.37
60 20 0.07
61 2 0.01
62 1 0.00
63 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (58 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAGT
Found at i:4568 original size:29 final size:30
Alignment explanation
Indices: 4522--4610 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 30
4512 GGAATGTTCG
* * *
4522 GGGGTAAAAATGTTATTTTTGAAATGTTTA
1 GGGGTCAAAATATAATTTTTGAAATGTTTA
* * * *
4552 GGTGT-TAAATATAATTTTGGAGAA-GTTTG
1 GGGGTCAAAATATAATTTTTGA-AATGTTTA
* *
4581 GGGGTCAAAATATAATTTTTGGACTGTTTA
1 GGGGTCAAAATATAATTTTTGAAATGTTTA
4611 AGGACCTTCG
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTTGAAATGTTTA
Done.