Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013724.1 Kokia drynarioides strain JFW-HI SEQ_128752, 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: 5164
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3392 original size:30 final size:30
Alignment explanation
Indices: 3356--3641 Score: 293
Period size: 30 Copynumber: 9.6 Consensus size: 30
3346 GCACGGGGGC
* * *
3356 AAAATGGTAGTTTTGGAAGGTTCGGAGTCA
1 AAAATGGGATTTTTGGAAGGTTCGGGGTCA
3386 AAAATGGGATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGGATTTTTGGAAGGTTCG-GGGTCA
* * * *
3414 AAAATGGTAATTTTCGAAAGGTTCGAGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGGGTCA
* *
3445 AAAATGGGATTTTTGGAAGTTTAGGGGT-A
1 AAAATGGGATTTTTGGAAGGTTCGGGGTCA
* * *
3474 AAAATGGTAATTTTTGAAAGGTTCGAGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGGGTCA
* *
3505 AAAATGGGATTTTTGGAAGTTTGGGGGT--
1 AAAATGGGATTTTTGGAAGGTTCGGGGTCA
*
3533 AAAATGGTGATTTTTAGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGGGTCA
3564 AAAATGGGATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGGATTTTTGGAAGGTTCG-GGGTCA
* **
3592 AAAATGGTAATTTTTAAAAGGTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGGGTCA
3623 AAAATGGGATTTTTGGAAG
1 AAAATGGGATTTTTGGAAG
3642 TTCAGGGATA
Statistics
Matches: 208, Mismatches: 33, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
28 21 0.10
29 59 0.28
30 99 0.48
31 29 0.14
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (30 bp):
AAAATGGGATTTTTGGAAGGTTCGGGGTCA
Found at i:3577 original size:119 final size:117
Alignment explanation
Indices: 3356--3664 Score: 437
Period size: 119 Copynumber: 2.6 Consensus size: 117
3346 GCACGGGGGC
* *
3356 AAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGAAAGGTTCGG-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
*
3420 GTAATTTTCGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAG-GGGT
65 GTAATTTTAGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTAGAGGGT
* *
3473 AAAAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT
1 -AAAATGGTAATTTTTGAAAGGTTCG-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
* * *
3538 GGTGATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
64 GGT-AATTTTAGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTAGAGGGT
*
3592 AAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGATAAAAT
1 AAAATGGTAATTTTTGAAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAAT
*
3656 AGTAATTTT
64 GGTAATTTT
3665 TGGAAAGTTT
Statistics
Matches: 172, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
117 8 0.05
118 68 0.40
119 89 0.52
120 7 0.04
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGAAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
TAATTTTAGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTAGAGGGT
Found at i:3665 original size:59 final size:58
Alignment explanation
Indices: 3372--3665 Score: 426
Period size: 59 Copynumber: 5.0 Consensus size: 58
3362 GTAGTTTTGG
* **
3372 AAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCGA
1 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAA
* * *
3431 AAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGTAATTTTTGA
1 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCA-GGGT-AAAATGGTAATTTTTAA
* ** * *
3491 AAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTGATTTTTAG
1 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCAGGGTAAAATGGTAATTTTTAA
3550 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAA
1 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAA
*
3609 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGATAAAATAGTAATTTTT
1 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG-TAAAATGGTAATTTTT
3666 GGAAAGTTTA
Statistics
Matches: 215, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
58 7 0.03
59 153 0.71
60 53 0.25
61 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33
Consensus pattern (58 bp):
AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGTAAAATGGTAATTTTTAA
Found at i:4596 original size:21 final size:23
Alignment explanation
Indices: 4561--4604 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
4551 AAAAAAAAAA
4561 CAGATCTAGCTCTAGAT-CAAAC
1 CAGATCTAGCTCTAGATCCAAAC
4583 CAGATCTAGC-CTAGATCCAAAC
1 CAGATCTAGCTCTAGATCCAAAC
4605 GGTTTTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (23 bp):
CAGATCTAGCTCTAGATCCAAAC
Done.