Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001487.1 Kokia drynarioides strain JFW-HI SEQ_113023, 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: 3389
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.31
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:390 original size:59 final size:59
Alignment explanation
Indices: 308--751 Score: 528
Period size: 59 Copynumber: 7.6 Consensus size: 59
298 GCACGGGGGC
* * * * *
308 AAAATGGT-AGTTTTGGAAAGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
366 AAAATGCTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
425 AAAATGGTAATTTTTAGAAGGTTCGAGGGT-----GTGGGGTTTTTTGGAAGTTCGGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCG-GGGTCAAAAAT-GGGATTTTTGGAAGTTC-GAGGGT
* * * * *
482 AAAATGATAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* ** *
541 AAAATGGTAATTTTTGGAATATTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
600 AAAATGGTAATTTTTAGAAGGTTCGAGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
658 AAAATGGTCATTTTTAGAAGGTTTGGGGCCAAAAATGAGATTTTTGGAAGGTTCG-GGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAA-GTTCGAGGGT
* *
717 AAAAAATGGTAATTTTTAGAAGTTTTGGGGT-AAAA
1 --AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAA
752 TGATAATTTT
Statistics
Matches: 336, Mismatches: 37, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
55 1 0.00
56 19 0.06
57 29 0.09
58 59 0.18
59 172 0.51
60 29 0.09
61 27 0.08
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:609 original size:175 final size:172
Alignment explanation
Indices: 318--751 Score: 550
Period size: 175 Copynumber: 2.5 Consensus size: 172
308 AAAATGGTAG
* * *
318 TTTTGGAAAGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGCTAATTTTTAG
1 TTTTGGAAGGTTCGG-GTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG
* *
383 AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTT
65 AAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTT
* ** *
448 CGAGGGT-GTGGGGTTTTTTGGAAGTTCGGGGGGTAAAATGATAAT
130 CGA-GGTAAT-GGAATTTTTGGAAGTTC-GAGGGTAAAATGATAAT
* * *
493 TTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TTTTGGAAGGTTCG-GGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG
* *
558 AATATTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTT
65 AAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTT
* *
623 CGAGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTCAT
130 CGAGGT---AATGGAATTTTTGGAAGTTCGAGGGTAAAATGATAAT
* * *
669 TTTTAGAAGGTTTGGGGCCAAAAATGAGATTTTTGGAAGGTTC-GGGGTAAAAAATGGTAATTTT
1 TTTTGGAAGG-TTCGGGTCAAAAATGAGATTTTTGGAA-GTTCGGGGGT--AAAATGGTAATTTT
* *
733 TAGAAGTTTTGGGGT-AAAA
62 TAGAAGATTCGGGGTCAAAA
752 TGATAATTTT
Statistics
Matches: 225, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
174 3 0.01
175 121 0.54
176 49 0.22
177 26 0.12
178 26 0.12
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (172 bp):
TTTTGGAAGGTTCGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGA
AGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTC
GAGGTAATGGAATTTTTGGAAGTTCGAGGGTAAAATGATAAT
Found at i:761 original size:29 final size:29
Alignment explanation
Indices: 303--761 Score: 324
Period size: 30 Copynumber: 15.7 Consensus size: 29
293 CGGATGCACG
* * *
303 GGGGCAAAATGGT-AGTTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
331 GGAGTCAAAAAT-G-AGATTTTTGGAA-GTTC
1 GGGGT--AAAATGGTA-ATTTTTGGAAGGTTC
* *
360 GAGGGTAAAATGCTAATTTTTAGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
*
390 GGGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
*
419 GGGGGTAAAATGGTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* ***
449 GAGGGT---GTGGGGTTTTTTGGAA-GTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
*
475 GGGGGGTAAAATGATAATTTTTGGAAGGTTC
1 --GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
506 GAGGTTAAAAATGG-GATTTTTGGAA-GTTC
1 G-GGGT-AAAATGGTAATTTTTGGAAGGTTC
**
535 GGGGGTAAAATGGTAATTTTTGGAATATTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
565 GGGGTCAAAAATGG-GATTTTTGGAA-GTTT
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
*
594 GAGGGTAAAATGGTAATTTTTAGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
*
624 GAGGTAAAAATGG-AATTTTTGGAA-GTTC
1 GGGGT-AAAATGGTAATTTTTGGAAGGTTC
* * *
652 GAGGGTAAAATGGTCATTTTTAGAAGGTTT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
*
682 GGGGCCAAAAAT-G-AGATTTTTGGAAGGTTC
1 GGGG--TAAAATGGTA-ATTTTTGGAAGGTTC
* * *
712 GGGGTAAAAAATGGTAATTTTTAGAAGTTTT
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
*
743 GGGGTAAAATGATAATTTT
1 GGGGTAAAATGGTAATTTT
762 CGGATAGTTT
Statistics
Matches: 342, Mismatches: 48, Indels: 81
0.73 0.10 0.17
Matches are distributed among these distances:
26 4 0.01
27 15 0.04
28 42 0.12
29 109 0.32
30 125 0.37
31 46 0.13
32 1 0.00
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTC
Found at i:1840 original size:10 final size:10
Alignment explanation
Indices: 1820--1848 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1810 CTCTTCATTT
1820 TTATT-ATTA
1 TTATTAATTA
1829 TTATTAATTA
1 TTATTAATTA
1839 TTATTAATTA
1 TTATTAATTA
1849 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTAATTA
Found at i:1840 original size:13 final size:14
Alignment explanation
Indices: 1822--1852 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1812 CTTCATTTTT
1822 ATTATTATT-ATTA
1 ATTATTATTAATTA
1835 ATTATTATTAATTA
1 ATTATTATTAATTA
1849 ATTA
1 ATTA
1853 ATAAATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATTATTAATTA
Found at i:2644 original size:11 final size:11
Alignment explanation
Indices: 2612--2645 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2602 AAAATAAATT
* *
2612 TAAACTTAAAT
1 TAAATTTAAAA
2623 TAAATTTAAAA
1 TAAATTTAAAA
2634 TAAATTTAAAA
1 TAAATTTAAAA
2645 T
1 T
2646 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2657 original size:46 final size:45
Alignment explanation
Indices: 2589--2677 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
2579 GTTTATTTTA
* *
2589 AAATTTAAATTTGAAAATAAATTTAAACTTAAATTAAATTTAAAAT
1 AAATTTAAATTTGAAAACAAATTT-AACTTAAAATAAATTTAAAAT
* *
2635 AAATTTAAAATTT-TAAACAAATTTAATTTAAAATAAATTTAAA
1 AAATTT-AAATTTGAAAACAAATTTAACTTAAAATAAATTTAAA
2678 GGGAGTATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 17 0.45
46 15 0.39
47 6 0.16
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (45 bp):
AAATTTAAATTTGAAAACAAATTTAACTTAAAATAAATTTAAAAT
Found at i:2663 original size:34 final size:35
Alignment explanation
Indices: 2610--2677 Score: 111
Period size: 34 Copynumber: 1.9 Consensus size: 35
2600 TGAAAATAAA
2610 TTTAAACTTAAATTAAATTTAAAATAAATTTAAAAT
1 TTTAAAC-TAAATTAAATTTAAAATAAATTTAAAAT
*
2646 TTTAAAC-AAATTTAATTTAAAATAAATTTAAA
1 TTTAAACTAAATTAAATTTAAAATAAATTTAAA
2678 GGGAGTATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 24 0.77
36 7 0.23
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (35 bp):
TTTAAACTAAATTAAATTTAAAATAAATTTAAAAT
Found at i:2674 original size:16 final size:16
Alignment explanation
Indices: 2608--2676 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
2598 TTTGAAAATA
* *
2608 AATTTAAACTTAAATTA
1 AATTTAAA-ATAAATTT
2625 AATTTAAAATAAATTT
1 AATTTAAAATAAATTT
* *
2641 AAAATTTTAAACAAATTT
1 --AATTTAAAATAAATTT
2659 AATTTAAAATAAATTT
1 AATTTAAAATAAATTT
2675 AA
1 AA
2677 AGGGAGTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 22 0.50
17 8 0.18
18 14 0.32
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATAAATTT
Done.