Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001393.1 Kokia drynarioides strain JFW-HI SEQ_112878, 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: 13645
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:410 original size:10 final size:10
Alignment explanation
Indices: 397--574 Score: 54
Period size: 10 Copynumber: 18.2 Consensus size: 10
387 TTAAATTTTG
397 ATAAAAAATT
1 ATAAAAAATT
*
407 ATAAAAAAAT
1 ATAAAAAATT
* **
417 ATTTAAATTTT
1 A-TAAAAAATT
428 ATTAAAAAATT
1 A-TAAAAAATT
*
439 AGGAAAAAA--
1 A-TAAAAAATT
*
448 ATATAAAATT
1 ATAAAAAATT
* **
458 TTTGAAAATT
1 ATAAAAAATT
*
468 ATAAAATA-T
1 ATAAAAAATT
477 AT-AAAAATT
1 ATAAAAAATT
486 A-AAAAAATT
1 ATAAAAAATT
*
495 -TATAAAATT
1 ATAAAAAATT
* * * *
504 TTATAAAGTG
1 ATAAAAAATT
514 ATAAGAAAATT
1 ATAA-AAAATT
* *
525 ATAGAAGATGT
1 ATAAAAAAT-T
536 A-AAAAAA-T
1 ATAAAAAATT
544 AT--AAAATT
1 ATAAAAAATT
*
552 CGTAAAATAATT
1 -ATAAAA-AATT
564 AT-AAAAATT
1 ATAAAAAATT
573 AT
1 AT
575 CATACTAAAA
Statistics
Matches: 120, Mismatches: 33, Indels: 31
0.65 0.18 0.17
Matches are distributed among these distances:
7 4 0.03
8 12 0.10
9 27 0.22
10 41 0.34
11 32 0.27
12 4 0.03
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:436 original size:33 final size:31
Alignment explanation
Indices: 365--459 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 31
355 GTGGTAAAAA
365 TGATAAAAAA-TAAAAAAAATATTTAAATTT
1 TGATAAAAAATTAAAAAAAATATTTAAATTT
395 TGATAAAAAATTATAAAAAAATATTTAAATTT
1 TGATAAAAAATTA-AAAAAAATATTTAAATTT
*
427 T-ATTAAAAAATTAGGAAAAAAATA-TAAAATTT
1 TGA-TAAAAAATTA--AAAAAAATATTTAAATTT
459 T
1 T
460 TGAAAATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.17
31 3 0.05
32 37 0.63
33 9 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (31 bp):
TGATAAAAAATTAAAAAAAATATTTAAATTT
Found at i:483 original size:18 final size:18
Alignment explanation
Indices: 443--550 Score: 58
Period size: 19 Copynumber: 5.8 Consensus size: 18
433 AAAATTAGGA
* * *
443 AAAAAATATAAAATTTTT
1 AAAAATTATAAAATATAT
*
461 GAAAATTATAAAATATAT
1 AAAAATTATAAAATATAT
* *
479 AAAAATTAAAAAAATTTAT
1 AAAAATT-ATAAAATATAT
* *
498 AAAATTTTATAAAGTGATA-
1 AAAA-ATTATAAAAT-ATAT
*
517 AGAAAATTATAGAAGATGTA-
1 A-AAAATTATA-AA-ATATAT
*
537 AAAAAATATAAAAT
1 AAAAATTATAAAAT
551 TCGTAAAATA
Statistics
Matches: 69, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
17 2 0.03
18 22 0.32
19 32 0.46
20 12 0.17
21 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAATATAT
Found at i:501 original size:9 final size:9
Alignment explanation
Indices: 449--510 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
439 AGGAAAAAAA
449 TATAAAATT
1 TATAAAATT
*
458 TTTGAAAA-T
1 TAT-AAAATT
*
467 TATAAAATA
1 TATAAAATT
476 TATAAAAATT
1 TAT-AAAATT
* *
486 AAAAAAATT
1 TATAAAATT
495 TATAAAATTT
1 TATAAAA-TT
505 TATAAA
1 TATAAA
511 GTGATAAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
8 4 0.10
9 19 0.46
10 18 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
TATAAAATT
Found at i:770 original size:10 final size:10
Alignment explanation
Indices: 757--891 Score: 52
Period size: 10 Copynumber: 13.6 Consensus size: 10
747 TTTTGATGCA
757 TTTTATAATTTT
1 TTTTATAA--TT
**
769 TTTTATAAAA
1 TTTTATAATT
* *
779 GTTTACAAT-
1 TTTTATAATT
788 TTTTATAATT
1 TTTTATAATT
*
798 TTTTACAATT
1 TTTTATAATT
*
808 TTTATAAAATT
1 TTT-TATAATT
*
819 TTCATTCTAATT
1 TT--TTATAATT
* *
831 TTTAATAA-A
1 TTTTATAATT
840 TTTTAT--TT
1 TTTTATAATT
848 TTTTAATAA--
1 TTTT-ATAATT
*
857 TATT-TAATT
1 TTTTATAATT
*
866 GTTTT-TATTT
1 -TTTTATAATT
876 TTTTATAATT
1 TTTTATAATT
886 TTTTAT
1 TTTTAT
892 CACATGCTAT
Statistics
Matches: 91, Mismatches: 20, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
7 3 0.03
8 4 0.04
9 21 0.23
10 39 0.43
11 8 0.09
12 15 0.16
13 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:820 original size:19 final size:19
Alignment explanation
Indices: 768--820 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
758 TTTATAATTT
*
768 TTTTTATAAAAGTTTACAA
1 TTTTTATAAAATTTTACAA
**
787 TTTTTATAATTTTTTACAA
1 TTTTTATAAAATTTTACAA
806 TTTTTATAAAATTTT
1 TTTTTATAAAATTTT
821 CATTCTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTATAAAATTTTACAA
Found at i:852 original size:18 final size:20
Alignment explanation
Indices: 829--872 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
819 TTCATTCTAA
*
829 TTTTTAATAA-ATTTTATT-
1 TTTTTAATAATATTTAATTG
847 TTTTTAATAATATTTAATTG
1 TTTTTAATAATATTTAATTG
867 TTTTTA
1 TTTTTA
873 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 7 0.30
20 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTAATAATATTTAATTG
Found at i:857 original size:28 final size:27
Alignment explanation
Indices: 826--888 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
816 ATTTTCATTC
826 TAATTTTTAATAAATTTTATTTTTTTAA
1 TAATTTTTAATAAATTTTATTTTTTT-A
* ***
854 TAATATTTAATTGTTTTTATTTTTTTA
1 TAATTTTTAATAAATTTTATTTTTTTA
881 TAATTTTT
1 TAATTTTT
889 TATCACATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TAATTTTTAATAAATTTTATTTTTTTA
Done.