Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010413.1 Kokia drynarioides strain JFW-HI SEQ_125299, 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, 960
Length: 1600
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.37
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:552 original size:305 final size:295
Alignment explanation
Indices: 1--576 Score: 1062
Period size: 305 Copynumber: 1.9 Consensus size: 295
1 ATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTTATTTAAAATTTAATAAT
1 ATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTTATTTAAAATTTAATAAT
66 GTTTAAATTTTGTTAGTTATTAACTTTATTATACAACTCATAAGATTGTTTAATAAAATGTGAAA
66 GTTTAAATTTTGTTAGTTATTAACTTTATTATACAACTCATAAGATTGTTTAATAAAATGTGAAA
131 GAAAATTATTACAAGTGTTTAATAAAATAAACAATAATCTATTTTTAAGTTATAATTAAAATTAG
131 GAAAATTATTACAAGTGTTTAATAAAATAAACAATAATCTATTTTTAAGTTATAATTAAAATTAG
196 TTACAAGTATGAAATTAAAAAATTTATTATTTTATAAAAATAAGAGAGTTTTAATAATTCACAAA
196 TTACAAGTATGAAATTAAAAAATTTATTATTTTATAAAAATAAGAGAGTTTTAATAATTCACAAA
261 AAATTAAACTTNNNNNNNNNNTTAATTTTACTAGTTAGTAATTTT
261 AAATTAAACTT----------TTAATTTTACTAGTTAGTAATTTT
306 ATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTTATTTAAAATTTAATAAT
1 ATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTTATTTAAAATTTAATAAT
371 GTTTAAATTTTGTTAGTTATTAACTTTATTATACAACTCATAAGATTGTTTAATAAAATGTGAAA
66 GTTTAAATTTTGTTAGTTATTAACTTTATTATACAACTCATAAGATTGTTTAATAAAATGTGAAA
436 GAAAATTATTACAAGTGTTTAATAAAATAAACAATAATCTATTTTTAAGTTATAATTAAAATTAG
131 GAAAATTATTACAAGTGTTTAATAAAATAAACAATAATCTATTTTTAAGTTATAATTAAAATTAG
501 TTACAAGTATGAAATTAAAAAATTTATTATTTTATAAAAATAAGAGAGTTTTAATAATTCACAAA
196 TTACAAGTATGAAATTAAAAAATTTATTATTTTATAAAAATAAGAGAGTTTTAATAATTCACAAA
566 AAATTAAACTT
261 AAATTAAACTT
577 AGCTAATTAA
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
305 271 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.42
Consensus pattern (295 bp):
ATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTTATTTAAAATTTAATAAT
GTTTAAATTTTGTTAGTTATTAACTTTATTATACAACTCATAAGATTGTTTAATAAAATGTGAAA
GAAAATTATTACAAGTGTTTAATAAAATAAACAATAATCTATTTTTAAGTTATAATTAAAATTAG
TTACAAGTATGAAATTAAAAAATTTATTATTTTATAAAAATAAGAGAGTTTTAATAATTCACAAA
AAATTAAACTTTTAATTTTACTAGTTAGTAATTTT
Found at i:616 original size:30 final size:30
Alignment explanation
Indices: 580--679 Score: 107
Period size: 30 Copynumber: 3.3 Consensus size: 30
570 TAAACTTAGC
580 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ****
610 TAATTAATTATCAAAA-ATAATAT-CCCCA
1 TAATTAATTACCAAAATATAATATAAAAAA
638 TCATATT-ATTGACCAAAATATAATATAAAAAA
1 T-A-ATTAATT-ACCAAAATATAATATAAAAAA
670 TAATTAATTA
1 TAATTAATTA
680 TGAAAATAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 2 0.04
29 11 0.20
30 28 0.52
31 11 0.20
32 2 0.04
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:627 original size:17 final size:17
Alignment explanation
Indices: 580--630 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
570 TAAACTTAGC
*
580 TAATTAATTA-CCAAAA
1 TAATTAATTATCAAAAA
*
596 T-A-TAA-TATAAAAAA
1 TAATTAATTATCAAAAA
610 TAATTAATTATCAAAAA
1 TAATTAATTATCAAAAA
627 TAAT
1 TAAT
631 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 2 0.07
16 4 0.14
17 12 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATTAATTATCAAAAA
Found at i:697 original size:59 final size:60
Alignment explanation
Indices: 589--715 Score: 229
Period size: 59 Copynumber: 2.1 Consensus size: 60
579 CTAATTAATT
589 ACCAAAATATAATATAAAAAATAATTAATTATCAAAAATAATATCCCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAAATAATATCCCCATCATATTATTG
* *
649 ACCAAAATATAATATAAAAAATAATTAATTAT-GAAAATAATATCCCCATCATATTATTT
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAAATAATATCCCCATCATATTATTG
708 ACCAAAAT
1 ACCAAAAT
716 GGTACAAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 33 0.51
60 32 0.49
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (60 bp):
ACCAAAATATAATATAAAAAATAATTAATTATCAAAAATAATATCCCCATCATATTATTG
Found at i:714 original size:29 final size:29
Alignment explanation
Indices: 623--715 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
613 TTAATTATCA
*
623 AAAATAATATCCCCATCATATTATTGACC
1 AAAATAATATCCCCATCATATTATTTACC
** ** * **
652 AAAATATAATAT--AAAAAATAATTAATTATG
1 -AAA-ATAATATCCCCATCAT-ATTATTTACC
682 AAAATAATATCCCCATCATATTATTTACC
1 AAAATAATATCCCCATCATATTATTTACC
711 AAAAT
1 AAAAT
716 GGTACAAAAT
Statistics
Matches: 44, Mismatches: 15, Indels: 9
0.65 0.22 0.13
Matches are distributed among these distances:
28 7 0.16
29 18 0.41
30 12 0.27
31 7 0.16
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATAATATCCCCATCATATTATTTACC
Done.