Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005646.1 Kokia drynarioides strain JFW-HI SEQ_119810, 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, 712
Length: 1188
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Found at i:540 original size:29 final size:29
Alignment explanation
Indices: 488--867 Score: 248
Period size: 29 Copynumber: 13.0 Consensus size: 29
478 TTCTAATCAT
*
488 ATTTGACCCC-AAACCTTCC-AAAATTACC
1 ATTTTACCCCTAAA-CTTCCAAAAATTACC
*
516 ATTTTACCCCTAAACTTCCAAAAA-TCCC
1 ATTTTACCCCTAAACTTCCAAAAATTACC
*
544 ATTTTTGACCCC-AAACCTTCCAAAAATTATC
1 A-TTTT-ACCCCTAAA-CTTCCAAAAATTACC
* *
575 ATTTTACCCCCAAACTTCCAAAAA-TCCC
1 ATTTTACCCCTAAACTTCCAAAAATTACC
** **
603 ATTTTTA-CCCTCAAAAGTCCAAAAA-CCCC
1 A-TTTTACCCCT-AAACTTCCAAAAATTACC
* *
632 AATTTTGACCCCTAACCTTCTAAAAATTACC
1 -ATTTT-ACCCCTAAACTTCCAAAAATTACC
* *
663 ATTTTA-CCCTCGAACTTCCAAAAA-TCCC
1 ATTTTACCCCT-AAACTTCCAAAAATTACC
691 ATTTTGACCCC-AAACCTTCCAAAAATTACC
1 ATTTT-ACCCCTAAA-CTTCCAAAAATTACC
** *
721 ATTTTACCCCCGAACTTCCAGAAA-T-CTC
1 ATTTTACCCCTAAACTTCCAAAAATTAC-C
* * *
749 ATTTTTGA-CTCTGAACCTTCCAAAAAATACC
1 A-TTTT-ACCCCT-AAACTTCCAAAAATTACC
** * *
780 ATTTTACCCCCGAAGTTCCAAAAATCT-CA
1 ATTTTACCCCTAAACTTCCAAAAAT-TACC
* * *
809 ATTTTTACCTCGAACCTTCCAAAAATTACC
1 A-TTTTACCCCTAAACTTCCAAAAATTACC
* *
839 ATTTTGACCCCGAAACATCCAAAAATTAC
1 ATTTT-ACCCCTAAACTTCCAAAAATTAC
868 TATCTTACTC
Statistics
Matches: 277, Mismatches: 45, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.00
28 41 0.15
29 112 0.40
30 110 0.40
31 12 0.04
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.28
Consensus pattern (29 bp):
ATTTTACCCCTAAACTTCCAAAAATTACC
Found at i:559 original size:58 final size:59
Alignment explanation
Indices: 493--864 Score: 286
Period size: 59 Copynumber: 6.3 Consensus size: 59
483 ATCATATTTG
* *
493 ACCC-CAAACCTTCCAAAATTACCATTTT-ACCCCTAAACTTCCAAAAA-TCCCATTTTT
1 ACCCTCAAA-CTTCCAAAAATACCATTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
* * *
550 GACCC-CAAACCTTCCAAAAATTATCATTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTT
1 -ACCCTCAAA-CTTCCAAAAA-TACCATTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
** ** * *
609 ACCCTCAAAAGTCCAAAAACCCCAATTTTGACCCCTAACCTTCTAAAAATTACCA-TTTT
1 ACCCTCAAACTTCCAAAAATACC-ATTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
* *
668 ACCCTCGAACTTCCAAAAATCCCATTTTGACCCC-AAACCTTCCAAAAATTACCA-TTTT
1 ACCCTCAAACTTCCAAAAATACCATTTTGACCCCTAAA-CTTCCAAAAATTACCATTTTT
* * * * * *
726 ACCCCCGAACTTCCAGAAAT-CTCATTTTTGA-CTCTGAACCTTCCAAAAAATACCA-TTTT
1 ACCCTCAAACTTCCAAAAATAC-CA-TTTTGACCCCT-AAACTTCCAAAAATTACCATTTTT
* * * * * * * *
785 ACCCCCGAAGTTCCAAAAAT-CTCAATTTTTACCTCGAACCTTCCAAAAATTACCATTTTG
1 ACCCTCAAACTTCCAAAAATAC-C-ATTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
*
845 ACCC-CGAAACATCCAAAAAT
1 ACCCTC-AAACTTCCAAAAAT
865 TACTATCTTA
Statistics
Matches: 268, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
57 4 0.01
58 87 0.32
59 149 0.56
60 28 0.10
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (59 bp):
ACCCTCAAACTTCCAAAAATACCATTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
Found at i:612 original size:88 final size:87
Alignment explanation
Indices: 489--864 Score: 338
Period size: 88 Copynumber: 4.3 Consensus size: 87
479 TCTAATCATA
*
489 TTTGA-CCCCAAACCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGAC
1 TTTGACCCCCAAA-CTTCCAAAAATACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-AC
* *
553 CCCAAACCTTCCAAAAATTATCAT
64 CCCGAACCTTCCAAAAATTACCAT
* ** * *
577 TTT-ACCCCCAAACTTCCAAAAATCCCATTTTTA-CCCTCAAAAGTCCAAAAACCCCAATTTTGA
1 TTTGACCCCCAAACTTCCAAAAATACCA-TTTTACCCCT-AAACTTCCAAAAATCCC-ATTTTTA
* *
640 CCCCTAACCTTCTAAAAATTACCAT
63 CCCCGAACCTTCCAAAAATTACCAT
* * * *
665 TTT-ACCCTCGAACTTCCAAAAATCCCATTTTGACCCC-AAACCTTCCAAAAATTACCA-TTTTA
1 TTTGACCCCCAAACTTCCAAAAATACCATTTT-ACCCCTAAA-CTTCCAAAAA-TCCCATTTTTA
*
727 CCCCCGAA-CTTCCAGAAA-T-CTCATT
63 -CCCCGAACCTTCCAAAAATTAC-CA-T
* ** * ** * *
752 TTTGACTCTGAACCTTCCAAAAAATACCATTTTACCCCCGAAGTTCCAAAAATCTCAATTTTTAC
1 TTTGACCCCCAAACTTCC-AAAAATACCATTTTACCCCTAAACTTCCAAAAATC-CCATTTTTAC
*
817 CTCGAACCTTCCAAAAATTACCAT
64 CCCGAACCTTCCAAAAATTACCAT
* *
841 TTTGACCCCGAAACATCCAAAAAT
1 TTTGACCCCCAAACTTCCAAAAAT
865 TACTATCTTA
Statistics
Matches: 235, Mismatches: 34, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
85 1 0.00
86 3 0.01
87 42 0.18
88 131 0.56
89 54 0.23
90 3 0.01
91 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.28
Consensus pattern (87 bp):
TTTGACCCCCAAACTTCCAAAAATACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTACCC
CGAACCTTCCAAAAATTACCAT
Done.