Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005452.1 Kokia drynarioides strain JFW-HI SEQ_119494, 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: 4522
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Found at i:523 original size:58 final size:59
Alignment explanation
Indices: 359--1018 Score: 935
Period size: 59 Copynumber: 11.3 Consensus size: 59
349 CTTTCCGAAG
* *
359 ATTACCATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACACCGAACCTTCTAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* *
418 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAACCCGAACCTTCTAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
*
477 ATTACCATTTT-CCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* * *
535 TTTACCATTTTACCCCCTAACTTCCAAAAATTCCATTTTTGA--CC---CCTTCTAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
** *
589 ATTACCATTTTACCCCTAAACTTCAAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* *
648 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCACGAACCTTCT-AAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
** *
706 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACATCGAACCTTCCAAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT-CTAAAA
* * * *
766 ATTACCATTTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCACGAACCTTCT-AAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* *
824 ATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACCTTCCAAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT-CTAAAA
* * *
884 ATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAACCTT-TCAGAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAA
** * *
943 ATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTC-CAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* * *
1001 ACTATCATTTTGCCCCCG
1 ATTACCATTTTACCCCCG
1019 TGCATCCGAA
Statistics
Matches: 535, Mismatches: 54, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
54 47 0.09
56 2 0.00
57 2 0.00
58 173 0.32
59 207 0.39
60 104 0.19
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
Found at i:1011 original size:29 final size:29
Alignment explanation
Indices: 359--1018 Score: 426
Period size: 29 Copynumber: 22.6 Consensus size: 29
349 CTTTCCGAAG
359 ATTACCATTTT-ACCTCCGAA-CTTCCAAA
1 ATTACCATTTTGACC-CCGAACCTTCCAAA
* * * *
387 AATCCCATTTTTGACACCGAACCTTCTAAAA
1 ATTACCA-TTTTGACCCCGAACCTTC-CAAA
418 ATTACCATTTT-ACCCTCGAA-CTTCCAAA
1 ATTACCATTTTGACCC-CGAACCTTCCAAA
* * * *
446 AATCCCATTTTTGAACCCGAACCTTCTAAAA
1 ATTACCA-TTTTGACCCCGAACCTTC-CAAA
*
477 ATTACCATTTT-CCCCCGAA-CTTCCAAA
1 ATTACCATTTTGACCCCGAACCTTCCAAA
* * * *
504 AATCCCATTTTTAACCCCGAACCTTCTAAA
1 ATTACCA-TTTTGACCCCGAACCTTCCAAA
*
534 ATTTACCATTTT-ACCCCCTAA-CTTCCAAAA
1 A-TTACCATTTTGA-CCCCGAACCTTCC-AAA
*
564 ATT-CCATTTTTGA--CC---CCTTCTAAAA
1 ATTACCA-TTTTGACCCCGAACCTTC-CAAA
* * *
589 ATTACCATTTT-ACCCCTAAACTTCAAAA
1 ATTACCATTTTGACCCCGAACCTTCCAAA
* * *
617 AATCCCATTTTTGACCCCGAACCTTCTAAAA
1 ATTACCA-TTTTGACCCCGAACCTTC-CAAA
648 ATTACCATTTT-ACCCTCGAA-CTTCCAAA
1 ATTACCATTTTGACCC-CGAACCTTCCAAA
* * * *
676 AATCCCATTTTTGACCACGAACCTTCTAAA
1 ATTACCA-TTTTGACCCCGAACCTTCCAAA
706 ATTACCATTTT-ACCCCCGAA-CTTCCAAA
1 ATTACCATTTTGA-CCCCGAACCTTCCAAA
* * **
734 AATCCCATTTTTGACATCGAACCTTCCAAAAA
1 ATTACCA-TTTTGACCCCGAACCTTCC--AAA
766 ATTACCATTTT-ACCCTCGAACC-TCCAAAA
1 ATTACCATTTTGACCC-CGAACCTTCC-AAA
* *
795 ATT-CCATTTTTGACCACGAACCTTCTAAA
1 ATTACCA-TTTTGACCCCGAACCTTCCAAA
824 ATTACCATTTT-ACCCCCGAA-CTTCCAAA
1 ATTACCATTTTGA-CCCCGAACCTTCCAAA
*
852 AAT-CCTATTTTTGACCCCGAACCTTCCAAAAA
1 ATTACC-A-TTTTGACCCCGAACCTTCC--AAA
884 ATTACCATTTT-ACCCCCGAA-CTTCCAAA
1 ATTACCATTTTGA-CCCCGAACCTTCCAAA
* * *
912 AAT-CTCATTTTTAACCCCGAACCTTTCAGAA
1 ATTAC-CA-TTTTGACCCCGAACCTTCCA-AA
*
943 ATTACCATTTT-ACCCTTGAA-CTTCCAAA
1 ATTACCATTTTGACCC-CGAACCTTCCAAA
* * *
971 AATCCCATTTTTGACTCCGAACCTTCCAAA
1 ATTACCA-TTTTGACCCCGAACCTTCCAAA
* * *
1001 ACTATCATTTTGCCCCCG
1 ATTACCATTTTGACCCCG
1019 TGCATCCGAA
Statistics
Matches: 500, Mismatches: 70, Indels: 123
0.72 0.10 0.18
Matches are distributed among these distances:
24 1 0.00
25 14 0.03
26 5 0.01
27 13 0.03
28 82 0.16
29 171 0.34
30 141 0.28
31 56 0.11
32 15 0.03
33 2 0.00
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.31
Consensus pattern (29 bp):
ATTACCATTTTGACCCCGAACCTTCCAAA
Done.