Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004674.1 Kokia drynarioides strain JFW-HI SEQ_118224, 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: 1738
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:350 original size:29 final size:29
Alignment explanation
Indices: 301--856 Score: 412
Period size: 29 Copynumber: 18.9 Consensus size: 29
291 GGAAGTCCCT
301 AAACTTCCAAAAAT-TCTATTTTTACCCCC
1 AAACTTCCAAAAATCTC-ATTTTTACCCCC
* * *
330 GAACTTTCAAAAATCTCATTTTTAACCCCA
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
* **
360 AAACTTCCAAAAATTTTNTTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* * *
389 GAACTTCCAAAAATTTCATTTTTACACCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* ** * **
418 GAACTTCTGAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
*
448 AAACTTCCAAAAAATC-CATTTTTACCCTC
1 AAACTTCC-AAAAATCTCATTTTTACCCCC
* * *
477 GAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
507 AAACTTCCAAAAAT-TCTATTTTTA-CCCC
1 AAACTTCCAAAAATCTC-ATTTTTACCCCC
* * * ***
535 GAACTTTCAAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
565 AAACTTCCAAAAAATC-CATTTTTACCCCC
1 AAACTTCC-AAAAATCTCATTTTTACCCCC
* * **
594 GAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
* * * *
624 AAACTTCTAAAAATTTCATTTTTAACCTC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
** * **
653 AAACTTCTGAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
* *
683 AAACTTCCAAAAAT-TCTATTTTTTCCCTC
1 AAACTTCCAAAAATCTC-ATTTTTACCCCC
* *
712 AAACTTCCAAAAAT-TCCATTTTTAACCTCA
1 AAACTTCCAAAAATCT-CATTTTT-ACCCCC
* **
742 AAACTTTCAAAAAT-TCTATTTTTACCTTC
1 AAACTTCCAAAAATCTC-ATTTTTACCCCC
* * *
771 GAACTTCCAAAAA-CACCATTTTTTACCCCG
1 AAACTTCCAAAAATC-TCA-TTTTTACCCCC
* * * *
801 AAACTTCCAGTAACA-CCCTTTTTTACCCCA
1 AAACTTCCA--AAAATCTCATTTTTACCCCC
831 AAACTTCCAAAAATCTCATTTTTACC
1 AAACTTCCAAAAATCTCATTTTTACC
857 ACGAATTTTC
Statistics
Matches: 423, Mismatches: 80, Indels: 48
0.77 0.15 0.09
Matches are distributed among these distances:
28 38 0.09
29 184 0.43
30 182 0.43
31 15 0.04
32 4 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATCTCATTTTTACCCCC
Found at i:393 original size:59 final size:60
Alignment explanation
Indices: 301--856 Score: 266
Period size: 59 Copynumber: 9.4 Consensus size: 60
291 GGAAGTCCCT
*
301 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATCTCATTTTTA-ACCCCA
1 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTACACCCCA
* * *
360 AAACTTCCAAAAATTTTNTTTTTACCCCCGAACTTCCAAAAATTTCATTTTTACA-CCC-
1 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTACACCCCA
* ** * * *** *
418 GAACTTCTGAAAATCCCATTTTTAACCCTAAAACTTCCAAAAAATC-CATTTTTAC-CCTC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCGAACTTCC-AAAAATCTCATTTTTACACCCCA
* * * **
477 GAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAAT-TCTATTTTT--ACCCC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCGAACTTCCAAAAATCTC-ATTTTTACACCCCA
* * * * **
535 GAACTTTCAAAAATCCCATTTTTGA-CCTTGAAACTTCCAAAAAATC-CATTTTTAC-CCCC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCG-AACTTCC-AAAAATCTCATTTTTACACCCCA
* * * *** * * *
594 GAACTTCCAAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTTCATTTTTA-ACCTC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCGAACTTCCAAAAATCTCATTTTTACACCCCA
** * * *** * *
653 AAACTTCTGAAAATCCCATTTTTAACCCTAAAACTTCCAAAAAT-TCTATTTTTTC-CCTC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCGAACTTCCAAAAATCTC-ATTTTTACACCCCA
* * ** * **
712 AAACTTCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAAT-TCTATTTTTAC-CTTC-
1 AAACTTCCAAAAATTCTATTTTT-ACCCCCGAACTTCCAAAAATCTC-ATTTTTACACCCCA
* ** * * * *
771 GAACTTCCAAAAACACCATTTTTTA-CCCCGAAACTTCCAGTAACA-C-CCTTTTT-TACCCCA
1 AAACTTCCAAAAATTCTA-TTTTTACCCCCG-AACTTCCA--AAAATCTCATTTTTACACCCCA
831 AAACTTCCAAAAA-TCTCATTTTTACC
1 AAACTTCCAAAAATTCT-ATTTTTACC
857 ACGAATTTTC
Statistics
Matches: 411, Mismatches: 60, Indels: 51
0.79 0.11 0.10
Matches are distributed among these distances:
57 2 0.00
58 72 0.18
59 304 0.74
60 30 0.07
61 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTACACCCCA
Found at i:657 original size:88 final size:88
Alignment explanation
Indices: 301--856 Score: 487
Period size: 88 Copynumber: 6.3 Consensus size: 88
291 GGAAGTCCCT
* * * * *
301 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATCTCATTTTTAACCCCAAAACTT
1 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTT
*** * *
366 CCAAAAATTTTNTTTTTACCCCC
66 CCAAAAATTCCATTTTTAACCTC
* * * * **
389 GAACTTCCAAAAATTTCATTTTTACACCCGAACTTCTGAAAATCCCATTTTTAACCCTAAAACTT
1 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTT
* *
454 CCAAAAAATCCATTTTTACCCTC
66 CCAAAAATTCCATTTTTAACCTC
* ** * * **
477 GAACTTCC-AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTT-ACCC-CGAAC
1 AAACTTCCAAAAAAT-CCATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAAC
* * * *
539 TTTCAAAAATCCCATTTTTGACCTTG
64 TTCCAAAAATTCCATTTTTAACC-TC
565 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTT
1 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTT
* *
630 CTAAAAATTTCATTTTTAACCTC
66 CCAAAAATTCCATTTTTAACCTC
** *** * * * *
653 AAACTT-CTGAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCTATTTTT-TCCCTCAAAC
1 AAACTTCCAAAAAAT-CCATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAAC
716 TTCCAAAAATTCCATTTTTAACCTC
64 TTCCAAAAATTCCATTTTTAACCTC
* * * ** * **
741 AAAACTTTCAAAAATTCTATTTTTACCTTCGAACTTCCAAAAA-CACCATTTTTTACCCCGAAAC
1 -AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATC-CCATTTTTAACCCTAAAAC
** ** * * *
805 TTCCAGTAACACCCTTTTTTACCCC
64 TTCCAAAAATTCCATTTTTAACCTC
830 AAAACTTCC-AAAAATCTCATTTTTACC
1 -AAACTTCCAAAAAATC-CATTTTTACC
857 ACGAATTTTC
Statistics
Matches: 378, Mismatches: 77, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
87 57 0.15
88 188 0.50
89 128 0.34
90 5 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (88 bp):
AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTT
CCAAAAATTCCATTTTTAACCTC
Done.