Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009231.1 Kokia drynarioides strain JFW-HI SEQ_123936, 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, 776
Length: 1294
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Found at i:527 original size:30 final size:30
Alignment explanation
Indices: 458--837 Score: 308
Period size: 29 Copynumber: 12.9 Consensus size: 30
448 CACTGGAGGT
*
458 CCCT-AAACCTTCCAAAAATTTCA-TTTTTA
1 CCCTGAAA-CTTCCAAAAATTCCATTTTTTA
** *
487 TCTTTG-AACTTCCAAAAATCCCATTTTTTA
1 -CCCTGAAACTTCCAAAAATTCCATTTTTTA
* *
517 CCCTGAAACTTCCAAAAATTCTATTTTTTT
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
* *
547 CCCCG-AACTTCCAAAAATTCCATTTTTAA
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
** * * *
576 CCCCAAAACTTCCACAAATCCCA-TTTTGA
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
* *
605 -CCTCAAAACTTCCAAAAA-TCTCATTTTTAA
1 CCCT-GAAACTTCCAAAAATTC-CATTTTTTA
* *
635 CCCTAAAACTTCCAAAAATTCTA-TTTTTA
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
* * *
664 CCCTCG-AACTTCTAAAAATCCCATTTTTGA
1 CCCT-GAAACTTCCAAAAATTCCATTTTTTA
*
694 CCCTGAAACTTTCAAAAATTCCA-TTTTTA
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
* *
723 CTCCCG-AACTTCCAAAAA-TCTCA-TTTTGA
1 C-CCTGAAACTTCCAAAAATTC-CATTTTTTA
*
752 CCCTAAAACTT-CAAAAATTCCA-TTTTTA
1 CCCTGAAACTTCCAAAAATTCCATTTTTTA
* *
780 CCTTCG-AACTTCCAAAAATGT-CATTTTTGA
1 CCCT-GAAACTTCCAAAAAT-TCCATTTTTTA
*
810 CCCCCGAAACTTCCAAAAATTCCATTTT
1 -CCCTGAAACTTCCAAAAATTCCATTTT
838 GCCCTCGAAC
Statistics
Matches: 284, Mismatches: 43, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
28 28 0.10
29 126 0.44
30 104 0.37
31 26 0.09
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTGAAACTTCCAAAAATTCCATTTTTTA
Found at i:558 original size:59 final size:58
Alignment explanation
Indices: 458--855 Score: 433
Period size: 59 Copynumber: 6.8 Consensus size: 58
448 CACTGGAGGT
* * *** *
458 CCCTAAACCTTCCAAAAATTTCATTTTTATCTTTGAACTTCCAAAAATCCCATTTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
517 CCCTGAAACTTCCAAAAATTCTATTTTTTTCCCCGAACTTCCAAAAATTCCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCA-TTTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * ** * *
576 CCCCAAAACTTCCACAAATCCCATTTTGACCTCAAAACTTCCAAAAATCTCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATCCCATTTTTGA
* *
635 CCCTAAAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTGA
* * *
694 CCCTGAAACTTTCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAATCTCA-TTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGA
* **
752 CCCTAAAACTT-CAAAAATTCCATTTTTACCTTCGAACTTCCAAAAATGTCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATCCCATTTTTGA
** *
810 CCCCCGAAACTTCCAAAAATTCCA-TTTTGCCCTCGAACTTCCAAAA
1 -CCCTAAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAA
856 TCTTCATATT
Statistics
Matches: 287, Mismatches: 43, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
56 1 0.00
57 36 0.13
58 29 0.10
59 203 0.71
60 18 0.06
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:884 original size:88 final size:85
Alignment explanation
Indices: 466--924 Score: 376
Period size: 88 Copynumber: 5.2 Consensus size: 85
456 GTCCCTAAAC
* * * ** * *
466 CTTCCAAAAATTTCATTTTTATCTTTGAACTTCCAAAAATCCCATTTTTTACCCTGAAACTTCCA
1 CTTCCAAAAATTCCATTTTTACCCTCAAACTT-CAAAAATCCCA-TTTTGACCCTCAAACTTCCA
**
531 AAAATTCTATTTTTTTCCCCGAA
64 AAAATTC-ATTTTTACCCCCGAA
*
554 CTTCCAAAAATTCCATTTTTAACCC-CAAAACTTCCACAAATCCCATTTTGA-CCTCAAAACTTC
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAACTT-CAAAAATCCCATTTTGACCCTC-AAACTTC
***
617 CAAAAATCTCATTTTTAACCCTAAAA
62 CAAAAAT-TCATTTTT-ACCCCCGAA
* * * *
643 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCTGAAACTTTCA
1 CTTCCAAAAATTCCATTTTTACCCTCAAACTTC-AAAAATCCCA-TTTTGACCCTCAAACTTCCA
*
708 AAAATTCCATTTTTACTCCCGAA
64 AAAATT-CATTTTTACCCCCGAA
* * * * * *
731 CTTCCAAAAA-TCTCATTTTGACCCTAAAACTTCAAAAATTCCATTTTTACCTTCGAACTTCCAA
1 CTTCCAAAAATTC-CATTTTTACCCTCAAACTTCAAAAATCCCATTTTGACCCTCAAACTTCCAA
795 AAATGTCATTTTTGACCCCCGAAA
65 AAAT-TCATTTTT-ACCCCCG-AA
* * * * * *
819 CTTCCAAAAATTCCA-TTTTGCCCTCGAACTTCCAAAATCTTCATATTCGA-CTTCAAAC-TCTC
1 CTTCCAAAAATTCCATTTTTACCCTCAAACTTCAAAAATC-CCAT-TTTGACCCTCAAACTTC-C
**
881 -AAAATTACCCTTTTACCCCCGAA
63 AAAAATT-CATTTTTACCCCCGAA
*
904 -TGTCTAAAAATTCCATTTTTA
1 CT-TCCAAAAATTCCATTTTTA
925 AACCCCAAAA
Statistics
Matches: 303, Mismatches: 47, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
84 1 0.00
85 14 0.05
86 39 0.13
87 52 0.17
88 119 0.39
89 75 0.25
90 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (85 bp):
CTTCCAAAAATTCCATTTTTACCCTCAAACTTCAAAAATCCCATTTTGACCCTCAAACTTCCAAA
AATTCATTTTTACCCCCGAA
Found at i:913 original size:116 final size:115
Alignment explanation
Indices: 466--923 Score: 387
Period size: 118 Copynumber: 3.9 Consensus size: 115
456 GTCCCTAAAC
* ** * ** *
466 CTTCCAAAAATTTCATTTTTA-TCTTTGAACTTCCAAAAATCCCATTTTTTACCCTGAAACTTCC
1 CTTCCAAAAATTCCATTTTTACTC-CCGAACTTCCAAAAATCTCA-TTTCGACCCTAAAACTT-C
* * * * * *
530 AAAAATTCTATTTTTTTCCC-CGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
63 AAAAATTCCA-CTTTTACCCTCGAACTTCTAAAAATT-CATTTTTGACCCCGAAA
* * * ** **
584 CTTCCACAAATCCCATTTTGAC-CTCAAAACTTCCAAAAATCTCATTTTTAACCCTAAAACTTCC
1 CTTCCAAAAATTCCATTTTTACTC-CCGAACTTCCAAAAATCTCA-TTTCGACCCTAAAACTT-C
* * * *
648 AAAAATTCTATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCTGAAA
63 AAAAATTCCACTTTTACCCTCGAACTTCTAAAAAT-TCATTTTTGACCCCGAAA
* *
702 CTTTCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAATCTCATTTTGACCCTAAAACTTCAAA
1 CTTCCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAATCTCATTTCGACCCTAAAACTTCAAA
* * *
767 AATTCCATTTTTACCTTCGAACTTCCAAAAATGTCATTTTTGACCCCCGAAA
66 AATTCCACTTTTACCCTCGAACTTCTAAAAAT-TCATTTTTGA-CCCCGAAA
* * *
819 CTTCCAAAAATTCCA-TTTTGC-CCTCGAACTTCC-AAAATCTTCATATTCGA-CTTCAAACTCT
1 CTTCCAAAAATTCCATTTTTACTCC-CGAACTTCCAAAAATC-TCAT-TTCGACCCTAAAACT-T
*
880 C-AAAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTT
62 CAAAAATT-CCACTTTTACCCTCGAACT-TCTAAAAATT-CATTTTT
924 AAACCCCAAA
Statistics
Matches: 290, Mismatches: 38, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
115 10 0.03
116 99 0.34
117 53 0.18
118 127 0.44
119 1 0.00
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (115 bp):
CTTCCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAATCTCATTTCGACCCTAAAACTTCAAA
AATTCCACTTTTACCCTCGAACTTCTAAAAATTCATTTTTGACCCCGAAA
Done.