Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010527.1 Kokia drynarioides strain JFW-HI SEQ_125443, 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: 2914
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:730 original size:30 final size:29
Alignment explanation
Indices: 694--939 Score: 264
Period size: 29 Copynumber: 8.3 Consensus size: 29
684 TTCAGCCTCG
694 AACTTCCAAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTTGACC-CAA
* *
724 AACTTCCAAAAAACCCATTTTT-ACCCTCA
1 AACTTCCAAAAATCCCATTTTTGACCC-AA
*
753 AACTTTCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATCCCATTTTTGACCC-AA
*
783 AACTTCC-AAAATCCCATTTTTAACCCAAA
1 AACTTCCAAAAATCCCATTTTTGACCC-AA
* *
812 AACATCCAAAAATCCCATTTTTGACCCTA
1 AACTTCCAAAAATCCCATTTTTGACCCAA
* * **
841 AACTTCCAAAGATTCCATTTTTGACCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCAA
* * **
870 ACCTTCAAAAAATATCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTTGA-CCCAA
* *
900 AACTTCCAAAAATTCCATTTTT-ACCCTCGA
1 AACTTCCAAAAATCCCATTTTTGA-CC-CAA
930 AACTTCCAAA
1 AACTTCCAAA
940 TTCATTTTTT
Statistics
Matches: 183, Mismatches: 28, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 98 0.54
30 84 0.46
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTGACCCAA
Found at i:763 original size:59 final size:59
Alignment explanation
Indices: 689--939 Score: 294
Period size: 59 Copynumber: 4.3 Consensus size: 59
679 CTATTTTCAG
* *
689 CCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAAACCCATTTTT-AC
1 CCTCAAACTTCCAAAAATCCCATTTTTGACC-CAAAACTTCCAAAAATCCCATTTTTAAC
*
748 CCTCAAACTTTCAAAAATCCCATTTTTGACCCTAAAACTTCC-AAAATCCCATTTTTAAC
1 CCTCAAACTTCCAAAAATCCCATTTTTGACCC-AAAACTTCCAAAAATCCCATTTTTAAC
** * * * * *
807 CCAAAAACATCCAAAAATCCCATTTTTGACCCTAAACTTCCAAAGATTCCATTTTTGAC
1 CCTCAAACTTCCAAAAATCCCATTTTTGACCCAAAACTTCCAAAAATCCCATTTTTAAC
* * * ** *
866 CC-CGACCTTCAAAAAATATCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-AC
1 CCTCAAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCAAAAATCCCATTTTTAAC
924 CCTCGAAACTTCCAAA
1 CCTC-AAACTTCCAAA
940 TTCATTTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
58 45 0.28
59 110 0.67
60 8 0.05
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (59 bp):
CCTCAAACTTCCAAAAATCCCATTTTTGACCCAAAACTTCCAAAAATCCCATTTTTAAC
Found at i:962 original size:59 final size:58
Alignment explanation
Indices: 659--1037 Score: 273
Period size: 59 Copynumber: 6.5 Consensus size: 58
649 CCCTGGAGGT
* * * *
659 CCCTAAAA-TGTCCCAAAATTCTATTTTCAGCCTCG-AACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTA-CCCCGAAACTT-CAAAAATCCCATTTTTGA
**
718 -CCTCAAAACTTCCAAAAAACCCATTTTTACCCTC-AAACTTTCAAAAATCCCATTTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCC-CGAAAC-TTCAAAAATCCCATTTTTGA
* ** *
777 CCCTAAAACTTCC-AAAATCCCATTTTTAACCCAAAAACATCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTT-ACCCCGAAAC-TTCAAAAATCCCATTTTTGA
* * **
836 CCCT-AAACTTCCAAAGATTCCATTTTTGACCCCG-ACCTTCAAAAAATATCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTC-AAAAATCCCATTTTTGA
* * * *
894 CCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAAACTTC-CAAAT-TCATTTTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCC-CGAAACTTCAAAAATCCCA-TTTTTGA
* * * * *
952 CCCTTGAAAC-TCTC-AAAATTACCCTTTTTACCCC-AAA-GT-AAAAATTCCATTTTTAAA
1 CCC-TAAAACTTC-CAAAAATT-CCATTTTTACCCCGAAACTTCAAAAATCCCATTTTT-GA
* * *
1009 CCTTAAAATTTCCCAAAATTACCATTTTT
1 CCCTAAAACTTCCAAAAATT-CCATTTTT
1038 GCCTCGAGAA
Statistics
Matches: 263, Mismatches: 35, Indels: 46
0.76 0.10 0.13
Matches are distributed among these distances:
56 15 0.06
57 29 0.11
58 72 0.27
59 136 0.52
60 11 0.04
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCAAAAATCCCATTTTTGA
Found at i:980 original size:30 final size:28
Alignment explanation
Indices: 672--1071 Score: 143
Period size: 29 Copynumber: 13.8 Consensus size: 28
662 TAAAATGTCC
* * *
672 CAAAATTCTATTTTCAGCCTCG-AACTT
1 CAAAATTCCATTTTTACCCTCGAAACTT
* *
699 CCAAAAATCCCATTTTTGA-CCTCAAAACTT
1 -C-AAAATTCCATTTTT-ACCCTCGAAACTT
**
729 CCAAAAAACCCATTTTTACCCTC-AAACTTT
1 -C-AAAATTCCATTTTTACCCTCGAAAC-TT
* *
759 CAAAAATCCCATTTTTGACCCT-AAAACTT
1 C-AAAATTCCATTTTT-ACCCTCGAAACTT
* ** *
788 CCAAAATCCCATTTTTAACCC-AAAAACATC
1 -CAAAATTCCATTTTT-ACCCTCGAAAC-TT
*
818 CAAAAATCCCATTTTTGACCCT--AAACTT
1 C-AAAATTCCATTTTT-ACCCTCGAAACTT
*
846 CCAAAGATTCCATTTTTGACCC-CG-ACCTT
1 -CAAA-ATTCCATTTTT-ACCCTCGAAACTT
*
875 CAAAAAATAT-CATTTTTGACCC-CAAAACTT
1 C--AAAAT-TCCATTTTT-ACCCTCGAAACTT
905 CCAAAAATTCCATTTTTACCCTCGAAACTT
1 -C-AAAATTCCATTTTTACCCTCGAAACTT
* *
935 CCAAATT-CATTTTTTTACCCTTGAAACTCT
1 CAAAATTCCA--TTTTTACCCTCGAAACT-T
* *
965 CAAAATTACCCTTTTTACCC-C-AAA-GT
1 CAAAATT-CCATTTTTACCCTCGAAACTT
* * ** *
991 AAAAATTCCATTTTTAAACCTTAAAATTT
1 CAAAATTCCATTTTT-ACCCTCGAAACTT
* *
1020 CCCAAAATTACCATTTTT-GCCTCGAGAA-TC
1 --CAAAATT-CCATTTTTACCCTCGA-AACTT
1050 CAAAATTACCA-TTTTACCCTCG
1 CAAAATT-CCATTTTTACCCTCG
1072 GGTACTCGAA
Statistics
Matches: 303, Mismatches: 32, Indels: 74
0.74 0.08 0.18
Matches are distributed among these distances:
25 7 0.02
26 10 0.03
27 6 0.02
28 33 0.11
29 123 0.41
30 106 0.35
31 9 0.03
32 9 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
CAAAATTCCATTTTTACCCTCGAAACTT
Done.