Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010434.1 Kokia drynarioides strain JFW-HI SEQ_125324, 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: 3278
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.36
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:78 original size:29 final size:29
Alignment explanation
Indices: 43--208 Score: 178
Period size: 29 Copynumber: 5.7 Consensus size: 29
33 TCCCTAAACT
43 TTCCAAAAATTCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* *
72 TTTCAAAAA-TCCATTTTTTAACCC-CAAAAC
1 TTCCAAAAATTCCA-TTTTT-ACCCTC-GAAC
*
102 TTCCAAAAATTCCTTTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* *
131 TTCCAAAAA-TCTAATTTTTAACCTCGAAAC
1 TTCCAAAAATTC-CATTTTTACCCTCG-AAC
* * *
161 TTCCAAAAATTCTATTTTTTCCCTTGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
*
190 TTCC-AAAATCCCATTTTTA
1 TTCCAAAAATTCCATTTTTA
209 ACCCGAGACT
Statistics
Matches: 114, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
28 18 0.16
29 48 0.42
30 43 0.38
31 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAC
Found at i:131 original size:59 final size:58
Alignment explanation
Indices: 38--212 Score: 219
Period size: 59 Copynumber: 3.0 Consensus size: 58
28 GGAGATCCCT
*
38 AAACTTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCATTTTTTAACCCCA
1 AAAC-TTCCAAAAATTCCTTTTTTACCCTCGAACTTTCAAAAATCCA-TTTTTAACCCCA
* * * *
98 AAACTTCCAAAAATTCCTTTTTTACCCTCGAACTTCCAAAAATCTAATTTTTAACCTCG
1 AAACTTCCAAAAATTCCTTTTTTACCCTCGAACTTTCAAAAATC-CATTTTTAACCCCA
* * *
157 AAACTTCCAAAAATT-CTATTTTTTCCCTTGAAC-TTCCAAAATCCCATTTTTAACCC
1 AAACTTCCAAAAATTCCT-TTTTTACCCTCGAACTTTCAAAAAT-CCATTTTTAACCC
213 GAGACTTNNN
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
58 19 0.19
59 77 0.76
60 5 0.05
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCTTTTTTACCCTCGAACTTTCAAAAATCCATTTTTAACCCCA
Found at i:453 original size:59 final size:57
Alignment explanation
Indices: 368--709 Score: 334
Period size: 59 Copynumber: 5.8 Consensus size: 57
358 CTAAACTTTT
* *
368 CAAAAATTCCGTTTTTACCCTCGAACTTTCAAAAATCCAATTTTTAACCCCAAAACTTC
1 CAAAAATTCCTTTTTTACCCTCGAACTTCCAAAAATCC-ATTTTTAACCCC-AAACTTC
*
427 CAAAAATTCCTTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCTCGAAACTTC
1 CAAAAATTCCTTTTTTACCCTCGAACTTCCAAAAATC-CATTTTTAACC-CCAAACTTC
* * * *
486 CAAAAATT-CTATTTTTTCCCCCGAACTTCC-AAAATCCCATTTTTAACCCGAGACTTC
1 CAAAAATTCCT-TTTTTACCCTCGAACTTCCAAAAAT-CCATTTTTAACCCCAAACTTC
* * *
543 CGAAAATTCCATTTTTATCCC-CGAACTTCCAAAAATCTCATTTTTAACCCTCAAACTTT
1 CAAAAATTCCTTTTTTA-CCCTCGAACTTCCAAAAATC-CATTTTTAACCC-CAAACTTC
* * * *
602 TAAAAATCCCATTTTTAACCC-CAAAACTTCCAAAAATCCCATTTTT-ACCCTCAAACTTC
1 CAAAAATTCC-TTTTTTACCCTC-GAACTTCCAAAAAT-CCATTTTTAACCC-CAAACTTC
* * ** *
661 CAAAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCCATTTTTAA
1 C-AAAAATTCC-TTTTTTACCCTCGAACTTCCAAAAA-TCCATTTTTAA
710 ACCCTAAATT
Statistics
Matches: 245, Mismatches: 22, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
57 30 0.12
58 39 0.16
59 106 0.43
60 67 0.27
61 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (57 bp):
CAAAAATTCCTTTTTTACCCTCGAACTTCCAAAAATCCATTTTTAACCCCAAACTTC
Found at i:709 original size:30 final size:30
Alignment explanation
Indices: 368--736 Score: 334
Period size: 30 Copynumber: 12.4 Consensus size: 30
358 CTAAACTTTT
* * *
368 CAAAAATTCCGTTTTT-ACCCTCGAACTTT
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
397 CAAAAA-TCCAATTTTTAACCC-CAAAACTTC
1 CAAAAATTCC-ATTTTTAACCCTC-AAACTTC
* *
427 CAAAAATTCC-TTTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
456 CAAAAA-TCTCATTTTTAA-CCTCGAAACTTC
1 CAAAAATTC-CATTTTTAACCCTC-AAACTTC
* * * *
486 CAAAAATTCTATTTTT-TCCCCCGAACTTC
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
* * *
515 C-AAAATCCCATTTTTAACCC-GAGACTTC
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
* * *
543 CGAAAATTCCATTTTTATCCC-CGAACTTC
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
*
572 CAAAAA-TCTCATTTTTAACCCTCAAACTTT
1 CAAAAATTC-CATTTTTAACCCTCAAACTTC
* *
602 TAAAAATCCCATTTTTAACCC-CAAAACTTC
1 CAAAAATTCCATTTTTAACCCTC-AAACTTC
*
632 CAAAAATCCCATTTTT-ACCCTCAAACTTC
1 CAAAAATTCCATTTTTAACCCTCAAACTTC
* *
661 CAAAAAATCCCATTTTTAACCCTAAAACTTC
1 C-AAAAATTCCATTTTTAACCCTCAAACTTC
* *
692 TAAAAATTCCATTTTTAAACCCT-AAATTTTC
1 CAAAAATTCCATTTTT-AACCCTCAAA-CTTC
*
723 CCAAAATTACCATT
1 CAAAAATT-CCATT
737 CTACCTCGGG
Statistics
Matches: 282, Mismatches: 36, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
28 25 0.09
29 99 0.35
30 120 0.43
31 33 0.12
32 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (30 bp):
CAAAAATTCCATTTTTAACCCTCAAACTTC
Done.