Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009935.1 Kokia drynarioides strain JFW-HI SEQ_124676, 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, 601
Length: 1002
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.38
Found at i:491 original size:30 final size:30
Alignment explanation
Indices: 450--713 Score: 271
Period size: 29 Copynumber: 8.9 Consensus size: 30
440 GACGTCCTTG
*
450 AACTGTCCAAAAATTCTATTTTTTACACCC-A
1 AACT-TCCAAAAATTCCATTTTTTAC-CCCAA
*
481 AACTTCCAAAAA-TCTCATTTTTGACCCCAA
1 AACTTCCAAAAATTC-CATTTTTTACCCCAA
* *
511 AACTTCCAAAAATTCCA-ATTTTACCCTC-G
1 AACTTCCAAAAATTCCATTTTTTACCC-CAA
*
540 AACTTCCAAAAATCCCA-TTTTTACCCCAA
1 AACTTCCAAAAATTCCATTTTTTACCCCAA
569 AACTTCCAAAAATT-CAGTTTTTTGACCCCAA
1 AACTTCCAAAAATTCCA-TTTTTT-ACCCCAA
* *
600 AACTTCCAAAAATTCCA-TTTATACCCTC-G
1 AACTTCCAAAAATTCCATTTTTTACCC-CAA
* *
629 AACTTCCAAAAATTCCA-ATTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTTACCCCAA
* * *
658 AACTTCAAAAAATGCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTTACCCCAA
688 AACTTTCC-AAAATTCCA-TTTTTACCC
1 AAC-TTCCAAAAATTCCATTTTTTACCC
714 TTGAACCTCC
Statistics
Matches: 198, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.02
29 100 0.51
30 62 0.31
31 30 0.15
32 2 0.01
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTTACCCCAA
Found at i:663 original size:118 final size:119
Alignment explanation
Indices: 450--709 Score: 345
Period size: 118 Copynumber: 2.2 Consensus size: 119
440 GACGTCCTTG
*
450 AACTGTCCAAAAATTCTATTTTTTACACCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
1 AACT-TCCAAAAATTCTATTTTTTACACCCAAACTTCCAAAAATCTCATTTATGACCCCAAAACT
* * *
515 TCCAAAAATTCCAATTTTACCCTCGAACTTCCAAAAATCCCATTTTT-ACCCCAA
65 TCCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAATCCCATTTTTGACCCCAA
*
569 AACTTCCAAAAATTC-AGTTTTTTGAC-CCCAAAACTTCCAAAAAT-TCCATTTAT-ACCCTC-G
1 AACTTCCAAAAATTCTA-TTTTTT-ACACCC-AAACTTCCAAAAATCT-CATTTATGACCC-CAA
*
629 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAATGCCATTTTTGACCCCAA
61 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAATCCCATTTTTGACCCCAA
*
688 AACTTTCC-AAAATTCCATTTTT
1 AAC-TTCCAAAAATTCTATTTTT
710 ACCCTTGAAC
Statistics
Matches: 127, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
117 1 0.01
118 72 0.57
119 49 0.39
120 5 0.04
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (119 bp):
AACTTCCAAAAATTCTATTTTTTACACCCAAACTTCCAAAAATCTCATTTATGACCCCAAAACTT
CCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAATCCCATTTTTGACCCCAA
Found at i:725 original size:88 final size:87
Alignment explanation
Indices: 449--737 Score: 393
Period size: 89 Copynumber: 3.3 Consensus size: 87
439 GGACGTCCTT
* *
449 GAACTGTCCAAAAATTCTATTTTTTACACCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAAC
1 GAACT-TCCAAAAATTCCA-TTTTTACCCCCAAACTTCCAAAAATC-CATTTTTGACCCCAAAAC
*
514 TTCCAAAAATTCCAATTTTACCCTC
63 TTCCAAAAATTCCATTTTTACCCTC
* * *
539 GAACTTCCAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATTCAGTTTTTTGACCCCAAAACT
1 GAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCA--TTTTTGACCCCAAAACT
*
604 TCCAAAAATTCCATTTATACCCTC
64 TCCAAAAATTCCATTTTTACCCTC
* *
628 GAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAATGCCATTTTTGACCCCAAAACTT
1 GAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCCCAAAAC-T
*
693 TCC-AAAATTCCATTTTTACCCTT
64 TCCAAAAATTCCATTTTTACCCTC
*
716 GAACCTCC-AAAATCTCCATTTT
1 GAACTTCCAAAAAT-TCCATTTT
738 CGACCTCGAA
Statistics
Matches: 178, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
87 7 0.04
88 71 0.40
89 93 0.52
90 7 0.04
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.31
Consensus pattern (87 bp):
GAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCCCAAAACTTC
CAAAAATTCCATTTTTACCCTC
Found at i:750 original size:59 final size:59
Alignment explanation
Indices: 450--772 Score: 281
Period size: 59 Copynumber: 5.5 Consensus size: 59
440 GACGTCCTTG
* * *
450 AACTGTCCAAAAATTCTATTTTTTACACCCAAACTTCCAAAAATCT-CATTTTTGACCCCAA
1 AACT-TCCAAAAATTCCA-ATTTTACCCCCAAACTTCCAAAAATCTCCA-TTTTGACCCCAA
* * *
511 AACTTCCAAAAATTCCAATTTTACCCTCGAACTTCCAAAAATC-CCATTTTTACCCCAA
1 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCTCCATTTTGACCCCAA
* * *
569 AACTTCCAAAAATT-CAGTTTTTTGACCCCAAAACTTCCAAAAAT-TCCATTTAT-ACCCTC-G
1 AACTTCCAAAAATTCCA--ATTTT-ACCCCCAAACTTCCAAAAATCTCCATTT-TGACCC-CAA
* *
629 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCAAAAAAT-GCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCTCCA-TTTTGACCCCAA
* *** * * *
688 AACTTTCC-AAAATTCCATTTTTACCCTTGAACCTCC-AAAATCTCCATTTTCGACCTCGA
1 AAC-TTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCTCCATTTT-GACCCCAA
**
747 AAC-TCTTAAAATTACC-ATTTTACCCC
1 AACTTCCAAAAATT-CCAATTTTACCCC
773 TGGGTATCCG
Statistics
Matches: 218, Mismatches: 28, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
57 4 0.02
58 71 0.33
59 78 0.36
60 57 0.26
61 8 0.04
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCTCCATTTTGACCCCAA
Done.