Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000190.1 Kokia drynarioides strain JFW-HI SEQ_110873, 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, 612
Length: 1021
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Found at i:670 original size:119 final size:119
Alignment explanation
Indices: 454--741 Score: 333
Period size: 119 Copynumber: 2.4 Consensus size: 119
444 GATATCCTTG
*
454 AACTGTCCAAAAATTCTATTTTTTACCCACAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
1 AACT-TCCAAAAATTCTATTTTTTACCCACAAACTTCCAAAAATCTCATTTCTGACCCCAAAACT
* * *
519 TCCAATAATTCCAATTTTACCCTCGAACTTCCAAAAAT-CTCATTTTTGACCCAAA
65 TCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATGC-CATTTTTGACCCAAA
*
574 AACTTCCAAAAATTC-AGTTTTTTGACCTC-GAAACTTCCAAAAAT-TCCATTTCT-ACCCTC-A
1 AACTTCCAAAAATTCTA-TTTTTT-ACC-CACAAACTTCCAAAAATCT-CATTTCTGACCC-CAA
**
634 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATGCCATTTTTGACCCCGA
61 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATGCCATTTTTGACCCAAA
* * * *
693 AACTTTCC-AAAATTCCA-TTTTTACCCTCGAACCTCC-AAAATCTCCATTT
1 AAC-TTCCAAAAATTCTATTTTTTACCCACAAACTTCCAAAAATCT-CATTT
742 TCGACCTCGA
Statistics
Matches: 148, Mismatches: 10, Indels: 23
0.82 0.06 0.13
Matches are distributed among these distances:
116 6 0.04
117 16 0.11
118 6 0.04
119 85 0.57
120 34 0.23
121 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (119 bp):
AACTTCCAAAAATTCTATTTTTTACCCACAAACTTCCAAAAATCTCATTTCTGACCCCAAAACTT
CCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATGCCATTTTTGACCCAAA
Found at i:738 original size:29 final size:29
Alignment explanation
Indices: 454--742 Score: 270
Period size: 29 Copynumber: 9.7 Consensus size: 29
444 GATATCCTTG
* *
454 AACTGTCCAAAAATTCTATTTTTTACCCACA
1 AACT-TCCAAAAATTCCA-TTTTTACCCTCA
485 AACTTCCAAAAA-TCTCATTTTTGACCC-CAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCTC-A
* * *
515 AACTTCCAATAATTCCAATTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCA
**
544 AACTTCCAAAAA-TCTCATTTTTGACCCAAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCTCA
574 AACTTCCAAAAATT-CAGTTTTTTGA-CCTCGA
1 AACTTCCAAAAATTCCA--TTTTT-ACCCTC-A
*
605 AACTTCCAAAAATTCCATTTCTACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
* *
634 AACTTCCAAAAATTCCAATTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
*
663 AACTTCCAAAAATGCCATTTTTGACCC-CGA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-A
*
693 AACTTTCC-AAAATTCCATTTTTACCCTCG
1 AAC-TTCCAAAAATTCCATTTTTACCCTCA
*
722 AACCTCC-AAAATCTCCATTTT
1 AACTTCCAAAAAT-TCCATTTT
743 CGACCTCGAA
Statistics
Matches: 220, Mismatches: 20, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.05
29 95 0.43
30 80 0.36
31 33 0.15
32 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCA
Found at i:749 original size:29 final size:28
Alignment explanation
Indices: 519--776 Score: 118
Period size: 29 Copynumber: 8.8 Consensus size: 28
509 CCCCAAAACT
*
519 TCCAATAATTCCAATTTT-ACCCTCGAACT
1 TCCAA-AATTCC-ATTTTGACCCTCGAACC
* *** *
548 TCCAAAAATCTCATTTTTGACCCAAAAACT
1 TCCAAAATTC-CA-TTTTGACCCTCGAACC
*
578 TCCAAAAATT-CAGTTTTTTGA-CCTCGAAACT
1 TCC-AAAATTCCA---TTTTGACCCTCG-AACC
* *
609 TCCAAAAATTCCATTTCT-ACCCTCAAACT
1 TCC-AAAATTCCATTT-TGACCCTCGAACC
* * *
638 TCCAAAAATTCCAATTTT-ACCCCCAAACT
1 TCC-AAAATTCC-ATTTTGACCCTCGAACC
* *
667 TCCAAAAATGCCATTTTTGACCC-CGAAACTT
1 TCC-AAAATTCCA-TTTTGACCCTCG-AAC-C
*
698 TCCAAAATTCCATTTTTACCCTCGAACC
1 TCCAAAATTCCATTTTGACCCTCGAACC
*
726 TCCAAAATCTCCATTTTCGA-CCTCGAAAC
1 TCCAAAAT-TCCATTTT-GACCCTCGAACC
*
755 TCTTAAAATTACCATTTT-ACCC
1 TC-CAAAATT-CCATTTTGACCC
777 CTGGGTATCC
Statistics
Matches: 190, Mismatches: 18, Indels: 42
0.76 0.07 0.17
Matches are distributed among these distances:
28 15 0.08
29 91 0.48
30 52 0.27
31 30 0.16
32 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCAAAATTCCATTTTGACCCTCGAACC
Found at i:755 original size:59 final size:60
Alignment explanation
Indices: 454--747 Score: 320
Period size: 59 Copynumber: 4.9 Consensus size: 60
444 GATATCCTTG
* * *
454 AACTGTCCAAAAATTCTATTTTTTACCCACAAACTTCCAAAAATCT-CATTTTTGACCCCAA
1 AACT-TCCAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTGACCCCAA
* * *
515 AACTTCCAATAATTCCAATTTTACCCTCGAACTTCCAAAAATCT-CATTTTTGACCCAAA
1 AACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTGACCCCAA
*
574 AACTTCCAAAAATT-CAGTTTTTTGA-CCTCGAAACTTCCAAAAAT-TCCATTTCT-ACCCTC-A
1 AACTTCCAAAAATTCCA--TTTTT-ACCCTCG-AACTTCCAAAAATCTCCATTTTTGACCC-CAA
* * * * *
634 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAAT-GCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTGACCCCAA
* *
693 AACTTTCC-AAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTCCATTTTCGACC
1 AAC-TTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTGACC
748 TCGAAACTCT
Statistics
Matches: 200, Mismatches: 21, Indels: 26
0.81 0.09 0.11
Matches are distributed among these distances:
58 29 0.14
59 101 0.50
60 44 0.22
61 26 0.13
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (60 bp):
AACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTGACCCCAA
Done.