Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000537.1 Kokia drynarioides strain JFW-HI SEQ_111436, 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, 720
Length: 1201
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Found at i:647 original size:59 final size:59
Alignment explanation
Indices: 486--846 Score: 258
Period size: 59 Copynumber: 6.1 Consensus size: 59
476 TAAATTGTCC
* * * *
486 AAAAATTTTGTTTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACC-CTAAAACTTCT
1 AAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTC-GAAACTTCT
* * * ** *
545 AAAATTTCTTTTTTTTTACACCTGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
1 AAAAATTC--TATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCT
* * *
606 TAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCTCATTTTT-ACCCCGAAACTTCA
1 AAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCT
**** *
664 AAAAATTCTATTTTTACCATTGAACTTCCAAAAAAAC-CAATTTTT-ACCCTC-AAACTT-T
1 AAAAATTCTATTTTTACCCCCAAACTTCC-AAAAATCTC-ATTTTTGA-CCTCGAAACTTCT
* * * * * * * *
722 CAAAAATTCCATTTTTAACCACGAACTTTCAAAAAT-TCCATTTTTGACCCCAAAACTTCC
1 -AAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCT-CATTTTTGACCTCGAAACTTCT
* * * * *
782 AAAATTTACCA-TTTTACCCCCAGA-TGTCCAAAAA-CTCTATTTTCGACTTCGAAAC-TCT
1 AAAAATT-CTATTTTTACCCCCAAACT-TCCAAAAATCTC-ATTTTTGACCTCGAAACTTCT
*
840 CAAAATT
1 AAAAATT
847 ACCCTTTTAC
Statistics
Matches: 240, Mismatches: 46, Indels: 33
0.75 0.14 0.10
Matches are distributed among these distances:
58 60 0.25
59 123 0.51
60 6 0.03
61 50 0.21
62 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCT
Found at i:786 original size:29 final size:28
Alignment explanation
Indices: 496--801 Score: 170
Period size: 29 Copynumber: 10.4 Consensus size: 28
486 AAAAATTTTG
*
496 TTTTTACCCCTAAACTTCCAAAAATCTCA
1 TTTTTACCCCTAAACTTCCAAAATTC-CA
* **
525 TTTTTGA-CCCTAAAACTTCTAAAATTTCTTTT
1 TTTTT-ACCCCT-AAACTTCCAAAA-TTC--CA
* * *
557 TTTTTACACCTGAACTTCCAAAAATCCCA
1 TTTTTACCCCTAAACTTCC-AAAATTCCA
* * * *
586 TTTTTGACCTCGAAACTTCTTAAAATTCTA
1 TTTTT-ACCCCTAAACTTC-CAAAATTCCA
* *
616 TTTTTACCCCCAAACTTCCAAAAATCTCA
1 TTTTTACCCCTAAACTTCCAAAATTC-CA
* * *
645 TTTTTACCCCGAAACTTCAAAAAATTCTA
1 TTTTTACCCCTAAACTTC-CAAAATTCCA
** * **
674 TTTTTACCATTGAACTTCCAAAAAAACCAA
1 TTTTTACCCCTAAACTTCC-AAAATTCC-A
*
704 TTTTTA-CCCTCAAACTTTCAAAAATTCCA
1 TTTTTACCCCT-AAAC-TTCCAAAATTCCA
* * *
733 TTTTTAACCAC-GAACTTTCAAAAATTCCA
1 TTTTT-ACCCCTAAAC-TTCCAAAATTCCA
*
762 TTTTTGACCCCAAAACTTCCAAAATTTACCA
1 TTTTT-ACCCCTAAACTTCCAAAA-TT-CCA
793 -TTTTACCCC
1 TTTTTACCCC
802 CAGATGTCCA
Statistics
Matches: 212, Mismatches: 46, Indels: 38
0.72 0.16 0.13
Matches are distributed among these distances:
28 6 0.03
29 109 0.51
30 65 0.31
31 19 0.09
32 13 0.06
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
TTTTTACCCCTAAACTTCCAAAATTCCA
Found at i:815 original size:88 final size:86
Alignment explanation
Indices: 568--803 Score: 212
Period size: 88 Copynumber: 2.7 Consensus size: 86
558 TTTTACACCT
* * * * * *
568 GAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCTTAAAATTCTA--TTTTTACCCCCAAAC
1 GAACTTTCAAAAATTCCATTTTTGACCACAAAACTTC-CAAAATT-TACCATTTTACCCCCAAAC
*
631 TTCCAAAAATCTCATTTTTACCCC
64 TTCCAAAAATC-CATTTTTACCAC
* *** ** *
655 GAAAC-TTCAAAAAATTCTATTTTT-ACCATTGAACTTCCAAAA-AAACCAATTTTTACCCTCAA
1 G-AACTTTC-AAAAATTCCATTTTTGACCACAAAACTTCCAAAATTTACC-A-TTTTACCCCCAA
*
717 ACTTTCAAAAATTCCATTTTTAACCAC
62 ACTTCCAAAAA-TCCATTTTT-ACCAC
*
744 GAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAATTTACCATTTTACCCCCA
1 GAACTTTCAAAAATTCCATTTTTGACCACAAAACTTCCAAAATTTACCATTTTACCCCCA
804 GATGTCCAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
84 1 0.01
86 4 0.03
87 12 0.10
88 71 0.61
89 25 0.22
90 3 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (86 bp):
GAACTTTCAAAAATTCCATTTTTGACCACAAAACTTCCAAAATTTACCATTTTACCCCCAAACTT
CCAAAAATCCATTTTTACCAC
Found at i:916 original size:59 final size:57
Alignment explanation
Indices: 701--917 Score: 170
Period size: 58 Copynumber: 3.7 Consensus size: 57
691 CCAAAAAAAC
* * * * *
701 CAATTTTTACCCTCAAACTTTCAAAAATT-CCATTTTTAACCACGAACTTTCAAAAATT
1 CAATTTTTAACCTCAAAATTTCCAAAATTACCA-TTTTACCCACGAA-TGTCAAAAATT
* * * * * *
759 CCATTTTTGACCCCAAAACTTCCAAAATTTACCATTTTACCC-CCAGATGTCCAAAAACT
1 CAATTTTTAACCTCAAAATTTCCAAAA-TTACCATTTTACCCACGA-ATGT-CAAAAATT
* ** * * * *
818 CTATTTTCGACTTCGAAA-CTCTCAAAATTACCCTTTTACCCACGAATGTCTAAAAATT
1 CAATTTTTAACCTCAAAATTTC-CAAAATTACCATTTTACCCACGAATGTC-AAAAATT
*
876 CAATTTTTAACCTTAAAATTTCCCAAAATTACCATTTTACCC
1 CAATTTTTAACCTCAAAATTT-CCAAAATTACCATTTTACCC
918 TTGAGAATCC
Statistics
Matches: 122, Mismatches: 28, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
57 1 0.01
58 61 0.50
59 56 0.46
60 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (57 bp):
CAATTTTTAACCTCAAAATTTCCAAAATTACCATTTTACCCACGAATGTCAAAAATT
Done.