Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001418.1 Kokia drynarioides strain JFW-HI SEQ_112915, 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, 945

Length: 1576
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35


Found at i:1025 original size:42 final size:42

Alignment explanation


    Indices: 961--1057  Score: 176
    Period size: 42  Copynumber: 2.3  Consensus size: 42

        951 CAAATATTTT

                *                   *                 
        961 TAAATCCAAATATAATTTCATTCTTAAAAAACACTTATAAAC
          1 TAAACCCAAATATAATTTCATTCTAAAAAAACACTTATAAAC

                                                      
       1003 TAAACCCAAATATAATTTCATTCTAAAAAAACACTTATAAAC
          1 TAAACCCAAATATAATTTCATTCTAAAAAAACACTTATAAAC

                         
       1045 TAAACCCAAATAT
          1 TAAACCCAAATAT

       1058 TTTTAAACTC


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  42   53  1.00

ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30


Consensus pattern (42 bp):   
TAAACCCAAATATAATTTCATTCTAAAAAAACACTTATAAAC

Found at i:1055 original size:100 final size:100

Alignment explanation


    Indices: 939--1120  Score: 296
    Period size: 100  Copynumber: 1.8  Consensus size: 100

        929 AAACCCATCC

                       *                                              *      
        939 ATAAACTAAACTCAAATATTTTTAAA-TCCAAATATAATTTCATTCTTAAAAAACACTTATAAAC
          1 ATAAACTAAACCCAAATATTTTTAAACT-CAAATATAATTTCATTCTTAAAAAACACTCATAAAC

                                                 
       1003 TAAACCCAAATAT-AATTTCATTCTAAAAAAACACTT
         65 TAAACCCAAA-ATCAATTTCATTCTAAAAAAACACTT

                                                                  *          
       1039 ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTAAAAAACTCTCATAAACT
          1 ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTAAAAAACACTCATAAACT

               *             
       1104 AAATCCAAAATCAATTT
         66 AAACCCAAAATCAATTT

       1121 TCTCTTCTTC


Statistics
Matches: 76,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  99    2  0.03
 100   73  0.96
 101    1  0.01

ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33


Consensus pattern (100 bp):   
ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTAAAAAACACTCATAAACT
AAACCCAAAATCAATTTCATTCTAAAAAAACACTT

Found at i:1071 original size:58 final size:58

Alignment explanation


    Indices: 1003--1112  Score: 175
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        993 ACTTATAAAC

                                               *                      
       1003 TAAACCCAAATATAATTTCATTCTAAAAAAACACTTATAAACTAAACCCAAATATTTT
          1 TAAACCCAAATATAATTTCATTCTAAAAAAACACTCATAAACTAAACCCAAATATTTT

                 *                  *       *             *     
       1061 TAAACTCAAATATAATTTCATTCTTAAAAAACTCTCATAAACTAAATCCAAA
          1 TAAACCCAAATATAATTTCATTCTAAAAAAACACTCATAAACTAAACCCAAA

       1113 ATCAATTTTC


Statistics
Matches: 47,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  58   47  1.00

ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31


Consensus pattern (58 bp):   
TAAACCCAAATATAATTTCATTCTAAAAAAACACTCATAAACTAAACCCAAATATTTT
Done.