Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009353.1 Kokia drynarioides strain JFW-HI SEQ_124060, 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: 1920
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39


Found at i:288 original size:15 final size:16

Alignment explanation


    Indices: 265--297  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

        255 TTGCTGAATC

                            
        265 ATATAAATTTTAA-AA
          1 ATATAAATTTTAATAA

                *           
        280 ATATTAATTTTAATAA
          1 ATATAAATTTTAATAA

              
        296 AT
          1 AT

        298 GATATTTTCT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   12  0.75
  16    4  0.25

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (16 bp):   
ATATAAATTTTAATAA

Found at i:1044 original size:30 final size:31

Alignment explanation


    Indices: 1001--1063  Score: 76
    Period size: 30  Copynumber: 2.1  Consensus size: 31

        991 TAAAAAAAGT

                             *              
       1001 AAAATTATAATTTAACCTTCTTAAAA-TTATA
          1 AAAATTATAATTTAACCAT-TTAAAAGTTATA

                    *      *               
       1032 AAAATT-TGATTTAATCATTTAAAAGTTATA
          1 AAAATTATAATTTAACCATTTAAAAGTTATA

              
       1062 AA
          1 AA

       1064 TATATAAAGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  29    6  0.21
  30   16  0.57
  31    6  0.21

ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41


Consensus pattern (31 bp):   
AAAATTATAATTTAACCATTTAAAAGTTATA

Found at i:1097 original size:32 final size:32

Alignment explanation


    Indices: 1052--1112  Score: 77
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       1042 TTAATCATTT

                *   *     *     *           
       1052 AAAAGTTATAAATATATAAAGTATTAAAAATA
          1 AAAAATTAAAAATACATAAACTATTAAAAATA

                              *          
       1084 AAAAATTAAAAATACATAGACTATTAAAA
          1 AAAAATTAAAAATACATAAACTATTAAAA

       1113 TTTGATTTAG


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  32   24  1.00

ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28


Consensus pattern (32 bp):   
AAAAATTAAAAATACATAAACTATTAAAAATA
Done.