Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000187.1 Kokia drynarioides strain JFW-HI SEQ_110870, 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, 690

Length: 1151
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42


Found at i:343 original size:30 final size:29

Alignment explanation


    Indices: 309--367  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        299 GAATTGGATC

                           *              
        309 AAATCAAAATTTCATGTATAAAATTGCACA
          1 AAATCAAAATTT-ATATATAAAATTGCACA

                 *  *          *         
        339 AAATCGAAGTTTATATATACAATTGCACA
          1 AAATCAAAATTTATATATAAAATTGCACA

        368 TTAAACTATA


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  29   15  0.60
  30   10  0.40

ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31


Consensus pattern (29 bp):   
AAATCAAAATTTATATATAAAATTGCACA

Found at i:1019 original size:23 final size:23

Alignment explanation


    Indices: 976--1018  Score: 63
    Period size: 22  Copynumber: 1.9  Consensus size: 23

        966 TAATAAAATC

                                   
        976 AATATAACATATAATATAAAAGA
          1 AATATAACATATAATATAAAAGA

                                  
        999 AATATAAC-TA-AGATATAAAA
          1 AATATAACATATA-ATATAAAA

       1019 AAAAAGATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  21    1  0.05
  22   10  0.53
  23    8  0.42

ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26


Consensus pattern (23 bp):   
AATATAACATATAATATAAAAGA

Found at i:1102 original size:59 final size:55

Alignment explanation


    Indices: 1026--1148  Score: 128
    Period size: 59  Copynumber: 2.2  Consensus size: 55

       1016 AAAAAAAAGA

                                                    *                   
       1026 TATT-TAATATATAGATAAAT-AATTAATATATATAATATTATAAAAAAATTTATAATAT
          1 TATTATAATATATAGAT-AATGAATT--TATATAT-ATATAATAAAAAAA-TTATAATAT

                                       *     *      *               
       1084 TATTATAATATA-ATGATAATGAATTTTTATATTTATAATTAAAAAATTATAATAT
          1 TATTATAATATATA-GATAATGAATTTATATATATATAATAAAAAAATTATAATAT

                       
       1139 TA-TATAATAT
          1 TATTATAATAT

       1149 TAA


Statistics
Matches: 58,  Mismatches: 4, Indels: 10
        0.81            0.06        0.14

Matches are distributed among these distances:
  54    8  0.14
  55   11  0.19
  56   11  0.19
  57    6  0.10
  58    8  0.14
  59   14  0.24

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (55 bp):   
TATTATAATATATAGATAATGAATTTATATATATATAATAAAAAAATTATAATAT

Found at i:1103 original size:55 final size:53

Alignment explanation


    Indices: 1044--1148  Score: 131
    Period size: 55  Copynumber: 1.9  Consensus size: 53

       1034 ATATAGATAA

                 *                         *                        
       1044 ATAATTAATATATATAATATTATAA-AAAAATTTATAATATTATTATAATATAATG
          1 ATAATGAATATATAT-AT-TTATAATAAAAAATTATAATATTA-TATAATATAATG

                     * *                                      
       1099 ATAATGAATTTTTATATTTATAATTAAAAAATTATAATATTATATAATAT
          1 ATAATGAATATATATATTTATAA-TAAAAAATTATAATATTATATAATAT

       1149 TAA


Statistics
Matches: 44,  Mismatches: 4, Indels: 5
        0.83            0.08        0.09

Matches are distributed among these distances:
  53    6  0.14
  54   10  0.23
  55   28  0.64

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (53 bp):   
ATAATGAATATATATATTTATAATAAAAAATTATAATATTATATAATATAATG
Done.