Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010381.1 Kokia drynarioides strain JFW-HI SEQ_125254, 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, 751

Length: 1253
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36


Found at i:535 original size:3 final size:3

Alignment explanation


    Indices: 529--592  Score: 67
    Period size: 3  Copynumber: 21.3  Consensus size: 3

        519 ATTATTAAAA

                             *  * *                                     
        529 ATT ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT AATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT

                      *  *           
        575 ATT A-T ATA AAT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT A

        593 ATAATATAAT


Statistics
Matches: 49,  Mismatches: 10, Indels: 4
        0.78            0.16        0.06

Matches are distributed among these distances:
   2    2  0.04
   3   44  0.90
   4    3  0.06

ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58


Consensus pattern (3 bp):   
ATT

Found at i:567 original size:27 final size:24

Alignment explanation


    Indices: 529--594  Score: 78
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        519 ATTATTAAAA

                         *             
        529 ATTATTATTATTAGTGTCATTATTATT
          1 ATTATTATTATTAAT-T-ATTATTA-T

                                    
        556 ATTATTATTATTAATTATTATTAT
          1 ATTATTATTATTAATTATTATTAT

              * *          
        580 ATAAATATTATTAAT
          1 ATTATTATTATTAAT

        595 AATATAATAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  24   14  0.39
  25    7  0.19
  26    1  0.03
  27   14  0.39

ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58


Consensus pattern (24 bp):   
ATTATTATTATTAATTATTATTAT

Found at i:597 original size:27 final size:27

Alignment explanation


    Indices: 517--597  Score: 80
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        507 ATCATTAATG

                                       *
        517 TTATTATTA-A-AAATTATTATTATTAG
          1 TTATTATTATATAAA-TATTATTATTAA

                            *            
        543 TGTCATTATTAT-T-ATTATTATTATTAA
          1 T-T-ATTATTATATAAATATTATTATTAA

                                   *   
        570 TTATTATTATATAAATATTATTAATAA
          1 TTATTATTATATAAATATTATTATTAA

             
        597 T
          1 T

        598 ATAATAATCA


Statistics
Matches: 45,  Mismatches: 4, Indels: 11
        0.75            0.07        0.18

Matches are distributed among these distances:
  25    8  0.18
  26    3  0.07
  27   26  0.58
  28    8  0.18

ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56


Consensus pattern (27 bp):   
TTATTATTATATAAATATTATTATTAA

Found at i:610 original size:24 final size:24

Alignment explanation


    Indices: 561--613  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        551 TTATTATTAT

                      *    *        
        561 TATTATTAATTATTATTATATAAA
          1 TATTATTAATAATTAATATATAAA

                                  *  
        585 TATTATTAATAATATAATA-ATCAA
          1 TATTATTAATAAT-TAATATATAAA

                 
        609 TATTA
          1 TATTA

        614 ACCTTAATGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   21  0.84
  25    4  0.16

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (24 bp):   
TATTATTAATAATTAATATATAAA
Done.