Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009195.1 Kokia drynarioides strain JFW-HI SEQ_123900, 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: 2093
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37


Found at i:740 original size:12 final size:12

Alignment explanation


    Indices: 719--804  Score: 57
    Period size: 12  Copynumber: 7.2  Consensus size: 12

        709 TTGGTTACTG

                 *    * 
        719 TTTTGGTGTTGT
          1 TTTTGCTGTTAT

                *      *
        731 TTTTACTGTTAC
          1 TTTTGCTGTTAT

                    *   
        743 TTTTGCTGCTAT
          1 TTTTGCTGTTAT

                 *     *
        755 TTTTGTTGTT-G
          1 TTTTGCTGTTAT

                        
        766 TTTTGCTGTTAT
          1 TTTTGCTGTTAT

                *  *  * 
        778 TTTTACTATTGT
          1 TTTTGCTGTTAT

               * *      
        790 TTTGGTTGTTAT
          1 TTTTGCTGTTAT

               
        802 TTT
          1 TTT

        805 GGTTGTTTGG


Statistics
Matches: 53,  Mismatches: 20, Indels: 2
        0.71            0.27        0.03

Matches are distributed among these distances:
  11    9  0.17
  12   44  0.83

ACGTcount: A:0.08, C:0.07, G:0.19, T:0.66


Consensus pattern (12 bp):   
TTTTGCTGTTAT

Found at i:798 original size:35 final size:35

Alignment explanation


    Indices: 714--805  Score: 96
    Period size: 35  Copynumber: 2.6  Consensus size: 35

        704 CTATTTTGGT

                                  *           * 
        714 TACTGTTTTGG-TGTTGTTTTTACTGTTACTTTTGC
          1 TACTGTTTTGGTTGTTG-TTTTGCTGTTACTTTTAC

             *  *    *                  *      
        749 TGCTATTTTTGTTGTTGTTTTGCTGTTATTTTTAC
          1 TACTGTTTTGGTTGTTGTTTTGCTGTTACTTTTAC

              *             *     
        784 TATTGTTTTGGTTGTTATTTTG
          1 TACTGTTTTGGTTGTTGTTTTG

        806 GTTGTTTGGA


Statistics
Matches: 45,  Mismatches: 11, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  35   40  0.89
  36    5  0.11

ACGTcount: A:0.09, C:0.08, G:0.20, T:0.64


Consensus pattern (35 bp):   
TACTGTTTTGGTTGTTGTTTTGCTGTTACTTTTAC

Found at i:803 original size:47 final size:44

Alignment explanation


    Indices: 717--826  Score: 105
    Period size: 47  Copynumber: 2.4  Consensus size: 44

        707 TTTTGGTTAC

                   *    *        *                         
        717 TGTTTTGGTGTTGTTTTTACTGTTACTTTTGCTGCTATTTTTGTTGT
          1 TGTTTTGATGTTATTTTTACTATTACTTTTGCTGCTA-TTTTG--GT

                   *                 *      *  *         
        764 TGTTTTGCTGTTATTTTTACTATT-GTTTTGGTTGTTATTTTGGT
          1 TGTTTTGATGTTATTTTTACTATTACTTTT-GCTGCTATTTTGGT

                 *             
        808 TGTTTGGATGTTATTTTTA
          1 TGTTTTGATGTTATTTTTA

        827 GGCATTTTTA


Statistics
Matches: 54,  Mismatches: 8, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  44   19  0.35
  46    9  0.17
  47   26  0.48

ACGTcount: A:0.09, C:0.05, G:0.21, T:0.65


Consensus pattern (44 bp):   
TGTTTTGATGTTATTTTTACTATTACTTTTGCTGCTATTTTGGT

Found at i:980 original size:10 final size:10

Alignment explanation


    Indices: 938--980  Score: 56
    Period size: 10  Copynumber: 4.6  Consensus size: 10

        928 AATCTAAAAT

                      
        938 TTTTTTAATA
          1 TTTTTTAATA

             *        
        948 TCTTTTAA-A
          1 TTTTTTAATA

                      
        957 TTTTTT--TA
          1 TTTTTTAATA

                      
        965 TTTTTTAATA
          1 TTTTTTAATA

                  
        975 TTTTTT
          1 TTTTTT

        981 TTAATGTTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
   8    7  0.25
   9    6  0.21
  10   15  0.54

ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74


Consensus pattern (10 bp):   
TTTTTTAATA
Done.