Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008092.1 Kokia drynarioides strain JFW-HI SEQ_122750, 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: 24048
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34

Warning! 18 characters in sequence are not A, C, G, or T


Found at i:7424 original size:14 final size:15

Alignment explanation


    Indices: 7405--7434  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       7395 GTTATTGTCT

                           
       7405 GACATTGAAA-CAGA
          1 GACATTGAAAGCAGA

                           
       7419 GACATTGAAAGCAGA
          1 GACATTGAAAGCAGA

             
       7434 G
          1 G

       7435 GAAGGAAATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   10  0.67
  15    5  0.33

ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13


Consensus pattern (15 bp):   
GACATTGAAAGCAGA

Found at i:13697 original size:61 final size:61

Alignment explanation


    Indices: 13622--13750  Score: 249
    Period size: 61  Copynumber: 2.1  Consensus size: 61

      13612 AATATTACCA

                                                                    *    
      13622 TTTTTACTCAAAATGGTAACATTTTTTAAAAAGTCCCTAAACCATCCATCATCACATTTTT
          1 TTTTTACTCAAAATGGTAACATTTTTTAAAAAGTCCCTAAACCATCCATCATCACACTTTT

                                                                         
      13683 TTTTTACTCAAAATGGTAACATTTTTTAAAAAGTCCCTAAACCATCCATCATCACACTTTT
          1 TTTTTACTCAAAATGGTAACATTTTTTAAAAAGTCCCTAAACCATCCATCATCACACTTTT

                   
      13744 TTTTTAC
          1 TTTTTAC

      13751 CCATAATCAT


Statistics
Matches: 67,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  61   67  1.00

ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40


Consensus pattern (61 bp):   
TTTTTACTCAAAATGGTAACATTTTTTAAAAAGTCCCTAAACCATCCATCATCACACTTTT

Found at i:21160 original size:34 final size:34

Alignment explanation


    Indices: 21117--21185  Score: 120
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      21107 AAATAGAAAC

                           *                  
      21117 TAAAAATACATGGTGGTTCACTATTTCACCTAAT
          1 TAAAAATACATGGTGATTCACTATTTCACCTAAT

                                         *    
      21151 TAAAAATACATGGTGATTCACTATTTCACTTAAT
          1 TAAAAATACATGGTGATTCACTATTTCACCTAAT

             
      21185 T
          1 T

      21186 GATGATTTTA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38


Consensus pattern (34 bp):   
TAAAAATACATGGTGATTCACTATTTCACCTAAT

Found at i:22745 original size:62 final size:62

Alignment explanation


    Indices: 22602--22792  Score: 253
    Period size: 62  Copynumber: 3.0  Consensus size: 62

      22592 AAAAATCCAA

                     *  **                                        *        
      22602 ATAACATGGTATGCTCTTTCTTGTGGTGTAATCTTAGCAT--A-ATAGATAATATTAATCTCC
          1 ATAACATGGCATATTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAA-AATAATCTCC

                        *                                                 
      22662 ATAACATGGCATGTTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAAAATAATCTCC
          1 ATAACATGGCATATTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAAAATAATCTCC

              *                        *                                     
      22724 ATGACATGGCATATTCTTTCTTGTGGTCTAATCTTAGCATAAGCACAGATAGATAAAATAATCTC
          1 ATAACATGGCATATTCTTTCTTGTGGTGTAATCTTAGCATAA--AC--ATAGATAAAATAATCTC

             
      22789 C
         62 C

               
      22790 ATA
          1 ATA

      22793 GAAATATTAA


Statistics
Matches: 117,  Mismatches: 7, Indels: 8
        0.89            0.05        0.06

Matches are distributed among these distances:
  60   38  0.32
  62   49  0.42
  63    8  0.07
  64    2  0.02
  66   20  0.17

ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36


Consensus pattern (62 bp):   
ATAACATGGCATATTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAAAATAATCTCC

Done.