Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000922.1 Kokia drynarioides strain JFW-HI SEQ_112069, 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, 650

Length: 1084
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.44


Found at i:373 original size:30 final size:30

Alignment explanation


    Indices: 313--486  Score: 206
    Period size: 30  Copynumber: 5.8  Consensus size: 30

        303 GTCCCTAAAT

                 *               ** *     
        313 TTTTCTAAAATTACATTTT-AAACACAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                                          
        342 TTTTCCAAAATTACATTTTGACCCCCAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                           *   *     *    
        372 TTTTCCAAAATTACAATTTAACCCCTAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                      ** *         * *    
        402 TTTTCCAAAAGCATATTTTGACCTCTAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                                           
        432 TTTTCCAAAATTACATTTTGACCCCTCAAAC
          1 TTTTCCAAAATTACATTTTGACCCC-CAAAC

                       * *          
        463 TTTTCCAAAATCATATTTTGACCC
          1 TTTTCCAAAATTACATTTTGACCC

        487 TTGAACTTCT


Statistics
Matches: 123,  Mismatches: 20, Indels: 2
        0.85            0.14        0.01

Matches are distributed among these distances:
  29   18  0.15
  30   79  0.64
  31   26  0.21

ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36


Consensus pattern (30 bp):   
TTTTCCAAAATTACATTTTGACCCCCAAAC

Found at i:420 original size:60 final size:60

Alignment explanation


    Indices: 313--486  Score: 242
    Period size: 60  Copynumber: 2.9  Consensus size: 60

        303 GTCCCTAAAT

                 *               * *                 * *                
        313 TTTTCTAAAATTACATTTTAAACAC-AAACTTTTCCAAAATTACATTTTGACCCCCAAAC
          1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

                           *                        *            * *    
        372 TTTTCCAAAATTACAATTTAACCCCTAAACTTTTCCAAAAGCATATTTTGACCTCTAAAC
          1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

                               *                                   
        432 TTTTCCAAAATTACATTTTGACCCCTCAAACTTTTCCAAAATCATATTTTGACCC
          1 TTTTCCAAAATTACATTTTAACCCCT-AAACTTTTCCAAAATCATATTTTGACCC

        487 TTGAACTTCT


Statistics
Matches: 100,  Mismatches: 13, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  59   21  0.21
  60   53  0.53
  61   26  0.26

ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36


Consensus pattern (60 bp):   
TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

Found at i:466 original size:31 final size:31

Alignment explanation


    Indices: 337--486  Score: 207
    Period size: 30  Copynumber: 4.9  Consensus size: 31

        327 ATTTTAAACA

                                           
        337 CAAACTTTTCCAAAATTACATTTTGACCCC-
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                                *   *      
        367 CAAACTTTTCCAAAATTACAATTTAACCCCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                           ** *         *  
        398 -AAACTTTTCCAAAAGCATATTTTGACCTCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                                           
        428 -AAACTTTTCCAAAATTACATTTTGACCCCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                            * *          
        458 CAAACTTTTCCAAAATCATATTTTGACCC
          1 CAAACTTTTCCAAAATTACATTTTGACCC

        487 TTGAACTTCT


Statistics
Matches: 104,  Mismatches: 14, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
  30   78  0.75
  31   26  0.25

ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35


Consensus pattern (31 bp):   
CAAACTTTTCCAAAATTACATTTTGACCCCT

Done.