Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006617.1 Kokia drynarioides strain JFW-HI SEQ_121207, 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, 747

Length: 1245
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39


Found at i:45 original size:30 final size:30

Alignment explanation


    Indices: 4--312  Score: 299
    Period size: 30  Copynumber: 10.3  Consensus size: 30

          1 AAT

                 *                       *
          4 TTTTCAAAAATTACATTTTAACCCTTAAAA
          1 TTTTCCAAAATTACATTTTAACCCTTAAAC

              *          **         *     
         34 TTGTCCAAAATTATGTTTTAACCCCTAAA-
          1 TTTTCCAAAATTACATTTTAACCCTTAAAC

            *     *             *           
         63 ATTTCTAAAAATTACATTTTGACACC-TAAAC
          1 TTTTC-CAAAATTACATTTTAAC-CCTTAAAC

                 *            *           
         94 TTTTCTAAAATTACATTTGAACCCTTAAAC
          1 TTTTCCAAAATTACATTTTAACCCTTAAAC

                 *                  *     
        124 TTTTCTAAAATTACATTTTAACCCATAAAC
          1 TTTTCCAAAATTACATTTTAACCCTTAAAC

                         **                
        154 TTTTCCAAAATTATTTTTTAA-CCTCTAAAC
          1 TTTTCCAAAATTACATTTTAACCCT-TAAAC

              *  *                         
        184 TTCTCTAAAATTACATTTTAA-CCTTCAAAC
          1 TTTTCCAAAATTACATTTTAACCCTT-AAAC

                                *          
        214 TTTTCCAAAATTGA-ATTTTTACCCTTAAAC
          1 TTTTCCAAAATT-ACATTTTAACCCTTAAAC

                        *      *   *      
        244 TTTTCCAAAATTGCATTTTGACCGTTAAAC
          1 TTTTCCAAAATTACATTTTAACCCTTAAAC

              *        *              *    
        274 TTCTCCAAAATCACATTTTCAA-CCTCAAA-
          1 TTTTCCAAAATTACATTTT-AACCCTTAAAC

                      
        303 TTTTCCAAAA
          1 TTTTCCAAAA

        313 GATTGACTTT


Statistics
Matches: 231,  Mismatches: 38, Indels: 21
        0.80            0.13        0.07

Matches are distributed among these distances:
  29   17  0.07
  30  202  0.87
  31   12  0.05

ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39


Consensus pattern (30 bp):   
TTTTCCAAAATTACATTTTAACCCTTAAAC

Found at i:362 original size:90 final size:91

Alignment explanation


    Indices: 7--384  Score: 248
    Period size: 90  Copynumber: 4.2  Consensus size: 91

          1 AATTTT

                                        *  *            **        *     *    
          7 TCAAAAATTACATTTT-AACCCTT-AAAATTGTCCAAAATT-ATGTTTTAACCCCTAAA-ATTTC
          1 TCAAAAATTACATTTTCAA-CCTTCAAACTTTTCCAAAATTGA-ACTTTAACCCTTAAACTTTTC

             *      *    * *             *
         68 TAAAAATTACATTTTGACACC-TAAACTTT
         64 -CAAAATTGCATTGTAAC-CCTTAAACTTC

              *             *                 *          *        *          
         97 TCTAAAATTACA-TTTGAACCCTT-AAACTTTTCTAAAATT-ACATTTTAACCCATAAACTTTTC
          1 TCAAAAATTACATTTTCAA-CCTTCAAACTTTTCCAAAATTGA-ACTTTAACCCTTAAACTTTTC

                   ***  *                
        159 CAAAATTATTTTTTAA-CCTCTAAACTTC
         64 CAAAATTGCATTGTAACCCT-TAAACTTC

              *                                        *   *                 
        187 TCTAAAATTACATTTT-AACCTTCAAACTTTTCCAAAATTGAATTTTTACCCTTAAACTTTTCCA
          1 TCAAAAATTACATTTTCAACCTTCAAACTTTTCCAAAATTGAACTTTAACCCTTAAACTTTTCCA

                      * *   *         
        251 AAATTGCATTTTGACCGTTAAACTTC
         66 AAATTGCATTGTAACCCTTAAACTTC

              *     *                                          *       *     
        277 TCCAAAATCACATTTTCAACC-TCAAA-TTTTCCAAAAGATTG-ACTTTAATCC-T-AAGTTTTC
          1 TCAAAAATTACATTTTCAACCTTCAAACTTTTCC-AAA-ATTGAACTTTAACCCTTAAACTTTTC

                    *                      
        337 CAAAAATTTCAATTGTAACCCTTAAA-TTCC
         64 C-AAAATTGC-ATTGTAACCCTTAAACTT-C

                      *       
        367 TCAAAAATTAGATTTTCA
          1 TCAAAAATTACATTTTCA

        385 TCCCTAATTC


Statistics
Matches: 240,  Mismatches: 34, Indels: 28
        0.79            0.11        0.09

Matches are distributed among these distances:
  88   10  0.04
  89   23  0.10
  90  189  0.79
  91   18  0.08

ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39


Consensus pattern (91 bp):   
TCAAAAATTACATTTTCAACCTTCAAACTTTTCCAAAATTGAACTTTAACCCTTAAACTTTTCCA
AAATTGCATTGTAACCCTTAAACTTC
Done.