Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009196.1 Kokia drynarioides strain JFW-HI SEQ_123901, 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, 749

Length: 1249
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31


Found at i:155 original size:10 final size:10

Alignment explanation


    Indices: 142--184  Score: 56
    Period size: 10  Copynumber: 4.6  Consensus size: 10

        132 AAAACATTAA

                      
        142 AAAAAATATT
          1 AAAAAATATT

                      
        152 AAAAAATA--
          1 AAAAAATATT

                      
        160 AAAAAAT-TT
          1 AAAAAATATT

                *     
        169 AAAAGATATT
          1 AAAAAATATT

                  
        179 AAAAAA
          1 AAAAAA

        185 ATTTTAGATT


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


Consensus pattern (10 bp):   
AAAAAATATT

Found at i:328 original size:12 final size:12

Alignment explanation


    Indices: 311--380  Score: 61
    Period size: 12  Copynumber: 5.9  Consensus size: 12

        301 ATAACATCCA

                  *    *
        311 AACAACCAAAAT
          1 AACAACAAAAAC

                  *     
        323 AACAACCAAAAC
          1 AACAACAAAAAC

              * **     *
        335 AATAGTAAAAAT
          1 AACAACAAAAAC

                *       
        347 AACAGC-AAAAC
          1 AACAACAAAAAC

                        
        358 AACAACAAAAAC
          1 AACAACAAAAAC

                       
        370 AACAACAAAAA
          1 AACAACAAAAA

        381 TAGCAGCAAA


Statistics
Matches: 47,  Mismatches: 10, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  11    9  0.19
  12   38  0.81

ACGTcount: A:0.70, C:0.21, G:0.03, T:0.06


Consensus pattern (12 bp):   
AACAACAAAAAC

Found at i:409 original size:12 final size:12

Alignment explanation


    Indices: 330--415  Score: 66
    Period size: 12  Copynumber: 7.2  Consensus size: 12

        320 AATAACAACC

                   *  * 
        330 AAAACAATAGTA
          1 AAAACAACAGCA

                *       
        342 AAAATAACAGC-
          1 AAAACAACAGCA

                     *  
        353 AAAACAACAACA
          1 AAAACAACAGCA

                     *  
        365 AAAACAACAACA
          1 AAAACAACAGCA

                * *     
        377 AAAATAGCAGCA
          1 AAAACAACAGCA

               **     * 
        389 AAAGTAACAGTA
          1 AAAACAACAGCA

                     *  
        401 AAAACAACACCA
          1 AAAACAACAGCA

               
        413 AAA
          1 AAA

        416 CAGTAACCAA


Statistics
Matches: 58,  Mismatches: 15, Indels: 2
        0.77            0.20        0.03

Matches are distributed among these distances:
  11    9  0.16
  12   49  0.84

ACGTcount: A:0.67, C:0.19, G:0.07, T:0.07


Consensus pattern (12 bp):   
AAAACAACAGCA

Found at i:415 original size:36 final size:35

Alignment explanation


    Indices: 317--415  Score: 99
    Period size: 35  Copynumber: 2.8  Consensus size: 35

        307 TCCAAACAAC

                 *      *       * **           
        317 CAAAATAACAACCAAAACAATAGTAAAAATAACAG
          1 CAAAACAACAACAAAAACAACAACAAAAATAACAG

                                           *   
        352 CAAAACAACAACAAAAACAACAACAAAAATAGCAG
          1 CAAAACAACAACAAAAACAACAACAAAAATAACAG

                  *    **          *     
        387 CAAAAGTAACAGTAAAAACAACACCAAAA
          1 CAAAA-CAACAACAAAAACAACAACAAAA

        416 CAGTAACCAA


Statistics
Matches: 53,  Mismatches: 10, Indels: 1
        0.83            0.16        0.02

Matches are distributed among these distances:
  35   34  0.64
  36   19  0.36

ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07


Consensus pattern (35 bp):   
CAAAACAACAACAAAAACAACAACAAAAATAACAG
Done.