Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001277.1 Kokia drynarioides strain JFW-HI SEQ_112664, 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: 4120
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:37 original size:30 final size:30

Alignment explanation


    Indices: 1--70  Score: 83
    Period size: 28  Copynumber: 2.4  Consensus size: 30

                                           
          1 AAATTACATTTTGACTCCT-AAACTTTTCCA
          1 AAATTACATTTTGAC-CCTCAAACTTTTCCA

                               * *        
         31 AAATTACA--TTGACCCTCGATCTTTTCCA
          1 AAATTACATTTTGACCCTCAAACTTTTCCA

                 *      
         59 AAATTTCATTTT
          1 AAATTACATTTT

         71 CATCCCGAGT


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  27    3  0.09
  28   21  0.62
  30   10  0.29

ACGTcount: A:0.31, C:0.23, G:0.04, T:0.41


Consensus pattern (30 bp):   
AAATTACATTTTGACCCTCAAACTTTTCCA

Found at i:999 original size:36 final size:35

Alignment explanation


    Indices: 912--1254  Score: 172
    Period size: 35  Copynumber: 9.5  Consensus size: 35

        902 AAAAACAAGA

                                            *  
        912 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGG

                     ***           *            
        947 TCTATCCCATTATTTTTAAGGTTATCTTAGACAAGG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGAC-AGG

             *       *              *       *  
        983 TTTATCCCAGCCTTTTTAAGGTTGCCTTAGACGGG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGG

                   *    *                    *  * * 
       1018 TCTATCCTAACATTTTTTAAAGGTT-TACCTTAAATAATG
          1 TCTATCCCAAC-CTTTTT-AAGGTTGT--CTTAGA-CAGG

                 * *   *            *      **  
       1057 TCTATTCTAACATTTTTAAGGTTGCCTTAGATGGG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGG

              *    *       *   *               
       1092 TCAATCCTAACCTTTATAATGTTGTCTTAGAC-GG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGG

                   **   **         *              * 
       1126 CTCTATCTTAATTTTTTTTAAAAAGTTGTCTTAGACAATG
          1 -TCTATCCCAA-CCTTTTT--AAGGTTGTCTTAGAC-AGG

                 ***           *              **
       1166 TCTATTTTAACCTTTTTAAAGTTG-CTTTAGACATA
          1 TCTATCCCAACCTTTTTAAGGTTGTC-TTAGACAGG

                  *                *  *         
       1201 TCTATCTCAACCTTTTTAAGGTTATCCTAGAC-GAG
          1 TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG-G

             *        *        
       1236 TTTATCCCAATCTTTTTAA
          1 TCTATCCCAACCTTTTTAA

       1255 AGGTCGACCT


Statistics
Matches: 236,  Mismatches: 56, Indels: 32
        0.73            0.17        0.10

Matches are distributed among these distances:
  34    2  0.01
  35  116  0.49
  36   56  0.24
  37   12  0.05
  38   29  0.12
  39   20  0.08
  40    1  0.00

ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42


Consensus pattern (35 bp):   
TCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGG

Found at i:1033 original size:71 final size:71

Alignment explanation


    Indices: 906--1123  Score: 229
    Period size: 71  Copynumber: 3.0  Consensus size: 71

        896 AAACTTAAAA

                 *                        *                 * **             
        906 ACAAGATCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGGTCTATCCCATTATTTTTAAGGTTA
          1 ACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACATTTTTAAGGTTA

                  
        971 TCTTAG
         66 TCTTAG

                   *       *                                                 
        977 ACAAGGTTTATCCCAGCCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACATTTTTTAAAGGT
          1 ACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACA-TTTTT-AAGG-

               *    *
       1042 TTACCTTAA
         63 TTATCTTAG

             *  *      * *   *                   *     *        *   *   *   *
       1051 ATAATGTCTATTCTAACATTTTTAAGGTTGCCTTAGATGGGTCAATCCTAACCTTTATAATGTTG
          1 ACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACATTTTTAAGGTTA

                  
       1116 TCTTAG
         66 TCTTAG

              
       1122 AC
          1 AC

       1124 GGCTCTATCT


Statistics
Matches: 119,  Mismatches: 25, Indels: 6
        0.79            0.17        0.04

Matches are distributed among these distances:
  71   53  0.45
  72    8  0.07
  73    8  0.07
  74   50  0.42

ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39


Consensus pattern (71 bp):   
ACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACATTTTTAAGGTTA
TCTTAG

Found at i:1143 original size:109 final size:109

Alignment explanation


    Indices: 993--1196  Score: 250
    Period size: 109  Copynumber: 1.9  Consensus size: 109

        983 TTTATCCCAG

                 *                  *                      *             *   
        993 CCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACATTTTTT-AAAGGTT-TACCTTAAATAAT
          1 CCTTTATAAGGTTGCCTTAGACGGCTCTATCCTAACATTTTTTAAAAAGTTGT--CTTAAACAAT

                                *                         
       1056 GTCTATTCTAACATTTTTAAGGTTGCCTTAGATGGGTCAATCCTAA
         64 GTCTATTCTAACATTTTTAAAGTTGCCTTAGATGGGTCAATCCTAA

                     *    *                *   **                    *       
       1102 CCTTTATAATGTTGTCTTAGACGGCTCTATCTTAATTTTTTTTAAAAAGTTGTCTTAGACAATGT
          1 CCTTTATAAGGTTGCCTTAGACGGCTCTATCCTAACATTTTTTAAAAAGTTGTCTTAAACAATGT

                 *    *             *     
       1167 CTATTTTAACCTTTTTAAAGTTGCTTTAGA
         66 CTATTCTAACATTTTTAAAGTTGCCTTAGA

       1197 CATATCTATC


Statistics
Matches: 79,  Mismatches: 14, Indels: 4
        0.81            0.14        0.04

Matches are distributed among these distances:
 109   72  0.91
 110    6  0.08
 111    1  0.01

ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44


Consensus pattern (109 bp):   
CCTTTATAAGGTTGCCTTAGACGGCTCTATCCTAACATTTTTTAAAAAGTTGTCTTAAACAATGT
CTATTCTAACATTTTTAAAGTTGCCTTAGATGGGTCAATCCTAA

Done.