Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001132.1 Kokia drynarioides strain JFW-HI SEQ_112422, 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, 923

Length: 1539
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30


Found at i:1115 original size:28 final size:30

Alignment explanation


    Indices: 1062--1122  Score: 90
    Period size: 29  Copynumber: 2.1  Consensus size: 30

       1052 ATCGGAGTTC

                     *                    
       1062 AAAATGAGACTTTTCGGATTCTCGGGGG-G
          1 AAAATGAGAATTTTCGGATTCTCGGGGGTG

                   *                      
       1091 AAAATGATAATTTT-GGATTCTCGGGGGTG
          1 AAAATGAGAATTTTCGGATTCTCGGGGGTG

               
       1120 AAA
          1 AAA

       1123 CGGTAATTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  28   13  0.45
  29   16  0.55

ACGTcount: A:0.30, C:0.10, G:0.31, T:0.30


Consensus pattern (30 bp):   
AAAATGAGAATTTTCGGATTCTCGGGGGTG

Found at i:1129 original size:28 final size:28

Alignment explanation


    Indices: 1072--1134  Score: 83
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       1062 AAAATGAGAC

                                   *     
       1072 TTTTCGGATTCTCGGGGGGAAAATGATAA
          1 TTTT-GGATTCTCGGGGGGAAAACGATAA

                                     *   
       1101 TTTTGGATTCTCGGGGGTG-AAACGGTAA
          1 TTTTGGATTCTCGGGGG-GAAAACGATAA

                  
       1129 TTTTGG
          1 TTTTGG

       1135 GAAATTCGAG


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  28   26  0.84
  29    5  0.16

ACGTcount: A:0.22, C:0.10, G:0.33, T:0.35


Consensus pattern (28 bp):   
TTTTGGATTCTCGGGGGGAAAACGATAA

Found at i:1212 original size:30 final size:30

Alignment explanation


    Indices: 1139--1372  Score: 191
    Period size: 29  Copynumber: 7.9  Consensus size: 30

       1129 TTTTGGGAAA

                *   *        *             
       1139 TTCGAGGTCAAAAATGGGATTTTT-AGAAG-
          1 TTCGGGGTTAAAAATGGAATTTTTGA-AAGT

                                      * *  
       1168 TTCGAGGG-TAAAAATGGAATTTTTGGAGGT
          1 TTCG-GGGTTAAAAATGGAATTTTTGAAAGT

                                         * 
       1198 TTCGGGGTTAAAAAT-GAGATTTTTGAAAAT
          1 TTCGGGGTTAAAAATGGA-ATTTTTGAAAGT

              *                           
       1228 TTAGGGG-TAAAAATGGAATTTTTGAAAGT
          1 TTCGGGGTTAAAAATGGAATTTTTGAAAGT

              * *             *             
       1257 TTTGAGGTCT-AAAATGGGA-TTTTGTAAAGT
          1 TTCGGGGT-TAAAAATGGAATTTTTG-AAAGT

                   *       *              
       1287 TT-GGGGGTAAAAATAGAATTTTTGAAAGT
          1 TTCGGGGTTAAAAATGGAATTTTTGAAAGT

                *              *      *    
       1316 TTCGAGGTTAAAAATGGGATTTTTTGGAAG-
          1 TTCGGGGTTAAAAAT-GGAATTTTTGAAAGT

                 *                      
       1346 TTCAGCGG-TAAAAATGGAATTTTTGAA
          1 TTC-GGGGTTAAAAATGGAATTTTTGAA

       1373 CAATTTAGGG


Statistics
Matches: 166,  Mismatches: 25, Indels: 28
        0.76            0.11        0.13

Matches are distributed among these distances:
  28    1  0.01
  29   80  0.48
  30   70  0.42
  31   15  0.09

ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35


Consensus pattern (30 bp):   
TTCGGGGTTAAAAATGGAATTTTTGAAAGT

Found at i:1212 original size:59 final size:59

Alignment explanation


    Indices: 1139--1372  Score: 278
    Period size: 59  Copynumber: 3.9  Consensus size: 59

       1129 TTTTGGGAAA

                    *                                             * *  
       1139 TTCGAGGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAGGT
          1 TTCGAGGTTAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT

                *           *         *  *  *                           
       1198 TTCGGGGTTAAAAATGAGATTTTTGAAAATTTAG-GGGTAAAAATGGAATTTTTGAAAGT
          1 TTCGAGGTTAAAAATGGGATTTTT-AGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT

              *                              * *          *              
       1257 TTTGAGGTCT-AAAATGGGATTTTGTA-AAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT
          1 TTCGAGGT-TAAAAATGGGATTTT-TAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT

                                     *                                
       1316 TTCGAGGTTAAAAATGGGATTTTTTGGAAGTTC-AGCGGTAAAAATGGAATTTTTGAA
          1 TTCGAGGTTAAAAATGGGA-TTTTTAGAAGTTCGAG-GGTAAAAATGGAATTTTTGAA

       1373 CAATTTAGGG


Statistics
Matches: 148,  Mismatches: 19, Indels: 15
        0.81            0.10        0.08

Matches are distributed among these distances:
  58    6  0.04
  59  105  0.71
  60   37  0.25

ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35


Consensus pattern (59 bp):   
TTCGAGGTTAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT

Done.