Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013177.1 Kokia drynarioides strain JFW-HI SEQ_128196, 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: 6413
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--26  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

                                                  
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

         27 CACTGAGATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:3803 original size:50 final size:49

Alignment explanation


    Indices: 3747--3908  Score: 128
    Period size: 50  Copynumber: 3.2  Consensus size: 49

       3737 AGGTAATCTA

                                    *                         
       3747 CCACAAAGGTTTCCCAAACATTACACCACATAGGATTTACAAGCAACCAG
          1 CCACAAAGGTTTCCCAAACATTACGCCACATAGGATTTA-AAGCAACCAG

             *       *   *     *    *          **     * *    * 
       3797 CTACAAAGGCTT-ACAAGATATTATGCCACATAAGCTTTTAACGTAACCTG
          1 CCACAAAGGTTTCCCAA-ACATTACGCCACAT-AGGATTTAAAGCAACCAG

                            *                 *   **        * 
       3847 CCACAAAGGTTTCCCAGACATTACGCCACATAGGCTTTTTAGCTAACCTG
          1 CCACAAAGGTTTCCCAAACATTACGCCACATAGGATTTAAAGC-AACCAG

            *           
       3897 TCACAAAGGTTT
          1 CCACAAAGGTTT

       3909 TACACAAACT


Statistics
Matches: 84,  Mismatches: 24, Indels: 8
        0.72            0.21        0.07

Matches are distributed among these distances:
  49    9  0.11
  50   67  0.80
  51    8  0.10

ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25


Consensus pattern (49 bp):   
CCACAAAGGTTTCCCAAACATTACGCCACATAGGATTTAAAGCAACCAG

Found at i:6206 original size:23 final size:23

Alignment explanation


    Indices: 6128--6316  Score: 130
    Period size: 23  Copynumber: 8.5  Consensus size: 23

       6118 TAAACGGAAC

                      *    *    *  
       6128 AAACAGAGAGTAC-CGAAGTACT
          1 AAACAGAGAGCACACAAAGTGCT

                   *       *       
       6150 AAACAGAAAGCACA-TAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

               *                      
       6172 GGGCAACAGAGAGCACACAAAGTGCT
          1 ---AAACAGAGAGCACACAAAGTGCT

                      *   *        
       6198 AAACAGAGAGTACATAAA--G-T
          1 AAACAGAGAGCACACAAAGTGCT

                  *         *      
       6218 --AC--TGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *                     
       6237 AATCAGAGAGCACA-AGAAGTGCT
          1 AAACAGAGAGCACACA-AAGTGCT

                   *                
       6260 AAACAGAAAGCACA-AGAAGTGCT
          1 AAACAGAGAGCACACA-AAGTGCT

                   *       *       
       6283 AAACAGAAAGCACACGAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

                       
       6306 AAACAGAGAGC
          1 AAACAGAGAGC

       6317 GCGCTAGTGT


Statistics
Matches: 132,  Mismatches: 21, Indels: 27
        0.73            0.12        0.15

Matches are distributed among these distances:
  16    8  0.06
  18    3  0.02
  19    1  0.01
  20    1  0.01
  21    2  0.02
  22   18  0.14
  23   80  0.61
  25   12  0.09
  26    7  0.05

ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11


Consensus pattern (23 bp):   
AAACAGAGAGCACACAAAGTGCT
Done.