Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010716.1 Kokia drynarioides strain JFW-HI SEQ_125666, 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: 3793
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2961 original size:96 final size:96

Alignment explanation


    Indices: 2777--2968  Score: 228
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       2767 TCTTTRCGAA

                     *                     **        *                      *
       2777 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTCGTAAGTTAAGGCGCAATATTTCG
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCA

            *  *         *                 
       2842 GAATCGAAGATAAGGAAACATTGCCTCGATT
         66 AAAACGAAGATAAAGAAACATTGCCTCGATT

                *           *                           *                    
       2873 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTC
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTC

                                 *            
       2937 AAAACACGAA-ATAAA-AGAATATTGCCTCGATT
         65 AAAA-ACGAAGATAAAGA-AACATTGCCTCGATT

       2969 TTAAAGTTTT


Statistics
Matches: 81,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  95    2  0.02
  96   75  0.93
  97    4  0.05

ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29


Consensus pattern (96 bp):   
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCA
AAAACGAAGATAAAGAAACATTGCCTCGATT

Found at i:3277 original size:59 final size:59

Alignment explanation


    Indices: 3180--3507  Score: 450
    Period size: 59  Copynumber: 5.6  Consensus size: 59

       3170 TTCGGATGTG

                  *          *    *                       *       *      
       3180 CGGGGGCAAAATGGT-AGTTTTGGTAA-GTTT-GGTGTCAAAAATGAGATTTTTTGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAG-AAGGTTTAGG-GTCAAAAATGGGATTTTTGGAAGTT

                                     *    *                            
       3238 CGGGGGTAAAATGGTAATTTTTAGATGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT

             *                             *     *                  *   
       3297 -TGGGGTAAAATGGTAATTTTTAGAAGG-TTCGAGGTAAAAAATGGGATTTTTGGAGGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAG-GGTCAAAAATGGGATTTTTGGAAGTT

                      *                              *                 
       3355 CGGGGGTAAATTGGTAATTTTTAGAAGGTTTAGGGTCAAAATTGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT

            *                        *     *                           
       3414 TGGGGGTAAAATGGTAATTTTTAGATGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT

                                               
       3473 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGG
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGG

       3508 ACCTCTAGGG


Statistics
Matches: 237,  Mismatches: 27, Indels: 11
        0.86            0.10        0.04

Matches are distributed among these distances:
  57    2  0.01
  58   64  0.27
  59  166  0.70
  60    5  0.02

ACGTcount: A:0.28, C:0.03, G:0.33, T:0.35


Consensus pattern (59 bp):   
CGGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT

Done.