Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002458.1 Kokia drynarioides strain JFW-HI SEQ_114578, 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, 872

Length: 1454
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:725 original size:29 final size:28

Alignment explanation


    Indices: 683--863  Score: 132
    Period size: 30  Copynumber: 6.1  Consensus size: 28

        673 TTCGAGGTCG

                                    *     
        683 AAAATGGAGA-TTTTGGAAGTTCAAGGGTA
          1 AAAATGGA-ATTTTTGGAAGTT-AGGGGTA

                                  *       
        712 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
          1 AAAATGGAATTTTTGGAAG-TTAGGGG-TA

                 *                  *       
        742 AAAA-AGAGATTTTATGGAAGTTTGGGGGTAA
          1 AAAATGGA-ATTTT-TGGAAG-TTAGGGGT-A

                     *             *  *  
        773 AAAATGGTATTTTTTGGAAGTTATGGTTA
          1 AAAATGG-AATTTTTGGAAGTTAGGGGTA

                 *                * *     
        802 AAAATAGAATTTTTGGAAGTTTTGAGGTCA
          1 AAAATGGAATTTTTGGAAG-TTAGGGGT-A

                   *       *             
        832 AAAATGGGATTTTTGAAAGTTTAGGGGTA
          1 AAAATGGAATTTTTGGAAG-TTAGGGGTA

               
        861 AAA
          1 AAA

        864 TAAAATTTTT


Statistics
Matches: 122,  Mismatches: 20, Indels: 20
        0.75            0.12        0.12

Matches are distributed among these distances:
  28   12  0.10
  29   37  0.30
  30   43  0.35
  31   24  0.20
  32    5  0.04
  33    1  0.01

ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34


Consensus pattern (28 bp):   
AAAATGGAATTTTTGGAAGTTAGGGGTA

Found at i:777 original size:90 final size:89

Alignment explanation


    Indices: 683--863  Score: 229
    Period size: 90  Copynumber: 2.0  Consensus size: 89

        673 TTCGAGGTCG

                                               *                  *   *      
        683 AAAATGG-AGATTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAAA
          1 AAAATGGTAGATTTTGGAAGTT-AAGGGTAAAAATAGAATTTTTGGAAGTTTCGAGGTCAAAAAA

                       *      *       
        747 GAGATTTTATGGAAGTTTGGGGGTAA
         65 GAGATTTT-TGAAAGTTTAGGGGTAA

                     **            *  *                        *           * 
        773 AAAATGGTATTTTTTGGAAGTTATGGTTAAAAATAGAATTTTTGGAAGTTTTGAGGTCAAAAATG
          1 AAAATGGTAGATTTTGGAAGTTAAGGGTAAAAATAGAATTTTTGGAAGTTTCGAGGTCAAAAAAG

            *                       
        838 GGATTTTTGAAAGTTTAGGGGTAA
         66 AGATTTTTGAAAGTTTAGGGGTAA

              
        862 AA
          1 AA

        864 TAAAATTTTT


Statistics
Matches: 78,  Mismatches: 12, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
  89   17  0.22
  90   49  0.63
  91   12  0.15

ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34


Consensus pattern (89 bp):   
AAAATGGTAGATTTTGGAAGTTAAGGGTAAAAATAGAATTTTTGGAAGTTTCGAGGTCAAAAAAG
AGATTTTTGAAAGTTTAGGGGTAA
Done.