Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008491.1 Kokia drynarioides strain JFW-HI SEQ_123166, 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: 4631
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:209 original size:27 final size:24

Alignment explanation


    Indices: 162--219  Score: 62
    Period size: 27  Copynumber: 2.3  Consensus size: 24

        152 AGAATTTTTA

                   *             *  
        162 TAATTTTTTTAAAATATAAAATTT
          1 TAATTTTATTAAAATATAAAAATT

                                       
        186 TAATTTTATTATAAATATTAAAAAATT
          1 TAATTTTATTA-AAATA-T-AAAAATT

            *      
        213 GAATTTT
          1 TAATTTT

        220 TGAAAATTAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  24   10  0.36
  25    5  0.18
  26    1  0.04
  27   12  0.43

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52


Consensus pattern (24 bp):   
TAATTTTATTAAAATATAAAAATT

Found at i:584 original size:46 final size:46

Alignment explanation


    Indices: 525--626  Score: 177
    Period size: 46  Copynumber: 2.2  Consensus size: 46

        515 ACTAATATTT

                                        *                  
        525 TTTTATTTTCAAGTAATTGAATTAGATATTTTTCAAAATCAAGGTTG
          1 TTTTA-TTTCAAGTAATTGAATTAGATAATTTTCAAAATCAAGGTTG

                                    *                     
        572 TTTTATTTCAAGTAATTGAATTAGCTAATTTTCAAAATCAAGGTTG
          1 TTTTATTTCAAGTAATTGAATTAGATAATTTTCAAAATCAAGGTTG

                     
        618 TTTTATTTC
          1 TTTTATTTC

        627 TTGTTGTTGT


Statistics
Matches: 53,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  46   48  0.91
  47    5  0.09

ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48


Consensus pattern (46 bp):   
TTTTATTTCAAGTAATTGAATTAGATAATTTTCAAAATCAAGGTTG

Found at i:4128 original size:22 final size:22

Alignment explanation


    Indices: 4103--4155  Score: 79
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4093 GTGTTAGGGA

                                  
       4103 AACAAAAGCACACACAATGCTG
          1 AACAAAAGCACACACAATGCTG

                *           *     
       4125 AACAGAAGCACACACAGTGCTG
          1 AACAAAAGCACACACAATGCTG

                *    
       4147 AACATAAGC
          1 AACAAAAGC

       4156 GCGCTAGCGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   28  1.00

ACGTcount: A:0.47, C:0.26, G:0.17, T:0.09


Consensus pattern (22 bp):   
AACAAAAGCACACACAATGCTG
Done.