Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007901.1 Kokia drynarioides strain JFW-HI SEQ_122542, 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, 638

Length: 1064
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40


Found at i:114 original size:21 final size:21

Alignment explanation


    Indices: 89--148  Score: 59
    Period size: 20  Copynumber: 2.9  Consensus size: 21

         79 TTAAGTCTAT

                                 
         89 TTTTTTTCTTCTTTGAATTGA
          1 TTTTTTTCTTCTTTGAATTGA

                   *  *    *      
        110 -TTTTTTGTTATTTAAAATTGA
          1 TTTTTTTCTTCTTT-GAATTGA

              *   *           
        131 TTCTTTGCTTCTTTGAAT
          1 TTTTTTTCTTCTTTGAAT

        149 CAATTCATTA


Statistics
Matches: 29,  Mismatches: 8, Indels: 4
        0.71            0.20        0.10

Matches are distributed among these distances:
  20   11  0.38
  21    9  0.31
  22    9  0.31

ACGTcount: A:0.18, C:0.08, G:0.10, T:0.63


Consensus pattern (21 bp):   
TTTTTTTCTTCTTTGAATTGA

Found at i:154 original size:21 final size:21

Alignment explanation


    Indices: 45--154  Score: 53
    Period size: 21  Copynumber: 5.2  Consensus size: 21

         35 ATTTTCGTTT

                                 
         45 ATTCTTTGCTTATTTGAATCA
          1 ATTCTTTGCTTATTTGAATCA

               *       *   *       
         66 ATTATTTG-TTGTTTTAAGTCTA
          1 ATTCTTTGCTTATTTGAA-TC-A

            *  *   *   *       **
         88 TTTTTTTTCTTCTTTGAATTG
          1 ATTCTTTGCTTATTTGAATCA

               *            *   **
        109 ATTTTTTG-TTATTTAAAATTG
          1 ATTCTTTGCTTATTT-GAATCA

                       *         
        130 ATTCTTTGCTTCTTTGAATCA
          1 ATTCTTTGCTTATTTGAATCA

                
        151 ATTC
          1 ATTC

        155 ATTATTGTTG


Statistics
Matches: 65,  Mismatches: 19, Indels: 10
        0.69            0.20        0.11

Matches are distributed among these distances:
  20   12  0.18
  21   34  0.52
  22   12  0.18
  23    7  0.11

ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59


Consensus pattern (21 bp):   
ATTCTTTGCTTATTTGAATCA

Found at i:173 original size:45 final size:43

Alignment explanation


    Indices: 45--202  Score: 144
    Period size: 45  Copynumber: 3.7  Consensus size: 43

         35 ATTTTCGTTT

                       *                           *    
         45 ATTCTTTGCTTATTTGAATCAATTA-TTTGTTGTTTTAAGTCT-
          1 ATTCTTTGCTTCTTTGAATCAATTATTTTGTTGTTTTAAAT-TG

                *   *           **           *   *      
         87 ATTTTTTTTCTTCTTTGAATTGATT-TTTTGTTATTTAAAATTG
          1 A-TTCTTTGCTTCTTTGAATCAATTATTTTGTTGTTTTAAATTG

                                                         
        130 ATTCTTTGCTTCTTTGAATCAATTCATTATTGTTGTTTTAAATTG
          1 ATTCTTTGCTTCTTTGAATCAATT-ATT-TTGTTGTTTTAAATTG

             * *       *        *        
        175 ACTATTTGCTTTTTTGAATCCATT-TTTT
          1 ATTCTTTGCTTCTTTGAATCAATTATTTT

        203 CTAGTTTTCT


Statistics
Matches: 92,  Mismatches: 18, Indels: 12
        0.75            0.15        0.10

Matches are distributed among these distances:
  42   23  0.25
  43   33  0.36
  44    2  0.02
  45   34  0.37

ACGTcount: A:0.21, C:0.09, G:0.10, T:0.59


Consensus pattern (43 bp):   
ATTCTTTGCTTCTTTGAATCAATTATTTTGTTGTTTTAAATTG
Done.