Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005953.1 Kokia drynarioides strain JFW-HI SEQ_120346, 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: 14871
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36


Found at i:52 original size:20 final size:20

Alignment explanation


    Indices: 5--58  Score: 56
    Period size: 20  Copynumber: 2.7  Consensus size: 20

          1 AAGT

                    *        *  
          5 GTTAAAATGATTTTGACTTA
          1 GTTAAAATAATTTTGACATA

               *    *           
         25 GTTCAAATTATTTTGACAT-
          1 GTTAAAATAATTTTGACATA

                           
         44 GTTTAAAATAATTTT
          1 G-TTAAAATAATTTT

         59 AACTTGATTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  19    1  0.04
  20   27  0.96

ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48


Consensus pattern (20 bp):   
GTTAAAATAATTTTGACATA

Found at i:10679 original size:20 final size:20

Alignment explanation


    Indices: 10656--10693  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      10646 ATAAAACTAT

                   *            
      10656 AGTTGTATCGATAGAAGTGG
          1 AGTTGTACCGATAGAAGTGG

                      *       
      10676 AGTTGTACCGGTAGAAGT
          1 AGTTGTACCGATAGAAGT

      10694 CTCATTGGAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.29, C:0.08, G:0.34, T:0.29


Consensus pattern (20 bp):   
AGTTGTACCGATAGAAGTGG

Found at i:14871 original size:20 final size:20

Alignment explanation


    Indices: 14792--14871  Score: 58
    Period size: 20  Copynumber: 4.0  Consensus size: 20

      14782 GGCCTAGAGC

                     *          *
      14792 TATTTTGACTTGTTTGAAAAA
          1 TATTTTGACATGTTT-AAAAT

            *                    
      14813 CATTTTGA-A-GTGTTAAAAT
          1 TATTTTGACATGT-TTAAAAT

            *        *      *    
      14832 GATTTTGACTTAG-TTCAAAT
          1 TATTTTGACAT-GTTTAAAAT

                                
      14852 TATTTTGACATGTTTAAAAT
          1 TATTTTGACATGTTTAAAAT


Statistics
Matches: 45,  Mismatches: 9, Indels: 11
        0.69            0.14        0.17

Matches are distributed among these distances:
  19   14  0.31
  20   23  0.51
  21    7  0.16
  22    1  0.02

ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46


Consensus pattern (20 bp):   
TATTTTGACATGTTTAAAAT
Done.