Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007255.1 Kokia drynarioides strain JFW-HI SEQ_121871, 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: 5990
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:271 original size:12 final size:12

Alignment explanation


    Indices: 244--278  Score: 54
    Period size: 12  Copynumber: 3.0  Consensus size: 12

        234 ATTGTTGTTC

                  *     
        244 TGAACTGTTT-T
          1 TGAACTTTTTGT

                        
        255 TGAACTTTTTGT
          1 TGAACTTTTTGT

                        
        267 TGAACTTTTTGT
          1 TGAACTTTTTGT

        279 AAAGTGTCCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  11    9  0.41
  12   13  0.59

ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57


Consensus pattern (12 bp):   
TGAACTTTTTGT

Found at i:565 original size:11 final size:12

Alignment explanation


    Indices: 544--568  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        534 TGAATTATTT

                        
        544 TTGAACTTTTTG
          1 TTGAACTTTTTG

                        
        556 TTGAACTTTTTG
          1 TTGAACTTTTTG

             
        568 T
          1 T

        569 AAAGTTTCCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60


Consensus pattern (12 bp):   
TTGAACTTTTTG

Found at i:1753 original size:4 final size:4

Alignment explanation


    Indices: 1744--1772  Score: 58
    Period size: 4  Copynumber: 7.2  Consensus size: 4

       1734 ATAATTATTC

                                                
       1744 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
          1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A

       1773 TATATATATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24


Consensus pattern (4 bp):   
ACAT

Found at i:2056 original size:74 final size:73

Alignment explanation


    Indices: 1932--2080  Score: 208
    Period size: 74  Copynumber: 2.0  Consensus size: 73

       1922 ATAATACTAT

                              *                    * * *           *         
       1932 AAATATGCCTCCGGGTACCAAGTCACCTATGTCTCAGGTGTTTGTAAAGGAAACTGTAGGGAAAT
          1 AAATATGCCTCCGGGTACAAAGTCACCTATGTCTCAGGTATCTATAAAGGAAACTATAGGGAAAT

                     
       1997 GAGCTATAA
         66 GAGCTA-AA

                      **                                 *       *           
       2006 AAATATGCCTTTGGGTACAAAGTCACCTATGTCTCAGGTATCTATGAAGGAAATTATAGGGAAAT
          1 AAATATGCCTCCGGGTACAAAGTCACCTATGTCTCAGGTATCTATAAAGGAAACTATAGGGAAAT

                    
       2071 GAGCTAAA
         66 GAGCTAAA

              
       2079 AA
          1 AA

       2081 GCCCAATGTG


Statistics
Matches: 66,  Mismatches: 9, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  73    4  0.06
  74   62  0.94

ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26


Consensus pattern (73 bp):   
AAATATGCCTCCGGGTACAAAGTCACCTATGTCTCAGGTATCTATAAAGGAAACTATAGGGAAAT
GAGCTAAA
Done.