Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002636.1 Kokia drynarioides strain JFW-HI SEQ_114865, 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: 42384
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:4138 original size:24 final size:24

Alignment explanation


    Indices: 4087--4141  Score: 65
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       4077 TCTTTCGGTT

                 *             *   *
       4087 AAACTATGTTTAATTGTTTTAATT
          1 AAACTCTGTTTAATTGTTTGAATC

                        *        *  
       4111 AAACTCTGTTTATTTGTTTGAGTC
          1 AAACTCTGTTTAATTGTTTGAATC

                   
       4135 AAACTCT
          1 AAACTCT

       4142 TATTAGTCTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49


Consensus pattern (24 bp):   
AAACTCTGTTTAATTGTTTGAATC

Found at i:31769 original size:14 final size:14

Alignment explanation


    Indices: 31750--31778  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      31740 CAGGAAATAT

                          
      31750 TTCTTAGAACCAAC
          1 TTCTTAGAACCAAC

                          
      31764 TTCTTAGAACCAAC
          1 TTCTTAGAACCAAC

             
      31778 T
          1 T

      31779 GGAGCCTAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31


Consensus pattern (14 bp):   
TTCTTAGAACCAAC

Found at i:41594 original size:23 final size:23

Alignment explanation


    Indices: 41546--41671  Score: 130
    Period size: 23  Copynumber: 5.5  Consensus size: 23

      41536 TATACGGAAC

                      *            
      41546 AAACAGAGAGTAC-CAAAGTACT
          1 AAACAGAGAGCACACAAAGTACT

                            *   *  
      41568 -AACAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTACT

                      *            
      41590 AAACAGAGAGTACACAAAGTACT
          1 AAACAGAGAGCACACAAAGTACT

              *                    
      41613 AATCAGAGAGCACACAAAGTACT
          1 AAACAGAGAGCACACAAAGTACT

             **  *          *   *  
      41636 AGTCAAAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTACT

                         
      41659 AATAACAGAGAGC
          1 -A-AACAGAGAGC

      41672 GCGCTAGTGT


Statistics
Matches: 85,  Mismatches: 15, Indels: 5
        0.81            0.14        0.05

Matches are distributed among these distances:
  21   11  0.13
  22    7  0.08
  23   59  0.69
  24    1  0.01
  25    7  0.08

ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12


Consensus pattern (23 bp):   
AAACAGAGAGCACACAAAGTACT

Done.