Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011793.1 Kokia drynarioides strain JFW-HI SEQ_126788, 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: 15424
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:6623 original size:15 final size:15

Alignment explanation


    Indices: 6600--6636  Score: 56
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       6590 ATTCTCTTAT

                *          
       6600 TCTTTTTCTTCCTTC
          1 TCTTCTTCTTCCTTC

                           
       6615 TCTTCTTCTTCCTTC
          1 TCTTCTTCTTCCTTC

                   
       6630 TCCTTCT
          1 T-CTTCT

       6637 ATTGGTTATC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15   15  0.75
  16    5  0.25

ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62


Consensus pattern (15 bp):   
TCTTCTTCTTCCTTC

Found at i:6633 original size:21 final size:21

Alignment explanation


    Indices: 6591--6636  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       6581 CTTCATTTCA

                         *       
       6591 TTCTCTTATTCTTTTTCTTCC
          1 TTCTCTTATTCTTCTTCTTCC

                   *              
       6612 TTCTCTTCTTCTTCCTTC-TCC
          1 TTCTCTTATTCTT-CTTCTTCC

                
       6633 TTCT
          1 TTCT

       6637 ATTGGTTATC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21   19  0.86
  22    3  0.14

ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63


Consensus pattern (21 bp):   
TTCTCTTATTCTTCTTCTTCC

Found at i:12073 original size:14 final size:13

Alignment explanation


    Indices: 12051--12090  Score: 55
    Period size: 14  Copynumber: 3.0  Consensus size: 13

      12041 TGCAACTTCT

                          
      12051 AAATAAATAAAAGA
          1 AAAT-AATAAAAGA

                          
      12065 AAATCAATAAAAGA
          1 AAAT-AATAAAAGA

                         
      12079 AAATAA-AAAAGA
          1 AAATAATAAAAGA

      12091 TTAGTAAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  12    6  0.24
  13    2  0.08
  14   17  0.68

ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12


Consensus pattern (13 bp):   
AAATAATAAAAGA

Found at i:12121 original size:20 final size:19

Alignment explanation


    Indices: 12078--12123  Score: 67
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      12068 TCAATAAAAG

                               
      12078 AAAATAAAAAAGATTAGTA
          1 AAAATAAAAAAGATTAGTA

                                
      12097 AAAATAAAAAAG-TTAAGTA
          1 AAAATAAAAAAGATT-AGTA

                    
      12116 AGAAATAA
          1 A-AAATAA

      12124 TTGCTACTAC


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  18    2  0.08
  19   17  0.68
  20    6  0.24

ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20


Consensus pattern (19 bp):   
AAAATAAAAAAGATTAGTA
Done.