Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007962.1 Kokia drynarioides strain JFW-HI SEQ_122610, 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: 9174
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34


Found at i:888 original size:20 final size:22

Alignment explanation


    Indices: 863--913  Score: 67
    Period size: 19  Copynumber: 2.5  Consensus size: 22

        853 TTGATATTAT

                                  
        863 TTAG-AAATTTTA-ATAATACA
          1 TTAGAAAATTTTATATAATACA

                                  
        883 TTAGAAAATTTTATATAAT--A
          1 TTAGAAAATTTTATATAATACA

                        
        903 TTA-AAAATTTT
          1 TTAGAAAATTTT

        914 GGTATCGATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    8  0.28
  20    8  0.28
  21    8  0.28
  22    5  0.17

ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45


Consensus pattern (22 bp):   
TTAGAAAATTTTATATAATACA

Found at i:1521 original size:29 final size:29

Alignment explanation


    Indices: 1468--1533  Score: 91
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1458 CAAAAAATTT

                        **                
       1468 AACTTTTAAGGGTTTTAAATTTTTTTTACC
          1 AACTTTTAAGGGACTTAAATTTTTTTT-CC

                                         
       1498 AACTTTTAA-GGACTTAAATTTTTTTTCC
          1 AACTTTTAAGGGACTTAAATTTTTTTTCC

                     
       1526 AA-TTTTAA
          1 AACTTTTAA

       1534 AAAAATCTAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  27    6  0.18
  28    4  0.12
  29   15  0.44
  30    9  0.26

ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52


Consensus pattern (29 bp):   
AACTTTTAAGGGACTTAAATTTTTTTTCC

Found at i:2880 original size:16 final size:16

Alignment explanation


    Indices: 2852--2890  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       2842 TTGAACCGAG

                            
       2852 ATTTTTGAGATTTTTA
          1 ATTTTTGAGATTTTTA

                             
       2868 ATTTGTTGA-ATTTTTA
          1 ATTT-TTGAGATTTTTA

                   
       2884 ATATTTT
          1 AT-TTTT

       2891 TAATCAAATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  16   15  0.71
  17    6  0.29

ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64


Consensus pattern (16 bp):   
ATTTTTGAGATTTTTA

Found at i:5975 original size:17 final size:17

Alignment explanation


    Indices: 5929--5978  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       5919 TTAAATTTTT

                              
       5929 AAATATTAATCATATAAA
          1 AAATATTAAT-ATATAAA

                               
       5947 AAATTATATAATA-ATAAA
          1 AAA-TAT-TAATATATAAA

                          
       5965 AAATCATTAATATA
          1 AAAT-ATTAATATA

       5979 ATTGAATCTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  17    6  0.21
  18   14  0.50
  19    4  0.14
  20    4  0.14

ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34


Consensus pattern (17 bp):   
AAATATTAATATATAAA
Done.