Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007792.1 Kokia drynarioides strain JFW-HI SEQ_122426, 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: 12916
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:1963 original size:15 final size:15

Alignment explanation


    Indices: 1929--1960  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       1919 ATGATTCATG

                           
       1929 AAATTTAATTATTTT
          1 AAATTTAATTATTTT

                           
       1944 AAATTTAATT-TTTT
          1 AAATTTAATTATTTT

               
       1958 AAA
          1 AAA

       1961 ATTCCATAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.41
  15   10  0.59

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (15 bp):   
AAATTTAATTATTTT

Found at i:2709 original size:21 final size:22

Alignment explanation


    Indices: 2684--2729  Score: 76
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       2674 ACTTAACATA

                                  
       2684 ATAATATTTTATAAGTA-ATAT
          1 ATAATATTTTATAAGTATATAT

                         *        
       2705 ATAATATTTTATATGTATATAT
          1 ATAATATTTTATAAGTATATAT

               
       2727 ATA
          1 ATA

       2730 TAAAGAAAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   16  0.70
  22    7  0.30

ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50


Consensus pattern (22 bp):   
ATAATATTTTATAAGTATATAT

Found at i:3548 original size:11 final size:11

Alignment explanation


    Indices: 3517--3588  Score: 72
    Period size: 11  Copynumber: 6.4  Consensus size: 11

       3507 ATTTATGATT

                *      
       3517 TGAATATGAAA
          1 TGAAAATGAAA

               * *     
       3528 TGACATTGAAA
          1 TGAAAATGAAA

               *        
       3539 TGAGAATGAAAA
          1 TGAAAATG-AAA

                     * 
       3551 TGAAAATGATA
          1 TGAAAATGAAA

                        
       3562 TGAAAATAGAAA
          1 TGAAAAT-GAAA

              *        
       3574 TGGAAATGAAA
          1 TGAAAATGAAA

                
       3585 TGAA
          1 TGAA

       3589 TGTTATAGTC


Statistics
Matches: 49,  Mismatches: 10, Indels: 4
        0.78            0.16        0.06

Matches are distributed among these distances:
  11   30  0.61
  12   19  0.39

ACGTcount: A:0.56, C:0.01, G:0.21, T:0.22


Consensus pattern (11 bp):   
TGAAAATGAAA

Found at i:3554 original size:17 final size:17

Alignment explanation


    Indices: 3534--3588  Score: 53
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       3524 GAAATGACAT

                             
       3534 TGAAATGAGAATGAAAA
          1 TGAAATGAGAATGAAAA

                      *       
       3551 TGAAAATGA-TATGAAAA
          1 TG-AAATGAGAATGAAAA

                               
       3568 TAGAAATG-GAAATG-AAA
          1 T-GAAATGAG-AATGAAAA

                
       3585 TGAA
          1 TGAA

       3589 TGTTATAGTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 9
        0.74            0.05        0.21

Matches are distributed among these distances:
  16    3  0.09
  17   19  0.59
  18   10  0.31

ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20


Consensus pattern (17 bp):   
TGAAATGAGAATGAAAA

Found at i:3564 original size:23 final size:23

Alignment explanation


    Indices: 3519--3588  Score: 70
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       3509 TTATGATTTG

                        * *        *
       3519 AATATGAAATGACATTGAAATGAG
          1 AATA-GAAATGAAAATGAAATGAA

                              *     
       3543 AAT-GAAAATGAAAATGATATGAA
          1 AATAG-AAATGAAAATGAAATGAA

                      *            
       3566 AATAGAAATGGAAATGAAATGAA
          1 AATAGAAATGAAAATGAAATGAA

       3589 TGTTATAGTC


Statistics
Matches: 38,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  22    1  0.03
  23   33  0.87
  24    4  0.11

ACGTcount: A:0.57, C:0.01, G:0.20, T:0.21


Consensus pattern (23 bp):   
AATAGAAATGAAAATGAAATGAA
Done.