Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011186.1 Kokia drynarioides strain JFW-HI SEQ_126162, 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, 685

Length: 1142
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42


Found at i:610 original size:30 final size:30

Alignment explanation


    Indices: 574--680  Score: 105
    Period size: 30  Copynumber: 3.6  Consensus size: 30

        564 TAAACTTGGC

                     *                    
        574 TAATTAATTTTCAAAATATAATATACAAAA
          1 TAATTAATTATCAAAATATAATATACAAAA

                                      *** 
        604 TAATTAATTATC-AAA-ATAATAT-CCCCA
          1 TAATTAATTATCAAAATATAATATACAAAA

                         *              *    
        631 TCATATT-ATTGACCAAAATATAATATAAAAAA
          1 T-A-ATTAATT-ATCAAAATATAATATACAAAA

                              
        663 TAATTAATTATCAAAATA
          1 TAATTAATTATCAAAATA

        681 ATATCCCCAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 14
        0.71            0.12        0.17

Matches are distributed among these distances:
  27    3  0.05
  28   11  0.18
  29    8  0.13
  30   25  0.42
  31   11  0.18
  32    2  0.03

ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35


Consensus pattern (30 bp):   
TAATTAATTATCAAAATATAATATACAAAA

Found at i:618 original size:16 final size:16

Alignment explanation


    Indices: 574--623  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

        564 TAAACTTGGC

                     *      
        574 TAATTAATTTTCAAAA
          1 TAATTAATTATCAAAA

                             
        590 T-A-TAA-TATACAAAA
          1 TAATTAATTAT-CAAAA

                            
        604 TAATTAATTATCAAAA
          1 TAATTAATTATCAAAA

                
        620 TAAT
          1 TAAT

        624 ATCCCCATCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  13    2  0.07
  14    9  0.31
  15    2  0.07
  16   13  0.45
  17    3  0.10

ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38


Consensus pattern (16 bp):   
TAATTAATTATCAAAA

Found at i:647 original size:29 final size:28

Alignment explanation


    Indices: 610--708  Score: 76
    Period size: 29  Copynumber: 3.4  Consensus size: 28

        600 AAAATAATTA

                *                       
        610 ATTATCAAAATAATATCCCCATCATATT
          1 ATTACCAAAATAATATCCCCATCATATT

                                 ** **      
        638 ATTGACCAAAATATAATAT--AAAAAATAATT
          1 ATT-ACC-AAA-ATAATATCCCCATCAT-ATT

                 *                       
        668 AATTATCAAAATAATATCCCCATCATATT
          1 -ATTACCAAAATAATATCCCCATCATATT

                        
        697 ATTTACCAAAAT
          1 A-TTACCAAAAT

        709 GGTACAAAAT


Statistics
Matches: 52,  Mismatches: 11, Indels: 15
        0.67            0.14        0.19

Matches are distributed among these distances:
  28   11  0.21
  29   20  0.38
  30   11  0.21
  31   10  0.19

ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33


Consensus pattern (28 bp):   
ATTACCAAAATAATATCCCCATCATATT

Found at i:648 original size:59 final size:59

Alignment explanation


    Indices: 585--708  Score: 230
    Period size: 59  Copynumber: 2.1  Consensus size: 59

        575 AATTAATTTT

                          *                                            
        585 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
          1 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC

                                                                    *  
        644 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTTAC
          1 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC

                  
        703 CAAAAT
          1 CAAAAT

        709 GGTACAAAAT


Statistics
Matches: 63,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  59   63  1.00

ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32


Consensus pattern (59 bp):   
CAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
Done.