Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005598.1 Kokia drynarioides strain JFW-HI SEQ_119727, 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: 29464
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:2094 original size:48 final size:46

Alignment explanation


    Indices: 2021--2132  Score: 136
    Period size: 46  Copynumber: 2.4  Consensus size: 46

       2011 ATAGTACTAT

                            *   *      *                     
       2021 AATACTAAGATTTTGCGACCTATACAATTGCTATAGTG-ATTCCAATAC
          1 AATACTAAGATTTTGCAACCAATAC-ACT--TATAGTGCATTCCAATAC

                                                         *
       2069 AATACTAAGATTTTGCAACCAATACACTTATAGTGCATTCCAATAT
          1 AATACTAAGATTTTGCAACCAATACACTTATAGTGCATTCCAATAC

             *      *         
       2115 AGTACTAACATTTTGCAA
          1 AATACTAAGATTTTGCAA

       2133 ATGAATAGTG


Statistics
Matches: 57,  Mismatches: 6, Indels: 4
        0.85            0.09        0.06

Matches are distributed among these distances:
  45    7  0.12
  46   25  0.44
  47    2  0.04
  48   23  0.40

ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33


Consensus pattern (46 bp):   
AATACTAAGATTTTGCAACCAATACACTTATAGTGCATTCCAATAC

Found at i:2577 original size:24 final size:24

Alignment explanation


    Indices: 2536--2586  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2526 AGTTTCACTG

                       *            
       2536 AAACAAATAAATAAAGTTTAATTA
          1 AAACAAATAAACAAAGTTTAATTA

                         *          
       2560 AAACAAATAAACAGAGTTTAATTA
          1 AAACAAATAAACAAAGTTTAATTA

               
       2584 AAA
          1 AAA

       2587 GATTATTTCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25


Consensus pattern (24 bp):   
AAACAAATAAACAAAGTTTAATTA

Found at i:9585 original size:3 final size:3

Alignment explanation


    Indices: 9577--9602  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       9567 AGTAAAGCTC

                                              
       9577 TAA TAA TAA TAA TAA TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TA

       9603 TGATTAGCAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:14410 original size:29 final size:29

Alignment explanation


    Indices: 14342--14411  Score: 81
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      14332 AAATTATATA

                   *                     
      14342 TTTTTAATAA-TTTTACTAATTTTTAATT
          1 TTTTTAAAAATTTTTACTAATTTTTAATT

               **  *                      
      14370 TTTAGAACAATTTTTAC-ATATTTTTAATT
          1 TTTTTAAAAATTTTTACTA-ATTTTTAATT

                         
      14399 TTTTTAAAAATTT
          1 TTTTTAAAAATTT

      14412 AAAAATAATT


Statistics
Matches: 34,  Mismatches: 6, Indels: 3
        0.79            0.14        0.07

Matches are distributed among these distances:
  28    8  0.24
  29   26  0.76

ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60


Consensus pattern (29 bp):   
TTTTTAAAAATTTTTACTAATTTTTAATT
Done.