Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009748.1 Kokia drynarioides strain JFW-HI SEQ_124467, 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: 27387
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34

Warning! 67 characters in sequence are not A, C, G, or T


Found at i:977 original size:13 final size:13

Alignment explanation


    Indices: 959--983  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        949 TGTTTCTTTC

                         
        959 TTAAAAAAAAAAA
          1 TTAAAAAAAAAAA

                        
        972 TTAAAAAAAAAA
          1 TTAAAAAAAAAA

        984 GTATTTCTTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (13 bp):   
TTAAAAAAAAAAA

Found at i:5771 original size:36 final size:36

Alignment explanation


    Indices: 5724--5797  Score: 148
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       5714 ATATGGGTAA

                                                
       5724 ATTACTTAGCTAGAAACAAGAATTGATTTTGGTTTT
          1 ATTACTTAGCTAGAAACAAGAATTGATTTTGGTTTT

                                                
       5760 ATTACTTAGCTAGAAACAAGAATTGATTTTGGTTTT
          1 ATTACTTAGCTAGAAACAAGAATTGATTTTGGTTTT

              
       5796 AT
          1 AT

       5798 CTTGTGCACT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   38  1.00

ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42


Consensus pattern (36 bp):   
ATTACTTAGCTAGAAACAAGAATTGATTTTGGTTTT

Found at i:25527 original size:17 final size:16

Alignment explanation


    Indices: 25484--25530  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

      25474 AAAATTGATT

                       *  * 
      25484 AAAATAAA-AATATCA
          1 AAAATAAATAAAATAA

                            
      25499 AAAATAAATAAAATAA
          1 AAAATAAATAAAATAA

                    *       
      25515 AAAATAGAGTAAAATA
          1 AAAATA-AATAAAATA

      25531 GACAAAGACA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  15    8  0.30
  16   11  0.41
  17    8  0.30

ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19


Consensus pattern (16 bp):   
AAAATAAATAAAATAA

Found at i:25738 original size:45 final size:45

Alignment explanation


    Indices: 25669--25758  Score: 171
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      25659 TCACCATCCT

                               *                         
      25669 TTGTGTAAATTAATTGTGGGAACATATATTATGCTCTTGTCATTA
          1 TTGTGTAAATTAATTGTGGCAACATATATTATGCTCTTGTCATTA

                                                         
      25714 TTGTGTAAATTAATTGTGGCAACATATATTATGCTCTTGTCATTA
          1 TTGTGTAAATTAATTGTGGCAACATATATTATGCTCTTGTCATTA

      25759 CATTTAGAGC


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44


Consensus pattern (45 bp):   
TTGTGTAAATTAATTGTGGCAACATATATTATGCTCTTGTCATTA
Done.