Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006234.1 Kokia drynarioides strain JFW-HI SEQ_120805, 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: 15555
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30


Found at i:4912 original size:27 final size:27

Alignment explanation


    Indices: 4874--4937  Score: 119
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       4864 CTACCACCAT

                         *             
       4874 TGCTGCCACAGGACAACATTCCTCCAA
          1 TGCTGCCACAGGAAAACATTCCTCCAA

                                       
       4901 TGCTGCCACAGGAAAACATTCCTCCAA
          1 TGCTGCCACAGGAAAACATTCCTCCAA

                      
       4928 TGCTGCCACA
          1 TGCTGCCACA

       4938 AGATTTACCA


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.30, C:0.36, G:0.16, T:0.19


Consensus pattern (27 bp):   
TGCTGCCACAGGAAAACATTCCTCCAA

Found at i:11037 original size:114 final size:115

Alignment explanation


    Indices: 10837--11064  Score: 341
    Period size: 114  Copynumber: 2.0  Consensus size: 115

      10827 CAAAACCTTT

                                                                          *  
      10837 ATCTCAAAATACTTCGACCACCCCTATTATGATTCCATCCACAACTCCATCGTCTTCATCCATAG
          1 ATCTCAAAATACTTCGACCACCCCTATTATGATTCCATCCACAACTCCATCGTCTTCATCCACAG

                                        *        *            
      10902 GCCCGTTTTATTTTTAACGACTAC-GACCAAGACAGATATCACAACATAC
         66 GCCCGTTTTATTTTTAACGACTACAGACAAAGACAGACATCACAACATAC

                  *            *        *      **             *              
      10951 ATCTCATAATACTTCGACCTCCCCTATTGTGATTCTGTCCACAACTCCATTGTCTTCATCCACAG
          1 ATCTCAAAATACTTCGACCACCCCTATTATGATTCCATCCACAACTCCATCGTCTTCATCCACAG

                     *                *      *               
      11016 GCCCGTTTTGTTTTTAACGACTACAGGCAAAGATAGACATCACAACATA
         66 GCCCGTTTTATTTTTAACGACTACAGACAAAGACAGACATCACAACATA

      11065 ATGTTGAAAC


Statistics
Matches: 101,  Mismatches: 12, Indels: 1
        0.89            0.11        0.01

Matches are distributed among these distances:
 114   81  0.80
 115   20  0.20

ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29


Consensus pattern (115 bp):   
ATCTCAAAATACTTCGACCACCCCTATTATGATTCCATCCACAACTCCATCGTCTTCATCCACAG
GCCCGTTTTATTTTTAACGACTACAGACAAAGACAGACATCACAACATAC

Found at i:12814 original size:17 final size:18

Alignment explanation


    Indices: 12794--12833  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      12784 TAAGTTTTAA

                              
      12794 TGCATTTT-TATTATCAC
          1 TGCATTTTATATTATCAC

                      *      *
      12811 TGCATTTTATTTTATCAT
          1 TGCATTTTATATTATCAC

                 
      12829 TGCAT
          1 TGCAT

      12834 CATTTTCTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55


Consensus pattern (18 bp):   
TGCATTTTATATTATCAC

Done.