Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006808.1 Kokia drynarioides strain JFW-HI SEQ_121407, 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: 24584
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:7906 original size:2 final size:2

Alignment explanation


    Indices: 7899--7931  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       7889 AGTTTTTATA

                                                             
       7899 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

       7932 TTTACTATCT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:13845 original size:17 final size:17

Alignment explanation


    Indices: 13823--13857  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      13813 ACACTCCGAA

                             
      13823 TTTATTTCTTTCTTTCT
          1 TTTATTTCTTTCTTTCT

                       *     
      13840 TTTATTTCTTTTTTTCT
          1 TTTATTTCTTTCTTTCT

             
      13857 T
          1 T

      13858 CTTCTTCTTC


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

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80


Consensus pattern (17 bp):   
TTTATTTCTTTCTTTCT

Found at i:14633 original size:16 final size:16

Alignment explanation


    Indices: 14595--14641  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

      14585 TTCTAGACAT

                *       *   
      14595 ATAATAAATAAATA-A
          1 ATAAAAAATAAAAATA

                             
      14610 ATAGAAAAATAAAAATA
          1 ATA-AAAAATAAAAATA

                   *       
      14627 ATAAAAATTAAAAAT
          1 ATAAAAAATAAAAAT

      14642 TGGGTTGTCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  15    3  0.11
  16   20  0.74
  17    4  0.15

ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23


Consensus pattern (16 bp):   
ATAAAAAATAAAAATA

Found at i:20196 original size:26 final size:26

Alignment explanation


    Indices: 20166--20220  Score: 110
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      20156 AGAGCTTTAA

                                      
      20166 CTTACCCTCCTATTAGCATTTAATAC
          1 CTTACCCTCCTATTAGCATTTAATAC

                                      
      20192 CTTACCCTCCTATTAGCATTTAATAC
          1 CTTACCCTCCTATTAGCATTTAATAC

               
      20218 CTT
          1 CTT

      20221 TAATCAATGG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.25, C:0.31, G:0.04, T:0.40


Consensus pattern (26 bp):   
CTTACCCTCCTATTAGCATTTAATAC

Found at i:21149 original size:19 final size:20

Alignment explanation


    Indices: 21127--21172  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      21117 TTTTATAAAC

                                
      21127 ATTTTGAA-TTTTAAAAATT
          1 ATTTTGAATTTTTAAAAATT

                 *       *      
      21146 ATTTTCAATTTTTGAAAATT
          1 ATTTTGAATTTTTAAAAATT

                   
      21166 ATTTTGA
          1 ATTTTGA

      21173 TTATTTTGTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  19    7  0.30
  20   16  0.70

ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54


Consensus pattern (20 bp):   
ATTTTGAATTTTTAAAAATT

Found at i:21338 original size:9 final size:9

Alignment explanation


    Indices: 21319--21359  Score: 55
    Period size: 9  Copynumber: 4.6  Consensus size: 9

      21309 TATTCAAGTC

                 *   
      21319 AACTCGAAT
          1 AACTCAAAT

                  *  
      21328 AACTCATAT
          1 AACTCAAAT

              *      
      21337 AATTCAAAT
          1 AACTCAAAT

                     
      21346 AACTCAAAT
          1 AACTCAAAT

                 
      21355 AACTC
          1 AACTC

      21360 GATTTGGTTA


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   9   27  1.00

ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27


Consensus pattern (9 bp):   
AACTCAAAT
Done.