Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014580.1 Kokia drynarioides strain JFW-HI SEQ_129619, 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: 29774
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:9783 original size:18 final size:18

Alignment explanation


    Indices: 9760--9795  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       9750 ACTCACACAG

                              
       9760 ACGCACATGCACATGCAT
          1 ACGCACATGCACATGCAT

                              
       9778 ACGCACATGCACATGCAT
          1 ACGCACATGCACATGCAT

       9796 TTATGTATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17


Consensus pattern (18 bp):   
ACGCACATGCACATGCAT

Found at i:20646 original size:76 final size:78

Alignment explanation


    Indices: 20541--20686  Score: 190
    Period size: 76  Copynumber: 1.9  Consensus size: 78

      20531 AACCCGGTTT

                             *            *   *  *                        *  
      20541 TTCATGTTTTATCGATAGTCTTATACCTTCGCAAGGTTTCAA-GATTCGAGTTTTACTAACAGTT
          1 TTCATGTTTTATCGATAATCTTATACCTTCACAAAGTATCAATG-TTCGAGTTTTACTAACAATT

                          
      20605 TCACTTCGTAAGTA
         65 TCACTTCGTAAGTA

                      *                                            *  *      
      20619 TTCATGTTTTCT-G-TAATCTTATACCTTCACAAAGTATCAATGTTCGAGTTTTATTAGCAATTT
          1 TTCATGTTTTATCGATAATCTTATACCTTCACAAAGTATCAATGTTCGAGTTTTACTAACAATTT

                 
      20682 CACTT
         66 CACTT

      20687 AGTTAGTACT


Statistics
Matches: 59,  Mismatches: 8, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  76   46  0.78
  77    2  0.03
  78   11  0.19

ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43


Consensus pattern (78 bp):   
TTCATGTTTTATCGATAATCTTATACCTTCACAAAGTATCAATGTTCGAGTTTTACTAACAATTT
CACTTCGTAAGTA

Found at i:21179 original size:2 final size:2

Alignment explanation


    Indices: 21172--21198  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      21162 ATTCAACCAT

                                                    
      21172 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      21199 GCAGCAGCAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:27818 original size:22 final size:22

Alignment explanation


    Indices: 27783--27827  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      27773 TCAATTGAGC

                          * *     
      27783 TAAGTAAAATTATTGATATTAT
          1 TAAGTAAAATTATTAACATTAT

                                   
      27805 TAAGT-AAATATATTAACATTAT
          1 TAAGTAAAAT-TATTAACATTAT

             
      27827 T
          1 T

      27828 TTTGGCTATG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21    4  0.20
  22   16  0.80

ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44


Consensus pattern (22 bp):   
TAAGTAAAATTATTAACATTAT

Found at i:28466 original size:17 final size:17

Alignment explanation


    Indices: 28446--28479  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      28436 TATTTAATAA

                   *         
      28446 ATTTATACAATTTTTTT
          1 ATTTATAAAATTTTTTT

                *            
      28463 ATTTTTAAAATTTTTTT
          1 ATTTATAAAATTTTTTT

      28480 TATATAGTCA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68


Consensus pattern (17 bp):   
ATTTATAAAATTTTTTT
Done.