Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008403.1 Kokia drynarioides strain JFW-HI SEQ_123072, 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: 11330
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34

Warning! 14 characters in sequence are not A, C, G, or T


Found at i:82 original size:25 final size:25

Alignment explanation


    Indices: 47--97  Score: 93
    Period size: 25  Copynumber: 2.0  Consensus size: 25

         37 AAAATTTATG

                                     
         47 TTTATAATTATTAGATTTTTAAGTT
          1 TTTATAATTATTAGATTTTTAAGTT

                  *                  
         72 TTTATATTTATTAGATTTTTAAGTT
          1 TTTATAATTATTAGATTTTTAAGTT

             
         97 T
          1 T

         98 GTTTCGATTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63


Consensus pattern (25 bp):   
TTTATAATTATTAGATTTTTAAGTT

Found at i:1681 original size:18 final size:17

Alignment explanation


    Indices: 1658--1696  Score: 51
    Period size: 19  Copynumber: 2.2  Consensus size: 17

       1648 ATAAAAAATT

                       *      
       1658 ATTTTTTAAACTTTTTAA
          1 ATTTTTTAAA-ATTTTAA

                              
       1676 ATTTTTTTAAAATTTTAA
          1 A-TTTTTTAAAATTTTAA

               
       1694 ATT
          1 ATT

       1697 AATAAAAATA


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  17    2  0.11
  18    8  0.42
  19    9  0.47

ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62


Consensus pattern (17 bp):   
ATTTTTTAAAATTTTAA

Found at i:3092 original size:24 final size:24

Alignment explanation


    Indices: 3042--3092  Score: 61
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       3032 CAATCATATT

                                 *  
       3042 TTAAATCTCTAAATTATCACAGAA
          1 TTAAATCTCTAAATTATCACAAAA

                                      
       3066 TTAAATC-CTAAA-TATCACCAAACA
          1 TTAAATCTCTAAATTATCA-CAAA-A

               
       3090 TTA
          1 TTA

       3093 TCTCTTATGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  22    5  0.21
  23    8  0.33
  24   11  0.46

ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31


Consensus pattern (24 bp):   
TTAAATCTCTAAATTATCACAAAA

Found at i:4116 original size:3 final size:3

Alignment explanation


    Indices: 4108--4137  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       4098 TTATCCATAT

                                                   
       4108 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

       4138 AATCAAATAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Done.