Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006474.1 Kokia drynarioides strain JFW-HI SEQ_121057, 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: 15913
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:4178 original size:18 final size:18

Alignment explanation


    Indices: 4157--4205  Score: 62
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       4147 TATGAAATCT

                      * *     
       4157 TTAATAAAATTATATTTA
          1 TTAATAAAATAAAATTTA

                              
       4175 TTAATAAAATAAAATTTA
          1 TTAATAAAATAAAATTTA

                  *      
       4193 TTTAATTAAATAA
          1 -TTAATAAAATAA

       4206 CCTAAAATTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  18   16  0.59
  19   11  0.41

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (18 bp):   
TTAATAAAATAAAATTTA

Found at i:4187 original size:23 final size:25

Alignment explanation


    Indices: 4159--4218  Score: 81
    Period size: 23  Copynumber: 2.5  Consensus size: 25

       4149 TGAAATCTTT

                                     
       4159 AATAAAATTATATTT-ATT-AATAA
          1 AATAAAATTATATTTAATTAAATAA

                                     
       4182 AATAAAATT-TATTTAATTAAATAA
          1 AATAAAATTATATTTAATTAAATAA

            **           
       4206 CCTAAAATTATAT
          1 AATAAAATTATAT

       4219 ATTTATAATC


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  22    5  0.16
  23   12  0.38
  24   12  0.38
  25    3  0.09

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (25 bp):   
AATAAAATTATATTTAATTAAATAA

Found at i:4644 original size:22 final size:22

Alignment explanation


    Indices: 4592--4644  Score: 52
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4582 ATTTTTATTA

                           **     
       4592 TTATTATTTTACTATTGTTTTG
          1 TTATTATTTTACTATCATTTTG

            * * *     *           
       4614 ATGTCATTTTGCTATCATTTTG
          1 TTATTATTTTACTATCATTTTG

                     
       4636 TTATTATTT
          1 TTATTATTT

       4645 GGTTATTATA


Statistics
Matches: 22,  Mismatches: 9, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.19, C:0.08, G:0.09, T:0.64


Consensus pattern (22 bp):   
TTATTATTTTACTATCATTTTG

Found at i:9867 original size:21 final size:21

Alignment explanation


    Indices: 9830--9883  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       9820 TTATATTTTA

                   *   *         
       9830 AAAAAAAGTTATA-AATAT-T
          1 AAAAAAATTTAAAGAATATAT

                                  
       9849 AAAAAAATTCTAAAGAATATAT
          1 AAAAAAATT-TAAAGAATATAT

               *         
       9871 AAAGAAATTTAAA
          1 AAAAAAATTTAAA

       9884 ATTAAAAAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  19    8  0.28
  20    3  0.10
  21    9  0.31
  22    9  0.31

ACGTcount: A:0.65, C:0.02, G:0.06, T:0.28


Consensus pattern (21 bp):   
AAAAAAATTTAAAGAATATAT

Found at i:14181 original size:2 final size:2

Alignment explanation


    Indices: 14174--14214  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      14164 AATTATTAAA

                                                                         
      14174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      14215 AAATAACAAC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.