Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006582.1 Kokia drynarioides strain JFW-HI SEQ_121170, 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: 13976
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:6225 original size:60 final size:60

Alignment explanation


    Indices: 6155--6333  Score: 254
    Period size: 60  Copynumber: 3.0  Consensus size: 60

       6145 TTATGTTCTG

                                              * *                        
       6155 ACCCT-AAACTTTCCAAAAATTCAAATTTAACCCCTAAACTTTCTAAAAAATTA-AATTTA
          1 ACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCT-AAAAATTAGAATTTA

                                         *                   *          
       6214 ACCCTCAAACTTTCCAAAAATTCAAATTTGACCCTTGAACTTTCTAAAATTTAGAATTTA
          1 ACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCTAAAAATTAGAATTTA

                                    *                    *  *    *      
       6274 ACCCTCAAACTTTCCAAAAAATTCCAATTTAACCCTTGAACTTTCCAACAATTTGAATTT
          1 ACCCTCAAACTTTCC-AAAAATTCAAATTTAACCCTTGAACTTTCTAAAAATTAGAATTT

       6334 GCCCTGATTT


Statistics
Matches: 107,  Mismatches: 10, Indels: 4
        0.88            0.08        0.03

Matches are distributed among these distances:
  59   12  0.11
  60   57  0.53
  61   38  0.36

ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34


Consensus pattern (60 bp):   
ACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCTAAAAATTAGAATTTA

Found at i:6306 original size:31 final size:31

Alignment explanation


    Indices: 6155--6321  Score: 186
    Period size: 30  Copynumber: 5.5  Consensus size: 31

       6145 TTATGTTCTG

                                           
       6155 ACCCT-AAACTTTCC-AAAAATTCAAATTTA
          1 ACCCTCAAACTTTCCAAAAAATTCAAATTTA

                           *                
       6184 ACCC-CTAAACTTTCTAAAAAATT-AAATTTA
          1 ACCCTC-AAACTTTCCAAAAAATTCAAATTTA

                                          *
       6214 ACCCTCAAACTTTCC-AAAAATTCAAATTTG
          1 ACCCTCAAACTTTCCAAAAAATTCAAATTTA

                 **         *      *        
       6244 ACCCTTGAACTTT-C-TAAAATTTAGAATTTA
          1 ACCCTCAAACTTTCCAAAAAATTCA-AATTTA

                                    *      
       6274 ACCCTCAAACTTTCCAAAAAATTCCAATTTA
          1 ACCCTCAAACTTTCCAAAAAATTCAAATTTA

                 **          
       6305 ACCCTTGAACTTTCCAA
          1 ACCCTCAAACTTTCCAA

       6322 CAATTTGAAT


Statistics
Matches: 115,  Mismatches: 15, Indels: 14
        0.80            0.10        0.10

Matches are distributed among these distances:
  29   19  0.17
  30   60  0.52
  31   30  0.26
  32    6  0.05

ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32


Consensus pattern (31 bp):   
ACCCTCAAACTTTCCAAAAAATTCAAATTTA

Found at i:6473 original size:20 final size:20

Alignment explanation


    Indices: 6429--6497  Score: 57
    Period size: 22  Copynumber: 3.1  Consensus size: 20

       6419 ATTGAATCCT

                  *  *            
       6429 TTTTATATGCTTGTGTATATTA
          1 TTTTATTTGTTTGT-TAT-TTA

                                
       6451 TTTTATTTGTTTGTTATTTA
          1 TTTTATTTGTTTGTTATTTA

                           *        
       6471 TTTATTCATTTGTTCGGTTATTTA
          1 -TT-TT-ATTTGTT-TGTTATTTA

               
       6495 TTT
          1 TTT

       6498 ACTTAATTTA


Statistics
Matches: 40,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  20    3  0.08
  21    5  0.12
  22   15  0.38
  23    9  0.22
  24    8  0.20

ACGTcount: A:0.17, C:0.04, G:0.12, T:0.67


Consensus pattern (20 bp):   
TTTTATTTGTTTGTTATTTA

Found at i:12340 original size:52 final size:52

Alignment explanation


    Indices: 12183--12365  Score: 228
    Period size: 52  Copynumber: 3.6  Consensus size: 52

      12173 AGCATATTTA

                                            * **           *    
      12183 ATACTCACGATGACACATAGTCATCGGACCTCTTGTTCCGTAAAGGAATCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

             *                     *         *                 *
      12235 ACACTCACGATGACAC--AGTCACCGGACCTCACAATCCGT-AAGGATTCAC
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                   *            *                  *            
      12284 ATACTCAAGATGACACATAGACATCGGACCTCATAATCCATAAAGGATTCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                         **               
      12336 ATACTCACGATGATGCATAGTCATCGGACC
          1 ATACTCACGATGACACATAGTCATCGGACC

      12366 CTTTTCATTT


Statistics
Matches: 109,  Mismatches: 19, Indels: 6
        0.81            0.14        0.04

Matches are distributed among these distances:
  49   22  0.20
  50   18  0.17
  51   19  0.17
  52   50  0.46

ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22


Consensus pattern (52 bp):   
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Done.