Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010451.1 Kokia drynarioides strain JFW-HI SEQ_125347, 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: 38497
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:107 original size:4 final size:4

Alignment explanation


    Indices: 100--149  Score: 73
    Period size: 4  Copynumber: 12.2  Consensus size: 4

         90 TCATTCTTCC

                                                  *              *      
        100 TTCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT
          1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT

             
        149 T
          1 T

        150 CATTTTTCGT


Statistics
Matches: 41,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
   4   38  0.93
   5    3  0.07

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (4 bp):   
TTCT

Found at i:155 original size:11 final size:12

Alignment explanation


    Indices: 107--156  Score: 50
    Period size: 12  Copynumber: 4.2  Consensus size: 12

         97 TCCTTCTTTC

                        
        107 TTTCTTTC-TTT
          1 TTTCTTTCATTT

                      *   
        118 CTTTCTTTCTCTTT
          1 -TTTCTTTC-ATTT

                    *   
        132 TTTCTTTCTTTT
          1 TTTCTTTCATTT

                        
        144 TTTC-TTCATTT
          1 TTTCTTTCATTT

              
        155 TT
          1 TT

        157 CGTTGGTCCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 5
        0.83            0.05        0.12

Matches are distributed among these distances:
  11    8  0.24
  12   15  0.44
  13    8  0.24
  14    3  0.09

ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78


Consensus pattern (12 bp):   
TTTCTTTCATTT

Found at i:4719 original size:112 final size:112

Alignment explanation


    Indices: 4575--4800  Score: 362
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       4565 ATGAATTAAT

                                                                      *      
       4575 TGTTGTAACTGTAATTGTCTTGAAATAGAACAAAATCTATTTTAATAAAAAATAACATCTATTAA
          1 TGTTGTAACTGTAATTGTCTTGAAATAGAACAAAATCTATTTTAATAAAAAATAACATATATTAA

                                        *    *             
       4640 TTCAATAACAATATTAATTGAAATTGAATCATTTACTTCAATTACCA
         66 TTCAATAACAATATTAATTGAAATTGAAGCATTAACTTCAATTACCA

                  * *                                  *  *       *          
       4687 TGTTGTGATTGTAATTGTCTTGAAATAGAACAAAATCTATTTTCATCAAAAATAGCATATATTAA
          1 TGTTGTAACTGTAATTGTCTTGAAATAGAACAAAATCTATTTTAATAAAAAATAACATATATTAA

                  *                            *           
       4752 TTCAATGACAATATTAATTGAAATTGAAGCATTAAGTTCAATTACCA
         66 TTCAATAACAATATTAATTGAAATTGAAGCATTAACTTCAATTACCA

              
       4799 TG
          1 TG

       4801 AATCTATATG


Statistics
Matches: 104,  Mismatches: 10, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 112  104  1.00

ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37


Consensus pattern (112 bp):   
TGTTGTAACTGTAATTGTCTTGAAATAGAACAAAATCTATTTTAATAAAAAATAACATATATTAA
TTCAATAACAATATTAATTGAAATTGAAGCATTAACTTCAATTACCA

Found at i:37517 original size:20 final size:21

Alignment explanation


    Indices: 37486--37529  Score: 72
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      37476 AGAAAAAAAT

                                 
      37486 TATTTAAATTTTAATATAATA
          1 TATTTAAATTTTAATATAATA

                        *        
      37507 TATTT-AATTTTTATATAATA
          1 TATTTAAATTTTAATATAATA

               
      37527 TAT
          1 TAT

      37530 AAAAGAAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20   17  0.77
  21    5  0.23

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (21 bp):   
TATTTAAATTTTAATATAATA
Done.