Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010079.1 Kokia drynarioides strain JFW-HI SEQ_124858, 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: 4351
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29


Found at i:253 original size:30 final size:29

Alignment explanation


    Indices: 194--328  Score: 157
    Period size: 29  Copynumber: 4.6  Consensus size: 29

        184 CCTTAAGCTG

                                         
        194 TCCAAAAATTCCATTTTTAGCCCCGAACT
          1 TCCAAAAATTCCATTTTTAGCCCCGAACT

                     *                     
        223 TCCAAAAATCCCATTTTTTA-CCCCGAAACT
          1 TCCAAAAATTCCA-TTTTTAGCCCCG-AACT

               *                  *      
        253 TCCCAAAATTCCATTTTTAGCCTCGAACT
          1 TCCAAAAATTCCATTTTTAGCCCCGAACT

                    *             *        
        282 TCCAAAAAATCCATTTTT-GACTCCGAAACT
          1 TCCAAAAATTCCATTTTTAG-CCCCG-AACT

               *             
        312 TCCTAAAATTACCATTT
          1 TCCAAAAATT-CCATTT

        329 CACCCCCGGA


Statistics
Matches: 90,  Mismatches: 10, Indels: 10
        0.82            0.09        0.09

Matches are distributed among these distances:
  28    1  0.01
  29   46  0.51
  30   37  0.41
  31    6  0.07

ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33


Consensus pattern (29 bp):   
TCCAAAAATTCCATTTTTAGCCCCGAACT

Found at i:288 original size:59 final size:59

Alignment explanation


    Indices: 198--449  Score: 235
    Period size: 59  Copynumber: 4.3  Consensus size: 59

        188 AAGCTGTCCA

                                                        *               
        198 AAAATTCCATTTTTAGCCCCGAACTTCC-AAAAATCCCATTTTTTACCCCGAAACTTCCC
          1 AAAATTCCATTTTTAGCCCCGAACTTCCAAAAAAT-CCATTTTTGACCCCGAAACTTCCC

                              *                           *           *
        257 AAAATTCCATTTTTAGCCTCGAACTTCCAAAAAATCCATTTTTGACTCCGAAACTTCCT
          1 AAAATTCCATTTTTAGCCCCGAACTTCCAAAAAATCCATTTTTGACCCCGAAACTTCCC

                          * *     *            * *      *   **          *
        316 AAAATTACCA-TTTCACCCCCGGA-TGTCCAAAAACTTCATTTTCGACTTCGAAACTTCCT
          1 AAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAAATCCATTTTTGACCCCGAAACTTCCC

                            *     *      *     *             *  *       *
        375 AAAATTACCA-TTTTACCCCCGGA-TGTCTAAAAACTCCATTTTTGACCTCGTAACTTCCT
          1 AAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAAATCCATTTTTGACCCCGAAACTTCCC

                            
        434 AAAATTACCATTTTTA
          1 AAAATT-CCATTTTTA

        450 CCCTCGAGAC


Statistics
Matches: 171,  Mismatches: 18, Indels: 7
        0.87            0.09        0.04

Matches are distributed among these distances:
  58    1  0.01
  59  156  0.91
  60   14  0.08

ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33


Consensus pattern (59 bp):   
AAAATTCCATTTTTAGCCCCGAACTTCCAAAAAATCCATTTTTGACCCCGAAACTTCCC

Found at i:3020 original size:15 final size:15

Alignment explanation


    Indices: 3000--3054  Score: 74
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       2990 TTTGCTAGTG

                           
       3000 TCAAGACAATACAGA
          1 TCAAGACAATACAGA

                      *     *
       3015 TCAAGACAATTCAAGTG
          1 TCAAGACAATAC-AG-A

                           
       3032 TCAAGACAATACAGA
          1 TCAAGACAATACAGA

                    
       3047 TCAAGACA
          1 TCAAGACA

       3055 GTTCATACCC


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  15   19  0.56
  16    4  0.12
  17   11  0.32

ACGTcount: A:0.49, C:0.20, G:0.15, T:0.16


Consensus pattern (15 bp):   
TCAAGACAATACAGA

Found at i:3037 original size:32 final size:32

Alignment explanation


    Indices: 2996--3059  Score: 119
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       2986 CACCTTTGCT

                                            
       2996 AGTGTCAAGACAATACAGATCAAGACAATTCA
          1 AGTGTCAAGACAATACAGATCAAGACAATTCA

                                       *    
       3028 AGTGTCAAGACAATACAGATCAAGACAGTTCA
          1 AGTGTCAAGACAATACAGATCAAGACAATTCA

       3060 TACCCGTTAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19


Consensus pattern (32 bp):   
AGTGTCAAGACAATACAGATCAAGACAATTCA
Done.