Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001272.1 Kokia drynarioides strain JFW-HI SEQ_112658, 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: 1725
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33


Found at i:1175 original size:23 final size:23

Alignment explanation


    Indices: 1149--1294  Score: 143
    Period size: 23  Copynumber: 6.3  Consensus size: 23

       1139 ACACTAGCGA

                                   
       1149 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    *          *    
       1172 GCTCTCTGTTTAGCAC-GTTTCGT
          1 GCTCTCTGATTAGCACTGTGT-GT

                                    
       1195 GCTCTCTGATTAGCACT-TCGTGT
          1 GCTCTCTGATTAGCACTGT-GTGT

                 *   *       *     
       1218 GCTCTTTGAGTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

               *         *   *     
       1241 GCTTTCTGATTAGTACTTTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

            *  * *  *        *     
       1264 ACTTTTTGTTTAGCACTATGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    
       1287 GCTCTCTG
          1 GCTCTCTG

       1295 TTGCCCAGCA


Statistics
Matches: 101,  Mismatches: 18, Indels: 8
        0.80            0.14        0.06

Matches are distributed among these distances:
  22    3  0.03
  23   96  0.95
  24    2  0.02

ACGTcount: A:0.12, C:0.21, G:0.23, T:0.45


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTGTGTGT

Found at i:1218 original size:46 final size:45

Alignment explanation


    Indices: 1149--1329  Score: 159
    Period size: 46  Copynumber: 3.9  Consensus size: 45

       1139 ACACTAGCGA

                                        *                  
       1149 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTTT-CGT
          1 GCTCTCTGATTAGCACT-TGTGTGCTCTTTGTTTAGCAC-TTTGCGT

                                           **          *  
       1195 GCTCTCTGATTAGCACTTCGTGTGCTCTTTGAGTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTT-GTGTGCTCTTTGTTTAGCACTTTGCGT

               *         *         *  *             *  *  
       1241 GCTTTCTGATTAGTACTTTGTGTACTTTTTGTTTAGCACTATGTGT
          1 GCTCTCTGATTAGCAC-TTGTGTGCTCTTTGTTTAGCACTTTGCGT

                                  *        *       *    
       1287 GCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTTAGTACTT
          1 GCTCTCTGATT----AGCACTTGTGTGCTCTTTGTTTAGCACTT

       1330 CGATACTCTC


Statistics
Matches: 109,  Mismatches: 19, Indels: 12
        0.78            0.14        0.09

Matches are distributed among these distances:
  45    6  0.06
  46   79  0.72
  47    2  0.02
  48   18  0.17
  49    4  0.04

ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44


Consensus pattern (45 bp):   
GCTCTCTGATTAGCACTTGTGTGCTCTTTGTTTAGCACTTTGCGT

Found at i:1296 original size:23 final size:22

Alignment explanation


    Indices: 1149--1329  Score: 141
    Period size: 23  Copynumber: 7.8  Consensus size: 22

       1139 ACACTAGCGA

                                   
       1149 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACT-TGTGT

                    *               
       1172 GCTCTCTGTTTAGCACGTT-TCGT
          1 GCTCTCTGATTAGCAC-TTGT-GT

                                   
       1195 GCTCTCTGATTAGCACTTCGTGT
          1 GCTCTCTGATTAGCACTT-GTGT

                 *   *             
       1218 GCTCTTTGAGTAGCACTTTGTGT
          1 GCTCTCTGATTAGCAC-TTGTGT

               *         *         
       1241 GCTTTCTGATTAGTACTTTGTGT
          1 GCTCTCTGATTAGCAC-TTGTGT

            *  * *  *              
       1264 ACTTTTTGTTTAGCACTATGTGT
          1 GCTCTCTGATTAGCACT-TGTGT

                                  *   
       1287 GCTCTCTG-TTGCCCAGCACTTATGT
          1 GCTCTCTGATT----AGCACTTGTGT

                    *    *    
       1312 GCTCTCTGTTTAGTACTT
          1 GCTCTCTGATTAGCACTT

       1330 CGATACTCTC


Statistics
Matches: 130,  Mismatches: 17, Indels: 23
        0.76            0.10        0.14

Matches are distributed among these distances:
  22   12  0.09
  23   94  0.72
  24    4  0.03
  25   12  0.09
  26    8  0.06

ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44


Consensus pattern (22 bp):   
GCTCTCTGATTAGCACTTGTGT
Done.