Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006686.1 Kokia drynarioides strain JFW-HI SEQ_121280, 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: 22862
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Found at i:4719 original size:18 final size:18

Alignment explanation


    Indices: 4696--4739  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       4686 GAAATTCTAT

                              
       4696 ATCCTTCAACGATTTTAA
          1 ATCCTTCAACGATTTTAA

                   *** *      
       4714 ATCCTTCTGGGGTTTTAA
          1 ATCCTTCAACGATTTTAA

                    
       4732 ATCCTTCA
          1 ATCCTTCA

       4740 GGGATTTCAT


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41


Consensus pattern (18 bp):   
ATCCTTCAACGATTTTAA

Found at i:17191 original size:25 final size:23

Alignment explanation


    Indices: 17154--17303  Score: 113
    Period size: 23  Copynumber: 6.4  Consensus size: 23

      17144 ACACTAGCGC

                                    
      17154 GCTCTCTGTTTAGCAC-GTCTCGT
          1 GCTCTCTGTTTAGCACTGTCT-GT

                                 *   
      17177 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTG-T-TTAGCACTGTCTGT

                    **       * *   
      17202 GCTCTCTGACTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTCTGT

                    **       * *   
      17225 GCTCTCTGACTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTCTGT

                    *    *   * *   
      17248 GCTCTCTGATTAGTACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTCTGT

            *  *           *   *   
      17271 ACTTTCTGTTTAGCATTGTGTGT
          1 GCTCTCTGTTTAGCACTGTCTGT

                      
      17294 GCTCTCTGTT
          1 GCTCTCTGTT

      17304 ACCCAGCACT


Statistics
Matches: 110,  Mismatches: 14, Indels: 6
        0.85            0.11        0.05

Matches are distributed among these distances:
  23   89  0.81
  24    1  0.01
  25   17  0.15
  26    3  0.03

ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44


Consensus pattern (23 bp):   
GCTCTCTGTTTAGCACTGTCTGT

Found at i:17256 original size:46 final size:46

Alignment explanation


    Indices: 17175--17347  Score: 158
    Period size: 46  Copynumber: 3.7  Consensus size: 46

      17165 AGCACGTCTC

                                 *                          
      17175 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGACTAGCACTTTGT
          1 GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGACTAGCACTTTGT

                       *                      *   *       
      17223 GTGCTCTCTGACTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
          1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGACTAGCACTTTGT

              *  *    *                            *           
      17269 GTACTTTCTGTTTAGCA-TTGTGTGTGCTCTCTGTTACCCAGCACTTATGT
          1 GTGCTCTCTGATTAGCACTT-TGTGTGCTCTCTG--A-CTAGCACTT-TGT

                           *         *       
      17319 GT--TCTCTG-TTAGTACTTTG-GTACTCTCTG
          1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTG

      17348 TTTGTTCTGT


Statistics
Matches: 105,  Mismatches: 14, Indels: 14
        0.79            0.11        0.11

Matches are distributed among these distances:
  45    2  0.02
  46   67  0.64
  47    7  0.07
  48   18  0.17
  49    6  0.06
  50    5  0.05

ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44


Consensus pattern (46 bp):   
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGACTAGCACTTTGT

Found at i:17298 original size:69 final size:72

Alignment explanation


    Indices: 17175--17350  Score: 197
    Period size: 69  Copynumber: 2.5  Consensus size: 72

      17165 AGCACGTCTC

                             *   *     *       **                         *  
      17175 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGACTAGCACTTTGTGTGCTCTCTG-A-CTAG
          1 GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTACCCAG

                     
      17238 CACTT-TGT
         64 CACTTATGT

                                        *                                    
      17246 GTGCTCTCTGATTAGTACTTTGTGTACTTTCTGTTTAGCA-TTGTGTGTGCTCTCTGTTACCCAG
          1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTT-TGTGTGCTCTCTG-TACCCAG

                     
      17310 CACTTATGT
         64 CACTTATGT

                                                
      17319 GT--TCTCTG-TTAGTACTTTG-GTACTCTCTGTTT
          1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTT

      17351 GTTCTGTATA


Statistics
Matches: 92,  Mismatches: 8, Indels: 12
        0.82            0.07        0.11

Matches are distributed among these distances:
  68    2  0.02
  69   49  0.53
  70   11  0.12
  71   17  0.18
  72    8  0.09
  73    5  0.05

ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45


Consensus pattern (72 bp):   
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTACCCAGCA
CTTATGT
Done.