Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007154.1 Kokia drynarioides strain JFW-HI SEQ_121766, 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: 4065
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:182 original size:30 final size:30

Alignment explanation


    Indices: 146--234  Score: 92
    Period size: 30  Copynumber: 3.0  Consensus size: 30

        136 TTTTGGTCAC

                       *                  
        146 TTGGGGGTAAATTGGTAATTTTGGGAAAAT
          1 TTGGGGGTAAAATGGTAATTTTGGGAAAAT

                                   **   *  
        176 TTGGGGGTAAAAATGG-AATTTTTAG-ACAT
          1 TTGGGGGT-AAAATGGTAATTTTGGGAAAAT

             **                     *     
        205 TCAGGGGTAAAATGGTAATTTTGGAAAAAT
          1 TTGGGGGTAAAATGGTAATTTTGGGAAAAT

        235 GAGGTCAAAA


Statistics
Matches: 46,  Mismatches: 10, Indels: 6
        0.74            0.16        0.10

Matches are distributed among these distances:
  28    7  0.15
  29   15  0.33
  30   18  0.39
  31    6  0.13

ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34


Consensus pattern (30 bp):   
TTGGGGGTAAAATGGTAATTTTGGGAAAAT

Found at i:226 original size:28 final size:27

Alignment explanation


    Indices: 126--229  Score: 93
    Period size: 28  Copynumber: 3.6  Consensus size: 27

        116 CCCGGGGGCA

                            *           
        126 AAAATGGTAATTTTGGTCACTTGGGGGT
          1 AAAATGGTAATTTTGGACA-TTGGGGGT

               *               *          
        154 AAATTGGTAATTTTGGGAAAATTTGGGGGT
          1 AAAATGGTAATTTT-GG-ACA-TTGGGGGT

                            *       *     
        184 AAAAATGG-AATTTTTAGACATTCAGGGGT
          1 -AAAATGGTAA-TTTTGGACATT-GGGGGT

                             
        213 AAAATGGTAATTTTGGA
          1 AAAATGGTAATTTTGGA

        230 AAAATGAGGT


Statistics
Matches: 61,  Mismatches: 9, Indels: 12
        0.74            0.11        0.15

Matches are distributed among these distances:
  28   28  0.46
  29   11  0.18
  30   12  0.20
  31   10  0.16

ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35


Consensus pattern (27 bp):   
AAAATGGTAATTTTGGACATTGGGGGT

Found at i:1391 original size:3 final size:3

Alignment explanation


    Indices: 1339--1376  Score: 60
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       1329 TATTTAATAT

                    *                                          
       1339 TTA TTA ATA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

       1377 ATGAATTTAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   31  0.94

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (3 bp):   
TTA

Found at i:2247 original size:17 final size:17

Alignment explanation


    Indices: 2202--2249  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       2192 TTTAAACACC

                 *           
       2202 AAATGGATTTAAATTTA
          1 AAATGAATTTAAATTTA

             *  *  *         
       2219 ATATAAACTTAAATTTA
          1 AAATGAATTTAAATTTA

                          
       2236 AAATGAATTTAAAT
          1 AAATGAATTTAAAT

       2250 CTGTTAGGCC


Statistics
Matches: 24,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40


Consensus pattern (17 bp):   
AAATGAATTTAAATTTA
Done.