Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009249.1 Kokia drynarioides strain JFW-HI SEQ_123954, 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: 2141
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38


Found at i:1140 original size:6 final size:6

Alignment explanation


    Indices: 1129--1210  Score: 57
    Period size: 6  Copynumber: 14.3  Consensus size: 6

       1119 TTTGGACATT

                                   * *                             *
       1129 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
          1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA

               *            *       *           *       
       1175 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA
          1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA

       1211 AAAAATTTCA


Statistics
Matches: 57,  Mismatches: 13, Indels: 12
        0.70            0.16        0.15

Matches are distributed among these distances:
   4    2  0.04
   5   12  0.21
   6   41  0.72
   7    2  0.04

ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44


Consensus pattern (6 bp):   
AATTTA

Found at i:1171 original size:17 final size:17

Alignment explanation


    Indices: 1129--1223  Score: 91
    Period size: 17  Copynumber: 5.6  Consensus size: 17

       1119 TTTGGACATT

                          * *
       1129 AATTTAAATTTAAATTT
          1 AATTTAAATTTAAAATA

              * *       *    
       1146 AACTCAAATTTATAATA
          1 AATTTAAATTTAAAATA

                       *  *  
       1163 AATTTAAATTTTAAGTA
          1 AATTTAAATTTAAAATA

                    *        
       1180 AATTTAAACTTAAAATA
          1 AATTTAAATTTAAAATA

                   *       * 
       1197 AATTTAATTTTAAAAAA
          1 AATTTAAATTTAAAATA

                 *    
       1214 AATTTCAATT
          1 AATTTAAATT

       1224 CTATTGGGTC


Statistics
Matches: 60,  Mismatches: 18, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  17   60  1.00

ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43


Consensus pattern (17 bp):   
AATTTAAATTTAAAATA

Found at i:1712 original size:47 final size:47

Alignment explanation


    Indices: 1643--1762  Score: 186
    Period size: 47  Copynumber: 2.6  Consensus size: 47

       1633 AATTCGGTTC

                        *                                  
       1643 ACTTCTCAGTATTTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
          1 ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT

                                                     **    
       1690 ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTTGACCT
          1 ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT

            *     *         *         
       1737 GCTTCTTAGTATCTCATCAGGAAGCT
          1 ACTTCTCAGTATCTCAACAGGAAGCT

       1763 GGGGTTTGAA


Statistics
Matches: 67,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  47   67  1.00

ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36


Consensus pattern (47 bp):   
ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
Done.