Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007408.1 Kokia drynarioides strain JFW-HI SEQ_122027, 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: 7526
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:3857 original size:176 final size:175

Alignment explanation


    Indices: 3490--3956  Score: 524
    Period size: 176  Copynumber: 2.7  Consensus size: 175

       3480 CAACTTTTCA

                         *          *            *   * *          *          
       3490 TAAAATATAGTAACAAGCAAACATAATAATATAACAAGCCATTGAATAATTAATTAATTTCACCA
          1 TAAAATA-A-TAAGAAGCAAACATGATAATATAACAAACCACTAAATAATTAATCAATTTCACCA

                         *   ***              *      *               *       
       3555 CATCTTCATAAAATATTTTGTGTCAATAAAATGTTGGCATATCAATCGCTTCACGGATAAATATT
         64 CATCTTCATAAAACATTCACTGTCAATAAAATGTAGGCATACCAATCGCTTCACGGACAAATATT

                       *   *   *              **   *       
       3620 CAAAAAGAAAACATCGCCACCCACCAAGTAGGCAGGAAATAAATTCC
        129 CAAAAAGAAAAAATCACCAACCACCAAGTAGGCAAAAAACAAATTCC

                                          *                             ** * 
       3667 TAAAATAATAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCATTATA
          1 TAAAATAATAAGAAGCAAACATGATAATATAACAAACCACTAAATAATTAATCAATTTCACCACA

                *                                          *   *         *   
       3732 TCTTTATAAAACATTCACTGTCAATAAAAATGTAGGCATACCAATCGTTTCGCGGACAAATGTTC
         66 TCTTCATAAAACATTCACTGTCAAT-AAAATGTAGGCATACCAATCGCTTCACGGACAAATATTC

             *              *                              
       3797 AGAAAGAAAAAATCACGAACCACCAAGT-GGACAAAAAACAAATTCC
        130 AAAAAGAAAAAATCACCAACCACCAAGTAGG-CAAAAAACAAATTCC

               *           *                    *                     * *    
       3843 TAACATAATAAGAAGGAAACATGATAATATAACAAATCACTAAATAATTAATCAATTTTAACACA
          1 TAAAATAATAAGAAGCAAACATGATAATATAACAAACCACTAAATAATTAATCAATTTCACCACA

                       *   ***                 *              
       3908 TCTTCATAAAATATTTTGTGTCAATAAAATGTCA-ACATACCAATCGCTT
         66 TCTTCATAAAACATTCACTGTCAATAAAATGT-AGGCATACCAATCGCTT

       3957 TGCGAATGAA


Statistics
Matches: 243,  Mismatches: 44, Indels: 8
        0.82            0.15        0.03

Matches are distributed among these distances:
 175   89  0.37
 176  147  0.60
 177    7  0.03

ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27


Consensus pattern (175 bp):   
TAAAATAATAAGAAGCAAACATGATAATATAACAAACCACTAAATAATTAATCAATTTCACCACA
TCTTCATAAAACATTCACTGTCAATAAAATGTAGGCATACCAATCGCTTCACGGACAAATATTCA
AAAAGAAAAAATCACCAACCACCAAGTAGGCAAAAAACAAATTCC

Found at i:5146 original size:19 final size:20

Alignment explanation


    Indices: 5118--5155  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       5108 CTGACCTTTA

                                
       5118 GAGGCGTTTTCT-AAAAAAC
          1 GAGGCGTTTTCTCAAAAAAC

                 *             
       5137 GAGGCTTTTTCTCAAAAAA
          1 GAGGCGTTTTCTCAAAAAA

       5156 ACGCCACTAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   11  0.65
  20    6  0.35

ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29


Consensus pattern (20 bp):   
GAGGCGTTTTCTCAAAAAAC

Found at i:5219 original size:41 final size:41

Alignment explanation


    Indices: 5154--5292  Score: 145
    Period size: 41  Copynumber: 3.3  Consensus size: 41

       5144 TTTCTCAAAA

                   *   *                    *     *  
       5154 AAACGCCACTATTGCTCTGACCTTTAGCGGCGCTTTCTCAT
          1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGATTTCTAAT

                  *         *  *         *            
       5195 AAACGCTGCTAATGCTTTGTCCTTTAGCGAC-ATTCTCTAAT
          1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGATT-TCTAAT

                                            *           
       5236 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTCTTATGAT
          1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGATTTC-TA--AT

                         
       5280 AAAACGCCGCTAA
          1 -AAACGCCGCTAA

       5293 AGGTCAGAGC


Statistics
Matches: 79,  Mismatches: 13, Indels: 8
        0.79            0.13        0.08

Matches are distributed among these distances:
  40    2  0.03
  41   59  0.75
  42    4  0.05
  44    2  0.03
  45   12  0.15

ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32


Consensus pattern (41 bp):   
AAACGCCGCTAATGCTCTGACCTTTAGCGGCGATTTCTAAT

Found at i:5234 original size:103 final size:103

Alignment explanation


    Indices: 5050--5240  Score: 267
    Period size: 103  Copynumber: 1.9  Consensus size: 103

       5040 CGTTTATGGG

                                                                             
       5050 AAAACGCCACTATTACTTAACCTTTAGCGGCGTCTATCTCATAAACGCCGCTAATGCTCTGACCT
          1 AAAACGCCACTATTACTTAACCTTTAGCGGCGTCTATCTCATAAACGCCGCTAATGCTCTGACCT

                  * *  *                          
       5115 TTAGAGGCGTTTTCTAAAAAACGAGGCTTTTTCTCAAA
         66 TTAGAGACATTCTCTAAAAAACGAGGCTTTTTCTCAAA

                          *    *                *            *         *  *  
       5153 AAAACGCCACTATTGCTCTGACCTTTAGCGGCG-CTTTCTCATAAACGCTGCTAATGCTTTGTCC
          1 AAAACGCCACTATTACT-TAACCTTTAGCGGCGTCTATCTCATAAACGCCGCTAATGCTCTGACC

                 *            *     
       5217 TTTAGCGACATTCTCTAATAAACG
         65 TTTAGAGACATTCTCTAAAAAACG

       5241 CCGCTAATGC


Statistics
Matches: 76,  Mismatches: 11, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
 103   62  0.82
 104   14  0.18

ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31


Consensus pattern (103 bp):   
AAAACGCCACTATTACTTAACCTTTAGCGGCGTCTATCTCATAAACGCCGCTAATGCTCTGACCT
TTAGAGACATTCTCTAAAAAACGAGGCTTTTTCTCAAA
Done.