Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002403.1 Kokia drynarioides strain JFW-HI SEQ_114491, 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, 895

Length: 1492
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37


Found at i:38 original size:24 final size:24

Alignment explanation


    Indices: 11--429  Score: 269
    Period size: 24  Copynumber: 17.7  Consensus size: 24

          1 CAGCTTGCAC

                              *     
         11 ACGTTTACGCTCGTCAGCCTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

                        ** * *   **  
         35 ACGTTTAC-CTTAATTAACTTGCAT
          1 ACGTTTACGC-TCGTCAGCTTATAT

             *         **           
         59 AGGTTTACGCTTTTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

                        *       ** *
         83 ACGTTTACGCTCATCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

             *                  ** *
        107 ATGTTTACGCTCGTCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

             *   *              ** *
        131 ATGTTCACGCTCGTCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

             *   *                  
        155 ATGTTCACGCTCGTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

              *        *            
        179 ACATTTACGCTTGTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

              *        *  *  *      *
        203 ACATTTACGCTTGTTAGATTGA-AC
          1 ACGTTTACGCTCGTCAGCTT-ATAT

                       *  *         
        227 ACGTTTACGCTTGTTAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

              *                 ** *
        251 ACATTTACGCTCGTCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

             * *                    
        275 ATGCTTACGCTCGTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

                       *        ** *
        299 ACGTTTACGCTTGTCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

                             *       
        323 A-GATTTACGCTCGTCAAC---T-T
          1 ACG-TTTACGCTCGTCAGCTTATAT

                   *   *        ** *
        343 A-GTTTATGCTTGTCAGCTTGCAC
          1 ACGTTTACGCTCGTCAGCTTATAT

             *     *                
        366 ATGTTTATGCTCGTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

                                    
        390 ACGTTTACGCTCGTCAGCTTATAT
          1 ACGTTTACGCTCGTCAGCTTATAT

              *        *    
        414 ACATTTACGCTTGTCA
          1 ACGTTTACGCTCGTCA

        430 ACTTCCACAT


Statistics
Matches: 314,  Mismatches: 71, Indels: 20
        0.78            0.18        0.05

Matches are distributed among these distances:
  19   12  0.04
  20    2  0.01
  23    4  0.01
  24  294  0.94
  25    2  0.01

ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37


Consensus pattern (24 bp):   
ACGTTTACGCTCGTCAGCTTATAT

Found at i:362 original size:43 final size:43

Alignment explanation


    Indices: 254--386  Score: 151
    Period size: 43  Copynumber: 3.0  Consensus size: 43

        244 CTTATATACA

                    *               *            *          
        254 TTTACGCTCGTCAGCTTGCACATGCTTACGCTCGTCAGCTTATATACG
          1 TTTACGCTTGTCAGCTTGCACATGTTTACGCTCGTCAAC---T-TA-G

                                                        
        302 TTTACGCTTGTCAGCTTGCACA-GATTTACGCTCGTCAACTTAG
          1 TTTACGCTTGTCAGCTTGCACATG-TTTACGCTCGTCAACTTAG

                *                       *        *    
        345 TTTATGCTTGTCAGCTTGCACATGTTTATGCTCGTCAGCTTA
          1 TTTACGCTTGTCAGCTTGCACATGTTTACGCTCGTCAACTTA

        387 TATACGTTTA


Statistics
Matches: 77,  Mismatches: 6, Indels: 9
        0.84            0.07        0.10

Matches are distributed among these distances:
  43   38  0.49
  44    3  0.04
  45    1  0.01
  47    1  0.01
  48   34  0.44

ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37


Consensus pattern (43 bp):   
TTTACGCTTGTCAGCTTGCACATGTTTACGCTCGTCAACTTAG

Found at i:391 original size:91 final size:91

Alignment explanation


    Indices: 254--433  Score: 270
    Period size: 91  Copynumber: 2.0  Consensus size: 91

        244 CTTATATACA

                                                                    *        
        254 TTTACGCTCGTCAGCTTGCACATGCTTACGCTCGTCAGCTTATATACGTTTACGCTTGTCAGCTT
          1 TTTACGCTCGTCAGCTTGCACATGCTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT

            *    *                    
        319 GCACAGATTTACGCTCGTCAACTTAG
         66 ACACACATTTACGCTCGTCAACTTAG

                *   *               *   *                                    
        345 TTTATGCTTGTCAGCTTGCACATGTTTATGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT
          1 TTTACGCTCGTCAGCTTGCACATGCTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT

             * *           *        
        410 ATATACATTTACGCTTGTCAACTT
         66 ACACACATTTACGCTCGTCAACTT

        434 CCACATATAC


Statistics
Matches: 79,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  91   79  1.00

ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38


Consensus pattern (91 bp):   
TTTACGCTCGTCAGCTTGCACATGCTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT
ACACACATTTACGCTCGTCAACTTAG

Found at i:1204 original size:12 final size:12

Alignment explanation


    Indices: 1187--1212  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1177 GAAATTTTTG

                        
       1187 TTTCTTTCCTTT
          1 TTTCTTTCCTTT

                        
       1199 TTTCTTTCCTTT
          1 TTTCTTTCCTTT

              
       1211 TT
          1 TT

       1213 ACCACTAATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (12 bp):   
TTTCTTTCCTTT
Done.