Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010431.1 Kokia drynarioides strain JFW-HI SEQ_125321, 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: 3813
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35


Found at i:302 original size:14 final size:15

Alignment explanation


    Indices: 259--302  Score: 65
    Period size: 14  Copynumber: 3.0  Consensus size: 15

        249 TTTTATTCTC

                            
        259 ATTTAATACTTATATT
          1 ATTTAATAC-TATATT

                           
        275 ATTTAATACT-TATT
          1 ATTTAATACTATATT

                           
        289 ATTTAATA-TATATT
          1 ATTTAATACTATATT

        303 TATTACATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  13    1  0.04
  14   16  0.59
  15    1  0.04
  16    9  0.33

ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57


Consensus pattern (15 bp):   
ATTTAATACTATATT

Found at i:971 original size:15 final size:15

Alignment explanation


    Indices: 953--1022  Score: 95
    Period size: 15  Copynumber: 4.7  Consensus size: 15

        943 TTTTGGGTAG

                           
        953 TTTGTAATTGGGCCA
          1 TTTGTAATTGGGCCA

                  *        
        968 TTTGTATTTGGGCCA
          1 TTTGTAATTGGGCCA

             * *        *  
        983 TCTATAATTGGGTCA
          1 TTTGTAATTGGGCCA

                 *         
        998 TTTGTTATTGGGCCA
          1 TTTGTAATTGGGCCA

                      
       1013 TTTGTAATTG
          1 TTTGTAATTG

       1023 AATTTTGTTT


Statistics
Matches: 45,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  15   45  1.00

ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46


Consensus pattern (15 bp):   
TTTGTAATTGGGCCA

Found at i:1061 original size:17 final size:17

Alignment explanation


    Indices: 1039--1089  Score: 84
    Period size: 17  Copynumber: 3.0  Consensus size: 17

       1029 GTTTTGGACT

                        *    
       1039 TTTTAAATTTAAGTTTA
          1 TTTTAAATTTAAATTTA

                             
       1056 TTTTAAATTTAAATTTA
          1 TTTTAAATTTAAATTTA

               *             
       1073 TTTGAAATTTAAATTTA
          1 TTTTAAATTTAAATTTA

       1090 AAATAAAATA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   32  1.00

ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57


Consensus pattern (17 bp):   
TTTTAAATTTAAATTTA

Found at i:1082 original size:7 final size:6

Alignment explanation


    Indices: 1040--1109  Score: 58
    Period size: 6  Copynumber: 12.2  Consensus size: 6

       1030 TTTTGGACTT

                        *      *                                    
       1040 TTTAAA TTTAAG TTT-AT TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA

                    *     * *            
       1086 TTTAAA -ATAAA ATAAAA TTTAAA T
          1 TTTAAA TTTAAA TTTAAA TTTAAA T

       1110 AAATTCAATT


Statistics
Matches: 51,  Mismatches: 8, Indels: 10
        0.74            0.12        0.14

Matches are distributed among these distances:
   4    4  0.08
   5    8  0.16
   6   35  0.69
   7    4  0.08

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (6 bp):   
TTTAAA
Done.