Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005263.1 Kokia drynarioides strain JFW-HI SEQ_119174, 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: 2905
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40


Found at i:2246 original size:31 final size:29

Alignment explanation


    Indices: 2175--2276  Score: 116
    Period size: 31  Copynumber: 3.4  Consensus size: 29

       2165 TCGATATATT

                                          
       2175 TTTTTTTAATTTAGTATATAAAATTTT-TA
          1 TTTTTTTAATTTAGTAT-TAAAATTTTATA

              **        *                  
       2204 TTAGTTTAATTTGGTATTAAAATTTGGTATA
          1 TTTTTTTAATTTAGTATTAAAATTT--TATA

                              *      *   
       2235 TTTTTTTAATTTAGTATTTAAATTTAATA
          1 TTTTTTTAATTTAGTATTAAAATTTTATA

                         
       2264 TTTTTTTTAATTT
          1 -TTTTTTTAATTT

       2277 GGTACATGAA


Statistics
Matches: 61,  Mismatches: 8, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  28    8  0.13
  29   17  0.28
  30   13  0.21
  31   23  0.38

ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62


Consensus pattern (29 bp):   
TTTTTTTAATTTAGTATTAAAATTTTATA

Found at i:2289 original size:30 final size:31

Alignment explanation


    Indices: 2235--2318  Score: 80
    Period size: 30  Copynumber: 2.7  Consensus size: 31

       2225 ATTTGGTATA

                        *   **         *   
       2235 TTTTTTTAATTTAGTATTTAAATTTAATA-T
          1 TTTTTTTAATTTGGTACATAAATTTAACACT

                               *     *     
       2265 TTTTTTTAATTTGGTACATGAATTTGACACT
          1 TTTTTTTAATTTGGTACATAAATTTAACACT

                        *     *    
       2296 TTTTTTTAAGTTGGGTACTTAAA
          1 TTTTTTTAA-TTTGGTACATAAA

       2319 CATTTTGAGG


Statistics
Matches: 43,  Mismatches: 9, Indels: 2
        0.80            0.17        0.04

Matches are distributed among these distances:
  30   23  0.53
  31   10  0.23
  32   10  0.23

ACGTcount: A:0.29, C:0.05, G:0.11, T:0.56


Consensus pattern (31 bp):   
TTTTTTTAATTTGGTACATAAATTTAACACT

Found at i:2621 original size:26 final size:26

Alignment explanation


    Indices: 2585--2656  Score: 103
    Period size: 26  Copynumber: 2.8  Consensus size: 26

       2575 TGCTAAGTTC

                 *                    
       2585 AGGTATCAAATTGAATAAAAAAAATT
          1 AGGTACCAAATTGAATAAAAAAAATT

                                   *  
       2611 AGGTACCAAATTGAATAAAAAAAGTT
          1 AGGTACCAAATTGAATAAAAAAAATT

             *                    
       2637 AAGTACCAAATT-AA-AAAAAA
          1 AGGTACCAAATTGAATAAAAAA

       2657 TGTCAAGTTC


Statistics
Matches: 43,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  24    6  0.14
  25    2  0.05
  26   35  0.81

ACGTcount: A:0.60, C:0.07, G:0.11, T:0.22


Consensus pattern (26 bp):   
AGGTACCAAATTGAATAAAAAAAATT

Found at i:2664 original size:24 final size:23

Alignment explanation


    Indices: 2600--2664  Score: 69
    Period size: 24  Copynumber: 2.7  Consensus size: 23

       2590 TCAAATTGAA

                         *         
       2600 TAAAAAAAAT-TAGGTACCAAAT
          1 TAAAAAAAATGTAAGTACCAAAT

                       *              
       2622 TGAATAAAAAAAGTTAAGTACCAAAT
          1 T-AA-AAAAAATG-TAAGTACCAAAT

                             
       2648 TAAAAAAAATGTCAAGT
          1 TAAAAAAAATGT-AAGT

       2665 TCTAATATTA


Statistics
Matches: 35,  Mismatches: 3, Indels: 8
        0.76            0.07        0.17

Matches are distributed among these distances:
  22    1  0.03
  23    3  0.09
  24   17  0.49
  25    2  0.06
  26   12  0.34

ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23


Consensus pattern (23 bp):   
TAAAAAAAATGTAAGTACCAAAT
Done.