Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1487

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: 9843
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31


Found at i:34 original size:21 final size:21

Alignment explanation


    Indices: 10--60  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

          1 ATTATCAAG

                       * *       
         10 GTTATCAAAATTAGATTAAAA
          1 GTTATCAAAATCAAATTAAAA

                 *               
         31 GTTATTAAAATCAAATTAAAA
          1 GTTATCAAAATCAAATTAAAA

            *   *    
         52 ATTACCAAA
          1 GTTATCAAA

         61 TTATATCAAA


Statistics
Matches: 24,  Mismatches: 6, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31


Consensus pattern (21 bp):   
GTTATCAAAATCAAATTAAAA

Found at i:424 original size:21 final size:20

Alignment explanation


    Indices: 235--476  Score: 108
    Period size: 21  Copynumber: 11.9  Consensus size: 20

        225 ATCTCAAATG

                 *    *          
        235 TACCACAATTGTATCAATAGT
          1 TACCAAAATTATATCAA-AGT

                        *         
        256 TACCAAAAAATTGTATCAAAGT
          1 TACC--AAAATTATATCAAAGT

                           *   * 
        278 GT--CAAAATTATA-AAAAAT
          1 -TACCAAAATTATATCAAAGT

              ***        *       
        296 TATTGAAATTATAGCAAATGT
          1 TACCAAAATTATATCAAA-GT

                    *           * 
        317 TACCAAAAGTATATCTAAGATT
          1 TACCAAAATTATATC-AA-AGT

                           *      
        339 TACCAAAATTAT-TGTAAATGT
          1 TACCAAAATTATAT-CAAA-GT

              *       *          
        360 TATCAAAATTTTATCAAAAG-
          1 TACCAAAATTATATC-AAAGT

                    *    **   * 
        380 TACCAAAACTA-AAAAAAAT
          1 TACCAAAATTATATCAAAGT

                                 
        399 TACCAAAATTATATCAAAGCT
          1 TACCAAAATTATATCAAAG-T

                     *            
        420 TACCAAAATCATAT-AAAGAAT
          1 TACCAAAATTATATCAAAG--T

                  *             
        441 TACC-ACA-TATATCAAAG-
          1 TACCAAAATTATATCAAAGT

              *                
        458 TATCAAAATTATATCAAAG
          1 TACCAAAATTATATCAAAG

        477 GCTATTAAAT


Statistics
Matches: 165,  Mismatches: 36, Indels: 42
        0.68            0.15        0.17

Matches are distributed among these distances:
  17    4  0.02
  18    9  0.05
  19   41  0.25
  20   26  0.16
  21   50  0.30
  22   21  0.13
  23   14  0.08

ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30


Consensus pattern (20 bp):   
TACCAAAATTATATCAAAGT

Found at i:6880 original size:52 final size:52

Alignment explanation


    Indices: 6810--6930  Score: 224
    Period size: 52  Copynumber: 2.3  Consensus size: 52

       6800 GAAAATTTAT

                                    *                           
       6810 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC

                                *                               
       6862 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC

                             
       6914 CTGCATGTATCGATACA
          1 CTGCATGTATCGATACA

       6931 AAGATCAGTG


Statistics
Matches: 67,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  52   67  1.00

ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Consensus pattern (52 bp):   
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC

Found at i:6943 original size:52 final size:51

Alignment explanation


    Indices: 6810--6950  Score: 212
    Period size: 52  Copynumber: 2.7  Consensus size: 51

       6800 GAAAATTTAT

                                                                
       6810 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC

                                *   *                           
       6862 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC

                              *                   
       6914 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
          1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA

       6951 ATGTATCGAT


Statistics
Matches: 82,  Mismatches: 5, Indels: 4
        0.90            0.05        0.04

Matches are distributed among these distances:
  51    2  0.02
  52   80  0.98

ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Consensus pattern (51 bp):   
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC

Found at i:6957 original size:13 final size:13

Alignment explanation


    Indices: 6939--6963  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       6929 CAAAGATCAG

                         
       6939 TGTATCGATACAA
          1 TGTATCGATACAA

                        
       6952 TGTATCGATACA
          1 TGTATCGATACA

       6964 TGTGAGTAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:7047 original size:13 final size:13

Alignment explanation


    Indices: 7029--7053  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7019 ACAAAAAATA

                         
       7029 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       7042 TGTATCGATACA
          1 TGTATCGATACA

       7054 ACATTTTATG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT
Done.