Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_445 ID=scaffold_445-JGI_221_v2.0

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: 7018
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.33

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:490 original size:25 final size:24

Alignment explanation


    Indices: 456--681  Score: 174
    Period size: 25  Copynumber: 9.6  Consensus size: 24

        446 TTAATGTATA

                                    
        456 ATGCTGTCCAATTTTGAGTATATT
          1 ATGCTGTCCAATTTTGAGTATATT

                            *         
        480 GATGCTGTCC-ATTTTAATGTATA--
          1 -ATGCTGTCCAATTTTGA-GTATATT

                           *        
        503 ATGCTGTCCAATTTTAAGTATATT
          1 ATGCTGTCCAATTTTGAGTATATT

                            *         
        527 GATGCTGTCC-ATTTTAATGTATA--
          1 -ATGCTGTCCAATTTTGA-GTATATT

            *                       
        550 GTGCTGTCCAATTTTGAGTATATT
          1 ATGCTGTCCAATTTTGAGTATATT

                       *    *         
        574 GATGCTGTCC-GTTTTAATGTATA--
          1 -ATGCTGTCCAATTTTGA-GTATATT

               *                     
        597 ATGTTGTCCAATTTTGAGTATATTT
          1 ATGCTGTCCAATTTTGAGTATA-TT

                     *                
        622 AAT-CTGTCTAA-TTTGATGTATA--
          1 -ATGCTGTCCAATTTTGA-GTATATT

                          *   *     
        644 ATGCTGTCC-ATTTAGAGCATATT
          1 ATGCTGTCCAATTTTGAGTATATT

                           
        667 ATTGCTGTCCAATTT
          1 A-TGCTGTCCAATTT

        682 GATGAATAAT


Statistics
Matches: 164,  Mismatches: 14, Indels: 46
        0.73            0.06        0.21

Matches are distributed among these distances:
  21    7  0.04
  22   49  0.30
  23   19  0.12
  24   31  0.19
  25   56  0.34
  26    2  0.01

ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45


Consensus pattern (24 bp):   
ATGCTGTCCAATTTTGAGTATATT

Found at i:514 original size:47 final size:47

Alignment explanation


    Indices: 445--701  Score: 340
    Period size: 47  Copynumber: 5.5  Consensus size: 47

        435 GTGTTATAAA

                                                           
        445 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT
          1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT

                                      *                    
        492 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
          1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT

                       *                                 * 
        539 TTTAATGTATAGTGCTGTCCAATTTTGAGTATATTGATGCTGTCCGT
          1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT

                          *                     *        * *
        586 TTTAATGTATAATGTTGTCCAATTTTGAGTATATTTAAT-CTGTCTAA
          1 TTTAATGTATAATGCTGTCCAATTTTGAGTATA-TTGATGCTGTCCAT

               *                     *   *                 *
        633 TTTGATGTATAATGCTGTCC-ATTTAGAGCATATT-ATTGCTGTCCAA
          1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCCAT

               *   *       *       
        679 TTTGATGAATAATTGTTGTCCAA
          1 TTTAATGTATAA-TGCTGTCCAA

        702 AATAGGGTTG


Statistics
Matches: 188,  Mismatches: 17, Indels: 9
        0.88            0.08        0.04

Matches are distributed among these distances:
  44    1  0.01
  45    3  0.02
  46   28  0.15
  47  151  0.80
  48    5  0.03

ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45


Consensus pattern (47 bp):   
TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT

Done.