Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold830

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: 5641
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Found at i:3917 original size:6 final size:7

Alignment explanation


    Indices: 3904--3936  Score: 50
    Period size: 7  Copynumber: 4.9  Consensus size: 7

       3894 AACAAAAGAG

                   
       3904 ATGAAAA
          1 ATGAAAA

             *     
       3911 AAG-AAA
          1 ATGAAAA

                   
       3917 ATGAAAA
          1 ATGAAAA

                   
       3924 ATGAAAA
          1 ATGAAAA

                  
       3931 ATGAAA
          1 ATGAAA

       3937 TAGTAAAATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   6    5  0.22
   7   18  0.78

ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12


Consensus pattern (7 bp):   
ATGAAAA

Found at i:3945 original size:13 final size:14

Alignment explanation


    Indices: 3904--3936  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       3894 AACAAAAGAG

                    *     
       3904 ATGAAAAAAG-AAA
          1 ATGAAAAATGAAAA

                          
       3917 ATGAAAAATGAAAA
          1 ATGAAAAATGAAAA

                  
       3931 ATGAAA
          1 ATGAAA

       3937 TAGTAAAATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13    9  0.50
  14    9  0.50

ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12


Consensus pattern (14 bp):   
ATGAAAAATGAAAA

Found at i:5303 original size:44 final size:44

Alignment explanation


    Indices: 5255--5465  Score: 151
    Period size: 44  Copynumber: 4.8  Consensus size: 44

       5245 AGAATCAGAT

                         *    *                         
       5255 CTTGCCTTCTTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
          1 CTTGCCTTCTTGCGTTGATAGCGAAGCAGATCGAAGACACAAAC

                       *          * *   * * *          * *
       5299 CTTGCCTCTCTCG-GTTG-TAGTGGAGCTGGTTGAAGACAACAGAT
          1 CTTGCCT-TCTTGCGTTGATAGCGAAGCAGATCGAAGAC-ACAAAC

                     *   *                              
       5343 CTTGCCTTCCTGCCTTGATAGCGAAGCAGATCGAAGACACAAAC
          1 CTTGCCTTCTTGCGTTGATAGCGAAGCAGATCGAAGACACAAAC

            *                     * *   * * *          * *
       5387 ATTGCCTCTCTTG-GTT-ATAGTGGAGCTGGTTGAAGACAGCAGAT
          1 CTTGCCT-TCTTGCGTTGATAGCGAAGCAGATCGAAGACA-CAAAC

                     *      * *                
       5431 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
          1 CTTGCCTTCTTGCGTTGATAGCGAAGCAGATCGAA

       5466 AACAAAGTCT


Statistics
Matches: 121,  Mismatches: 38, Indels: 15
        0.70            0.22        0.09

Matches are distributed among these distances:
  43   38  0.31
  44   48  0.40
  45   35  0.29

ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25


Consensus pattern (44 bp):   
CTTGCCTTCTTGCGTTGATAGCGAAGCAGATCGAAGACACAAAC

Found at i:5536 original size:86 final size:86

Alignment explanation


    Indices: 5165--5595  Score: 521
    Period size: 88  Copynumber: 5.0  Consensus size: 86

       5155 ATGAAGTTGT

                                                 *                 *         
       5165 AGATCTTGCCTTCCTTG-GTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTTCATCGGTTG
          1 AGATCTTGCCTT-CTTGCGTTAACAGCGAAGCAGATCGAAAACAAA-CCTTGCCTCCATCGGTTG

            *    *               * 
       5229 CAGTGAAGCTGGTTAAAGA-ATC
         64 TAGTGGAGCTGGTTAAAGACAGC

                             *  *                                            
       5251 AGATCTTGCCTTCTTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTC-TCGGTT
          1 AGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAACCTTGCCTC-CATCGGTT

                           *      * 
       5315 GTAGTGGAGCTGGTTGAAGACAAC
         63 GTAGTGGAGCTGGTTAAAGACAGC

                         *   *  * *                         *           *    
       5339 AGATCTTGCCTTCCTGCCTTGATAGCGAAGCAGATCGAAGACACAAACATTGCCTCTC-TTGGTT
          1 AGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAACCTTGCCTC-CATCGGTT

            *              *        
       5403 ATAGTGGAGCTGGTTGAAGACAGC
         63 GTAGTGGAGCTGGTTAAAGACAGC

                         *                                *             *   *
       5427 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGATTGC
          1 AGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAAAACAAA-CCTTGCCTCCATCGGTTGT

                                  
       5492 AGTGGAGCTGGTTAAAGA-AGC
         65 AGTGGAGCTGGTTAAAGACAGC

                              *              *   *                           
       5513 AGATCTTGCCTTCTTGCGCTAACAGCGAAGCAGGTCGGAAACAAAACCTTGCCTCCATCGGTTGT
          1 AGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAAAAC-AAACCTTGCCTCCATCGGTTGT

                              
       5578 AGTGGAGCTGGTTAAAGA
         65 AGTGGAGCTGGTTAAAGA

       5596 TCGTATCAGA


Statistics
Matches: 305,  Mismatches: 32, Indels: 16
        0.86            0.09        0.05

Matches are distributed among these distances:
  85    4  0.01
  86  112  0.37
  87   64  0.21
  88  125  0.41

ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25


Consensus pattern (86 bp):   
AGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTCCATCGGTTGTA
GTGGAGCTGGTTAAAGACAGC
Done.