Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2811

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, 506

Length: 844
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.29

Warning! 268 characters in sequence are not A, C, G, or T


Found at i:77 original size:29 final size:29

Alignment explanation


    Indices: 24--206  Score: 232
    Period size: 29  Copynumber: 6.4  Consensus size: 29

         14 AAGCCAAAAA

                                          
         24 AATTTAGGTTA-GTTT-AGGTTTTTTAATT
          1 AATTTAGGTTAGGTTTAAGG-TTTTTAATT

                                         
         52 AATTTAGGTTAGGTTTAAGGTTTTTAATT
          1 AATTTAGGTTAGGTTTAAGGTTTTTAATT

                    *    *   *        *  
         81 AATTTAGGATA-GATTAGGGTTTTTAGTT
          1 AATTTAGGTTAGGTTTAAGGTTTTTAATT

                             *           
        109 AATTTAGGTTAGGTTTAGGGTTTTTAATT
          1 AATTTAGGTTAGGTTTAAGGTTTTTAATT

                         *             *  
        138 AATTTAGGTTA-GATT-AGCGTTTTTAGTT
          1 AATTTAGGTTAGGTTTAAG-GTTTTTAATT

                  *          *           
        166 AATTTATGTTAGGTTTAGGGTTTTTAATT
          1 AATTTAGGTTAGGTTTAAGGTTTTTAATT

                        
        195 AATTTAGGTTAG
          1 AATTTAGGTTAG

        207 ATTAGGGTTT


Statistics
Matches: 134,  Mismatches: 15, Indels: 11
        0.84            0.09        0.07

Matches are distributed among these distances:
  27    1  0.01
  28   57  0.43
  29   72  0.54
  30    4  0.03

ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51


Consensus pattern (29 bp):   
AATTTAGGTTAGGTTTAAGGTTTTTAATT

Found at i:98 original size:57 final size:57

Alignment explanation


    Indices: 24--217  Score: 325
    Period size: 57  Copynumber: 3.4  Consensus size: 57

         14 AAGCCAAAAA

                        *     *      *                   *           
         24 AATTTAGGTTAGTTTAGGTTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTTAATT
          1 AATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT

                    *                                                
         81 AATTTAGGATAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT
          1 AATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT

                             *                *                      
        138 AATTTAGGTTAGATTAGCGTTTTTAGTTAATTTATGTTAGGTTTAGGGTTTTTAATT
          1 AATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT

                                   
        195 AATTTAGGTTAGATTAGGGTTTT
          1 AATTTAGGTTAGATTAGGGTTTT

        218 NNNNNNNNNN


Statistics
Matches: 128,  Mismatches: 9, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  57  128  1.00

ACGTcount: A:0.26, C:0.01, G:0.22, T:0.52


Consensus pattern (57 bp):   
AATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT

Found at i:619 original size:26 final size:25

Alignment explanation


    Indices: 584--636  Score: 79
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        574 TTTTCTTAAA

                                      
        584 AAATTTCTATGCGTATTACATCAAAT
          1 AAATTTCTAT-CGTATTACATCAAAT

                      **             
        610 AAATTTCTATTTTATTACATCAAAT
          1 AAATTTCTATCGTATTACATCAAAT

              
        635 AA
          1 AA

        637 TAAATTTAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  25   15  0.60
  26   10  0.40

ACGTcount: A:0.42, C:0.13, G:0.04, T:0.42


Consensus pattern (25 bp):   
AAATTTCTATCGTATTACATCAAAT

Found at i:777 original size:24 final size:24

Alignment explanation


    Indices: 750--802  Score: 79
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        740 AGCGGTTGTT

                                    
        750 CTTCCTCTGGTGCTGATTGTGGTC
          1 CTTCCTCTGGTGCTGATTGTGGTC

                        *  *       *
        774 CTTCCTCTGGTGGTGGTTGTGGTT
          1 CTTCCTCTGGTGCTGATTGTGGTC

                 
        798 CTTCC
          1 CTTCC

        803 AGTTCAGCAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.02, C:0.25, G:0.30, T:0.43


Consensus pattern (24 bp):   
CTTCCTCTGGTGCTGATTGTGGTC
Done.