Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold730

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: 19959
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:4089 original size:15 final size:15

Alignment explanation


    Indices: 4071--4100  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4061 TTCCATCACT

                      *    
       4071 CTTCTTTACTTTTTG
          1 CTTCTTTACTCTTTG

                           
       4086 CTTCTTTACTCTTTG
          1 CTTCTTTACTCTTTG

       4101 TTTATTGCCC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.07, C:0.23, G:0.07, T:0.63


Consensus pattern (15 bp):   
CTTCTTTACTCTTTG

Found at i:8045 original size:34 final size:34

Alignment explanation


    Indices: 7980--8163  Score: 262
    Period size: 34  Copynumber: 5.4  Consensus size: 34

       7970 ACGGTTCAAT

                            *          *      
       7980 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                   *         *                
       8013 TTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                                              
       8047 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

              *             *        * *      
       8081 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                   *                   *  *   
       8115 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                           
       8149 TTGTTGATTAAATGG
          1 TTGTTGATTAAATGG

       8164 TGGTTTTTAC


Statistics
Matches: 133,  Mismatches: 17, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  33   12  0.09
  34  121  0.91

ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40


Consensus pattern (34 bp):   
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

Found at i:8524 original size:19 final size:19

Alignment explanation


    Indices: 8468--8530  Score: 90
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       8458 TGGTTGTCGA

                             **
       8468 GGTACTATTCACGTATATA
          1 GGTACTATTCACGTATACG

                               
       8487 GGTACTATTCACGTATACG
          1 GGTACTATTCACGTATACG

                       *       
       8506 GGTACTATTCAAGTATACG
          1 GGTACTATTCACGTATACG

             *    
       8525 GTTACT
          1 GGTACT

       8531 GTACACGTGA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  19   40  1.00

ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Consensus pattern (19 bp):   
GGTACTATTCACGTATACG

Found at i:12662 original size:34 final size:34

Alignment explanation


    Indices: 12596--12780  Score: 264
    Period size: 34  Copynumber: 5.5  Consensus size: 34

      12586 AAGTGGGAGA

                             *          *     
      12596 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
          1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

                    *         *               
      12629 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
          1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

                                              
      12663 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
          1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

               *             *        * *     
      12697 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
          1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

                    *                   *  *  
      12731 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
          1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

                            
      12765 ATTGTTGATTAAATGG
          1 ATTGTTGATTAAATGG

      12781 TGGTTTTTAC


Statistics
Matches: 134,  Mismatches: 17, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  33   13  0.10
  34  121  0.90

ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40


Consensus pattern (34 bp):   
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC

Done.