Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4032

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: 16291
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:3920 original size:27 final size:27

Alignment explanation


    Indices: 3887--4063  Score: 189
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       3877 ATTAAATTAC

                                       
       3887 AGCACTAAGTGTGCGATTTGACTATGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

            *               **    *    
       3914 TGCACTAAGTGTGCGAAATGA-AATG-
          1 AGCACTAAGTGTGCGATTTGACTATGT

                             *     *   *
       3939 ATGCACTAAGTGTGCGAATTGACCATGC
          1 A-GCACTAAGTGTGCGATTTGACTATGT

            *                           
       3967 GGCACT-AGTGTGCGAGTTTGACTATGT
          1 AGCACTAAGTGTGCGA-TTTGACTATGT

                                 *  *  
       3994 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                            *    *   * 
       4021 AGCACTAAGTGTGCGAGTTGATTATAT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                  *         
       4048 AGCACTGAGTGTGCGA
          1 AGCACTAAGTGTGCGA

       4064 CTCAATATAC


Statistics
Matches: 127,  Mismatches: 18, Indels: 10
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   31  0.24
  27   87  0.69
  28    9  0.07

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGATTTGACTATGT

Found at i:7447 original size:51 final size:51

Alignment explanation


    Indices: 7392--7491  Score: 139
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       7382 CTACCACATA

                                       *                        
       7392 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCAACAAGCTTGGATGTT
          1 ACATG-AATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATGTT

                     *       *              *     *          
       7443 ACATGAATCGCATCCATTATGAACTCAGACCTTTCAACGAGCTTGGATG
          1 ACATGAATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATG

       7492 CTCGCATCCA


Statistics
Matches: 43,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  50    2  0.05
  51   41  0.95

ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26


Consensus pattern (51 bp):   
ACATGAATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATGTT

Found at i:12446 original size:50 final size:50

Alignment explanation


    Indices: 12326--12569  Score: 289
    Period size: 50  Copynumber: 4.9  Consensus size: 50

      12316 GCTATTGTGA

                                   *         *                
      12326 GGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAAC-T
          1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT

                * *                                  *        
      12375 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG-GTACCTGATAACTT
          1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT

              *                               **    *      **  
      12424 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGAT-GGTT
          1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT

                                              *      **        
      12474 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAA-TT
          1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT

                * *                            *          
      12524 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
          1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA

      12570 GCTTCGGCTA


Statistics
Matches: 164,  Mismatches: 27, Indels: 8
        0.82            0.14        0.04

Matches are distributed among these distances:
  48   11  0.07
  49   72  0.44
  50   74  0.45
  51    7  0.04

ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29


Consensus pattern (50 bp):   
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT

Found at i:12568 original size:99 final size:99

Alignment explanation


    Indices: 12328--12569  Score: 301
    Period size: 99  Copynumber: 2.4  Consensus size: 99

      12318 TATTGTGAGG

                *                *                             *             
      12328 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAACTGGTCGCATGTGTAGTACT
          1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT

                           *                  
      12393 AAGTGCAGGCTACTATGGTACCTGATAACTTCGA
         66 AAGTGCAGGCTACTACGGTACCTGATAACTTCGA

                *                           *    *     ***        *          
      12427 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACGTGTGTAGTAC
          1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACT-GGTCACATGTGTAGTAC

                                                *
      12492 TAAGTGCAGGCTACTACGTGTA-CTGGATAA-TT-GG
         65 TAAGTGCAGGCTACTACG-GTACCT-GATAACTTCGA

              *                            * *          
      12526 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
          1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA

      12570 GCTTCGGCTA


Statistics
Matches: 123,  Mismatches: 17, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  99   79  0.64
 100   36  0.29
 101    8  0.07

ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29


Consensus pattern (99 bp):   
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTACGGTACCTGATAACTTCGA
Done.