Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3575

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: 28876
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:3264 original size:50 final size:49

Alignment explanation


    Indices: 3132--3315  Score: 228
    Period size: 50  Copynumber: 3.7  Consensus size: 49

       3122 CGAAGCTATC

                  * *                                      * 
       3132 TGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-TCAA-AAA
          1 TGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTCAACATA

                *    *                             *       *   *
       3179 TCGTGTACATGTAGTAGCCTGCACTTAGTACTACACATGTGACCTCATCATT
          1 T-G-ATACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CTCAACATA

                                                      *       
       3231 TGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAATA
          1 TGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTCAAC-ATA

                              *                
       3281 TGATACACGTAGTAGCCTACACTTAGTACTACACA
          1 TGATACACGTAGTAGCCTGCACTTAGTACTACACA

       3316 CGTGTATTCA


Statistics
Matches: 116,  Mismatches: 15, Indels: 9
        0.83            0.11        0.06

Matches are distributed among these distances:
  47    1  0.01
  48    1  0.01
  49   37  0.32
  50   71  0.61
  51    4  0.03
  52    2  0.02

ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27


Consensus pattern (49 bp):   
TGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTCAACATA

Found at i:8734 original size:43 final size:43

Alignment explanation


    Indices: 8681--8818  Score: 174
    Period size: 43  Copynumber: 3.3  Consensus size: 43

       8671 ATACCCAGAT

                       *  *                **          
       8681 ATGGTCTTACATGTTATCATATATCGATGCCTCTGTCCTAGAC
          1 ATGGTCTTACACGTAATCATATATCGATGCCAATGTCCTAGAC

             *                                         
       8724 AGGGTCTTACACG-AATCATATAT-GATGCCAATGTCCTAGAC
          1 ATGGTCTTACACGTAATCATATATCGATGCCAATGTCCTAGAC

                        *                 *        *    
       8765 ATGGTCTTACACATAATC-TCATATCGATGTCAATGTCCCAGAC
          1 ATGGTCTTACACGTAATCAT-ATATCGATGCCAATGTCCTAGAC

                       
       8808 ATGGTCTTACA
          1 ATGGTCTTACA

       8819 TGAAATCACA


Statistics
Matches: 83,  Mismatches: 9, Indels: 6
        0.85            0.09        0.06

Matches are distributed among these distances:
  41   28  0.34
  42   17  0.20
  43   38  0.46

ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32


Consensus pattern (43 bp):   
ATGGTCTTACACGTAATCATATATCGATGCCAATGTCCTAGAC

Found at i:8751 original size:41 final size:42

Alignment explanation


    Indices: 8696--8818  Score: 151
    Period size: 41  Copynumber: 2.9  Consensus size: 42

       8686 CTTACATGTT

                            **                        
       8696 ATCATATATCGATGCCTCTGTCCTAGACAGGGTCTTACACGA
          1 ATCATATATCGATGCCAATGTCCTAGACAGGGTCTTACACGA

                                         *           * 
       8738 ATCATATAT-GATGCCAATGTCCTAGACATGGTCTTACACATA
          1 ATCATATATCGATGCCAATGTCCTAGACAGGGTCTTACAC-GA

                           *        *     *         
       8780 ATC-TCATATCGATGTCAATGTCCCAGACATGGTCTTACA
          1 ATCAT-ATATCGATGCCAATGTCCTAGACAGGGTCTTACA

       8819 TGAAATCACA


Statistics
Matches: 72,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  41   28  0.39
  42   17  0.24
  43   27  0.38

ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30


Consensus pattern (42 bp):   
ATCATATATCGATGCCAATGTCCTAGACAGGGTCTTACACGA

Found at i:10103 original size:18 final size:20

Alignment explanation


    Indices: 10080--10123  Score: 65
    Period size: 20  Copynumber: 2.3  Consensus size: 20

      10070 TGTAAGTAGG

                                
      10080 CCGTGTGG-TC-GCACACGC
          1 CCGTGTGGCTCGGCACACGC

                         *      
      10098 CCGTGTGGCTCGGGACACGC
          1 CCGTGTGGCTCGGCACACGC

                  
      10118 CCGTGT
          1 CCGTGT

      10124 CCTCAGCCTG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    8  0.35
  19    2  0.09
  20   13  0.57

ACGTcount: A:0.09, C:0.36, G:0.36, T:0.18


Consensus pattern (20 bp):   
CCGTGTGGCTCGGCACACGC

Found at i:11666 original size:45 final size:45

Alignment explanation


    Indices: 11581--11667  Score: 120
    Period size: 45  Copynumber: 1.9  Consensus size: 45

      11571 AACATGTGTC

                                         * *             
      11581 ACATACATCATGAACTCAGACCACAACTCCATGAGCTCAGATGTT
          1 ACATACATCATGAACTCAGACCACAACTCAAAGAGCTCAGATGTT

                 *          *      *           *      
      11626 ACATATATCATGAACTTAGACCATAACTCAAAGAGTTCAGAT
          1 ACATACATCATGAACTCAGACCACAACTCAAAGAGCTCAGAT

      11668 CACATAGTTC


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  45   36  1.00

ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24


Consensus pattern (45 bp):   
ACATACATCATGAACTCAGACCACAACTCAAAGAGCTCAGATGTT

Found at i:16185 original size:30 final size:29

Alignment explanation


    Indices: 16151--16214  Score: 110
    Period size: 30  Copynumber: 2.2  Consensus size: 29

      16141 ATGGATCGGA

                       *                  
      16151 AGCTTTGGCACTAAGTGTGCGATTTAGACT
          1 AGCTTTGGCACGAAGTGTGCGATTTA-ACT

                                         
      16181 AGCTTTGGCACGAAGTGTGCGATTTAACT
          1 AGCTTTGGCACGAAGTGTGCGATTTAACT

                 
      16210 AGCTT
          1 AGCTT

      16215 CGGCTACTTG


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  29    8  0.24
  30   25  0.76

ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33


Consensus pattern (29 bp):   
AGCTTTGGCACGAAGTGTGCGATTTAACT
Done.