Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1345

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: 9174
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33


Found at i:3751 original size:20 final size:20

Alignment explanation


    Indices: 3728--3774  Score: 58
    Period size: 21  Copynumber: 2.3  Consensus size: 20

       3718 GAGGGTGCTG

                    **          
       3728 AACATGCTGTAAATGCATGA
          1 AACATGCTCAAAATGCATGA

                                 
       3748 AACATAGCTCAAAATGCATGA
          1 AACAT-GCTCAAAATGCATGA

             *    
       3769 ATCATG
          1 AACATG

       3775 GGCTGTTATA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  20    6  0.26
  21   17  0.74

ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23


Consensus pattern (20 bp):   
AACATGCTCAAAATGCATGA

Found at i:7523 original size:19 final size:19

Alignment explanation


    Indices: 7499--7560  Score: 67
    Period size: 19  Copynumber: 3.4  Consensus size: 19

       7489 GGGATGTGTT

                               
       7499 TGTGTTGGTGTGTTGGTTG
          1 TGTGTTGGTGTGTTGGTTG

                  *            
       7518 TGTGTTTGTGTGTTGGTT-
          1 TGTGTTGGTGTGTTGGTTG

             *           *     
       7536 TTTG-TGGTG-GTGGGTTG
          1 TGTGTTGGTGTGTTGGTTG

              *     
       7553 TGGGTTGG
          1 TGTGTTGG

       7561 GGGTGTGATT


Statistics
Matches: 35,  Mismatches: 6, Indels: 5
        0.76            0.13        0.11

Matches are distributed among these distances:
  16    6  0.17
  17    6  0.17
  18    6  0.17
  19   17  0.49

ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52


Consensus pattern (19 bp):   
TGTGTTGGTGTGTTGGTTG

Found at i:9101 original size:36 final size:37

Alignment explanation


    Indices: 9050--9121  Score: 110
    Period size: 36  Copynumber: 1.9  Consensus size: 37

       9040 CATATAGTTG

                      *         *                
       9050 TATTGTATCGCGACATAAGTGTTT-TATCGATACATA
          1 TATTGTATCGAGACATAAGTCTTTGTATCGATACATA

                                                
       9086 TATTGTATCGAGACATAAGTCTTTGGTATCGATACA
          1 TATTGTATCGAGACATAAGTCTTT-GTATCGATACA

       9122 AATAGCTATG


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  36   22  0.69
  38   10  0.31

ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38


Consensus pattern (37 bp):   
TATTGTATCGAGACATAAGTCTTTGTATCGATACATA
Done.