Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1968

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: 3820
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32


Found at i:27 original size:21 final size:20

Alignment explanation


    Indices: 1--53  Score: 72
    Period size: 19  Copynumber: 2.6  Consensus size: 20

                            **   
          1 GTATCGATACAATTTGGCCAT
          1 GTATCGATACAA-TTGAACAT

                                
         22 GTATCGATACAA-TGAACAT
          1 GTATCGATACAATTGAACAT

                         
         41 GTATCGATACAAT
          1 GTATCGATACAAT

         54 GTATCGATAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  19   17  0.59
  21   12  0.41

ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Consensus pattern (20 bp):   
GTATCGATACAATTGAACAT

Found at i:57 original size:13 final size:13

Alignment explanation


    Indices: 39--65  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

         29 TACAATGAAC

                         
         39 ATGTATCGATACA
          1 ATGTATCGATACA

                         
         52 ATGTATCGATACA
          1 ATGTATCGATACA

             
         65 A
          1 A

         66 AGCAGCATGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30


Consensus pattern (13 bp):   
ATGTATCGATACA

Found at i:80 original size:33 final size:32

Alignment explanation


    Indices: 20--84  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 32

         10 CAATTTGGCC

                          *                 
         20 ATGTATCGATACAATGAACATGTATCGATACA
          1 ATGTATCGATACAAAGAACATGTATCGATACA

                              *              
         52 ATGTATCGATACAAAGCAGCATGTATCGATACA
          1 ATGTATCGATACAAAG-AACATGTATCGATACA

         85 TCTGGGTGTG


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   15  0.50
  33   15  0.50

ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26


Consensus pattern (32 bp):   
ATGTATCGATACAAAGAACATGTATCGATACA

Found at i:1520 original size:95 final size:97

Alignment explanation


    Indices: 1294--1536  Score: 337
    Period size: 95  Copynumber: 2.5  Consensus size: 97

       1284 TTTATTTATC

                *                               *    *  *                    
       1294 GGGATACTCCAACCCTATTCCTCCGAGGGGATACTCTAACCCCGCTTTTAAACACATCAAAGTTT
          1 GGGACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGTTTTTAAACACATCAAAGTTT

                                            
       1359 AAATTTTATTCTCACTTAAATTGTAATCATCG
         66 AAATTTTATTCTCACTTAAATTGTAATCATCG

                    *      *       *             *    **        **           
       1391 GGGACACTTCAACCCCATTCCTCTGAGGGGATACTCCGACCTAATTTTTAAATGCATCAAAGTTT
          1 GGGACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGTTTTTAAACACATCAAAGTTT

                                    *       
       1456 AAATTTTA-T-TCACTTAAATTGTCATCATCG
         66 AAATTTTATTCTCACTTAAATTGTAATCATCG

                         *              *                      
       1486 GGGACACTCCAACTCTATTCCTCCGAGGAGATACTCCAACCTCGTTTTTAA
          1 GGGACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGTTTTTAA

       1537 TCAAAAATTA


Statistics
Matches: 125,  Mismatches: 21, Indels: 2
        0.84            0.14        0.01

Matches are distributed among these distances:
  95   63  0.50
  96    1  0.01
  97   61  0.49

ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32


Consensus pattern (97 bp):   
GGGACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGTTTTTAAACACATCAAAGTTT
AAATTTTATTCTCACTTAAATTGTAATCATCG
Done.