Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold600

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: 7661
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31


Found at i:1370 original size:76 final size:76

Alignment explanation


    Indices: 1268--1448  Score: 271
    Period size: 78  Copynumber: 2.4  Consensus size: 76

       1258 CAACCCCTCG

                                                                      *      
       1268 GGGGAATCAGCACATAGCAACCCCCTTT-CATTTCAAAGATATGGTGGAT-ATCGCACTTAGCAC
          1 GGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATATGGTGGATCA-CGCACATAGCAC

                         
       1331 CACCAATG-AACC
         65 CACC-ATGAAACC

                                                                             
       1343 GGGGAATCAGCAACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGGATCACGCACATAGCA
          1 GGGGAATCAGC-ACATAGCAACCCCCTTT-ACATTTCAAAGATATGGTGGATCACGCACATAGCA

                       * 
       1408 CCACCATGAAATC
         64 CCACCATGAAACC

                          *              
       1421 GGGGAATCAGCACACAGCAA-CCCCTTTA
          1 GGGGAATCAGCACATAGCAACCCCCTTTA

       1449 TATACAACAT


Statistics
Matches: 98,  Mismatches: 3, Indels: 10
        0.88            0.03        0.09

Matches are distributed among these distances:
  75   12  0.12
  76   24  0.24
  77   11  0.11
  78   50  0.51
  79    1  0.01

ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19


Consensus pattern (76 bp):   
GGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATATGGTGGATCACGCACATAGCACC
ACCATGAAACC

Found at i:1798 original size:29 final size:29

Alignment explanation


    Indices: 1765--1828  Score: 76
    Period size: 30  Copynumber: 2.2  Consensus size: 29

       1755 TAATCCACCA

                                          
       1765 CCCAACTTTTTG-AAAATTACAATTTTGCC
          1 CCCAAC-TTTTGCAAAATTACAATTTTGCC

                          *       *     * 
       1794 CCCAAACTTTTGCATAATTACACTTTTGTC
          1 CCC-AACTTTTGCAAAATTACAATTTTGCC

                 
       1824 CCCAA
          1 CCCAA

       1829 GCTCGGAAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  29   10  0.33
  30   20  0.67

ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36


Consensus pattern (29 bp):   
CCCAACTTTTGCAAAATTACAATTTTGCC

Found at i:1802 original size:30 final size:30

Alignment explanation


    Indices: 1772--1828  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1762 CCACCCAACT

                                          
       1772 TTTTG-AAAATTACAATTTTGCCCCCAAAC
          1 TTTTGCAAAATTACAATTTTGCCCCCAAAC

                   *       *     *      
       1801 TTTTGCATAATTACACTTTTGTCCCCAA
          1 TTTTGCAAAATTACAATTTTGCCCCCAA

       1829 GCTCGGAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29    5  0.21
  30   19  0.79

ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39


Consensus pattern (30 bp):   
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.