Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold960

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: 12582
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:736 original size:47 final size:47

Alignment explanation


    Indices: 667--763  Score: 149
    Period size: 47  Copynumber: 2.1  Consensus size: 47

        657 GATTTTATTT

                                     *  *                  
        667 TAGGGAATGTAAGGCTATTAGAATTGTATAAACATATTTGTTTTCTA
          1 TAGGGAATGTAAGGCTATTAGAATTCTACAAACATATTTGTTTTCTA

                                           * * *           
        714 TAGGGAATGTAAGGCTATTAGAATTCTACAACCTTGTTTGTTTTCTA
          1 TAGGGAATGTAAGGCTATTAGAATTCTACAAACATATTTGTTTTCTA

               
        761 TAG
          1 TAG

        764 TTTAATGGTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  47   45  1.00

ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40


Consensus pattern (47 bp):   
TAGGGAATGTAAGGCTATTAGAATTCTACAAACATATTTGTTTTCTA

Found at i:1874 original size:31 final size:32

Alignment explanation


    Indices: 1798--1882  Score: 91
    Period size: 32  Copynumber: 2.7  Consensus size: 32

       1788 GAATTATTCT

                     *      *    *          
       1798 AAACAATAACTATTCTAAATAGGAGTTGTTTC
          1 AAACAATAATTATTCTGAATAAGAGTTGTTTC

              **  *                         
       1830 AAGGAAAAATTATTCTGAATAAGAGTTG-TTC
          1 AAACAATAATTATTCTGAATAAGAGTTGTTTC

                    *     *       
       1861 AAACAATAGTTATTTTGAATAA
          1 AAACAATAATTATTCTGAATAA

       1883 TAGCTATTCT


Statistics
Matches: 42,  Mismatches: 11, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  31   20  0.48
  32   22  0.52

ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34


Consensus pattern (32 bp):   
AAACAATAATTATTCTGAATAAGAGTTGTTTC

Found at i:8782 original size:15 final size:15

Alignment explanation


    Indices: 8762--8791  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       8752 TATTTATAGG

                           
       8762 CTAGAATGTTGACAT
          1 CTAGAATGTTGACAT

                           
       8777 CTAGAATGTTGACAT
          1 CTAGAATGTTGACAT

       8792 ACTCGTTGGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33


Consensus pattern (15 bp):   
CTAGAATGTTGACAT

Found at i:9122 original size:20 final size:22

Alignment explanation


    Indices: 9099--9139  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 22

       9089 CAAAGCAATA

                                  
       9099 TGTATCGATA-TTTCT-GGGTC
          1 TGTATCGATACTTTCTAGGGTC

                                 
       9119 TGTATCGATACTTTCTAGGGT
          1 TGTATCGATACTTTCTAGGGT

       9140 TTTGACCTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20   10  0.53
  21    5  0.26
  22    4  0.21

ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44


Consensus pattern (22 bp):   
TGTATCGATACTTTCTAGGGTC
Done.