Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1490

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: 14507
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Found at i:155 original size:33 final size:32

Alignment explanation


    Indices: 91--158  Score: 91
    Period size: 33  Copynumber: 2.1  Consensus size: 32

         81 GTAGCCAAAC

                             **             
         91 TTGTATCGATACACACAGTATGTATCAATACA
          1 TTGTATCGATACACACAAAATGTATCAATACA

                            *          *     
        123 TTGTATCGATACACCATAAAATGTATCGATACA
          1 TTGTATCGATACA-CACAAAATGTATCAATACA

               
        156 TTG
          1 TTG

        159 GCTTGTAACG


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  32   13  0.42
  33   18  0.58

ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32


Consensus pattern (32 bp):   
TTGTATCGATACACACAAAATGTATCAATACA

Found at i:8702 original size:20 final size:20

Alignment explanation


    Indices: 8677--8801  Score: 97
    Period size: 20  Copynumber: 5.7  Consensus size: 20

       8667 TTTTAACTAG

                                
       8677 ATGTATCGATACATTGAAAA
          1 ATGTATCGATACATTGAAAA

                                           
       8697 ATGTATCGATACATCTAGGTAAAAAGACAGA
          1 ATGTATCGATACAT-T--G-----A-A-A-A

                 *            * 
       8728 ATGTAACGATACATTGAAGA
          1 ATGTATCGATACATTGAAAA

                           * * *
       8748 ATGTATCGATACATTCATAC
          1 ATGTATCGATACATTGAAAA

                                
       8768 ATGTATCGATACATTGAAAA
          1 ATGTATCGATACATTGAAAA

                   *      
       8788 ATGTATCAATACAT
          1 ATGTATCGATACAT

       8802 CTAGGTACTT


Statistics
Matches: 83,  Mismatches: 11, Indels: 22
        0.72            0.09        0.19

Matches are distributed among these distances:
  20   60  0.72
  21    1  0.01
  22    1  0.01
  23    2  0.02
  28    2  0.02
  29    1  0.01
  30    2  0.02
  31   14  0.17

ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29


Consensus pattern (20 bp):   
ATGTATCGATACATTGAAAA

Found at i:10202 original size:14 final size:14

Alignment explanation


    Indices: 10183--10210  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      10173 ATTTCAATGA

                          
      10183 AAAAAATGAAAAAC
          1 AAAAAATGAAAAAC

                          
      10197 AAAAAATGAAAAAC
          1 AAAAAATGAAAAAC

      10211 TCATAAAAAT


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07


Consensus pattern (14 bp):   
AAAAAATGAAAAAC
Done.