Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1975

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: 13680
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31


Found at i:5661 original size:26 final size:26

Alignment explanation


    Indices: 5631--5682  Score: 95
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       5621 CACCAATGAA

                           *          
       5631 TCGGGGAATCAGCACTTAGCAACCCC
          1 TCGGGGAATCAGCACATAGCAACCCC

                                      
       5657 TCGGGGAATCAGCACATAGCAACCCC
          1 TCGGGGAATCAGCACATAGCAACCCC

       5683 CTTTCACATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13


Consensus pattern (26 bp):   
TCGGGGAATCAGCACATAGCAACCCC

Found at i:5716 original size:103 final size:104

Alignment explanation


    Indices: 5495--5760  Score: 455
    Period size: 103  Copynumber: 2.6  Consensus size: 104

       5485 TAACCGTTAT

                     *                **                                     
       5495 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                   
       5560 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA

                                                                             
       5599 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGG
          1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG

                                                    
       5662 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
         65 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA

                           *                               **          
       5702 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
          1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT

       5761 TTATATACAA


Statistics
Matches: 154,  Mismatches: 6, Indels: 5
        0.93            0.04        0.03

Matches are distributed among these distances:
 103   97  0.63
 104   57  0.37

ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19


Consensus pattern (104 bp):   
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA

Found at i:12838 original size:13 final size:12

Alignment explanation


    Indices: 12820--12873  Score: 74
    Period size: 12  Copynumber: 4.4  Consensus size: 12

      12810 CCGTATGCAA

                          
      12820 TTTTTTTCAAATTT
          1 TTTTTTTC-AA-TT

                        
      12834 TTTTTTTCAATT
          1 TTTTTTTCAATT

                    *   
      12846 TTTTTTTCGATT
          1 TTTTTTTCAATT

                        
      12858 TTTTTTTC-ATT
          1 TTTTTTTCAATT

                 
      12869 TTTTT
          1 TTTTT

      12874 GAATCTACAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  11    8  0.21
  12   21  0.54
  13    2  0.05
  14    8  0.21

ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78


Consensus pattern (12 bp):   
TTTTTTTCAATT
Done.