Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2539

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: 7021
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33


Found at i:447 original size:13 final size:13

Alignment explanation


    Indices: 429--453  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        419 CATAAAGTAT

                         
        429 TGTATCGATACAA
          1 TGTATCGATACAA

                        
        442 TGTATCGATACA
          1 TGTATCGATACA

        454 TATTTTTTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:451 original size:33 final size:33

Alignment explanation


    Indices: 409--475  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

        399 TTCAACGATT

                                             
        409 TGTATCGATACATAAAGTATTGTATCGATACAA
          1 TGTATCGATACATAAAGTATTGTATCGATACAA

                          *** *              
        442 TGTATCGATACATATTTTTTTGTATCGATACAA
          1 TGTATCGATACATAAAGTATTGTATCGATACAA

             
        475 T
          1 T

        476 TTAAGCTACT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40


Consensus pattern (33 bp):   
TGTATCGATACATAAAGTATTGTATCGATACAA

Found at i:534 original size:13 final size:13

Alignment explanation


    Indices: 516--540  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        506 ATCACTTAAA

                         
        516 TGTATCGATACAT
          1 TGTATCGATACAT

                        
        529 TGTATCGATACA
          1 TGTATCGATACA

        541 CTGATCTTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:3971 original size:47 final size:46

Alignment explanation


    Indices: 3917--4018  Score: 116
    Period size: 47  Copynumber: 2.2  Consensus size: 46

       3907 ATCGACACAA

                            *      *                        
       3917 TCTAGAAACCCAGATGTATCAATGCATTATT-CATTATATCAATACAT
          1 TCTAGAAACCCAGATGGATCAATACATT-TTGC-TTATATCAATACAT

                     *           *             *    *      
       3964 TCTAGAAAATCCAGATGGATCGATACATTTTGCTTGTATCGATACAT
          1 TCTAG-AAACCCAGATGGATCAATACATTTTGCTTATATCAATACAT

                    
       4011 TCTAGAAA
          1 TCTAGAAA

       4019 AACTCAGATA


Statistics
Matches: 47,  Mismatches: 6, Indels: 5
        0.81            0.10        0.09

Matches are distributed among these distances:
  46    3  0.06
  47   24  0.51
  48   20  0.43

ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33


Consensus pattern (46 bp):   
TCTAGAAACCCAGATGGATCAATACATTTTGCTTATATCAATACAT

Found at i:4019 original size:47 final size:48

Alignment explanation


    Indices: 3904--4051  Score: 140
    Period size: 48  Copynumber: 3.1  Consensus size: 48

       3894 CATTAGTGAG

                    *   *                 *      *          
       3904 TGTATCGACACAATCTAG-AAACCCAGATGTATCAATGCATTATTCAT
          1 TGTATCGATACATTCTAGAAAACCCAGATGGATCAATACATTATTCAT

             *    *               *           *              
       3951 TATATCAATACATTCTAGAAAATCCAGATGGATCGATACATT-TTGC-T
          1 TGTATCGATACATTCTAGAAAACCCAGATGGATCAATACATTATT-CAT

                                    *     **          **     
       3998 TGTATCGATACATTCTAGAAAAACTCAGATATATCAATACATCGTTCAT
          1 TGTATCGATACATTCTAG-AAAACCCAGATGGATCAATACATTATTCAT

                 
       4047 TGTAT
          1 TGTAT

       4052 TGATTCAAAA


Statistics
Matches: 80,  Mismatches: 16, Indels: 8
        0.77            0.15        0.08

Matches are distributed among these distances:
  47   33  0.41
  48   39  0.49
  49    8  0.10

ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33


Consensus pattern (48 bp):   
TGTATCGATACATTCTAGAAAACCCAGATGGATCAATACATTATTCAT
Done.