Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1822

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: 1013428
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


File 7 of 7

Found at i:1010382 original size:47 final size:46

Alignment explanation


    Indices: 1010328--1010429  Score: 116
    Period size: 47  Copynumber: 2.2  Consensus size: 46

    1010318 ATCGACACAA

                            *      *                        
    1010328 TCTAGAAACCCAGATGTATCAATGCATTATT-CATTATATCAATACAT
          1 TCTAGAAACCCAGATGGATCAATACATT-TTGC-TTATATCAATACAT

                     *           *             *    *      
    1010375 TCTAGAAAATCCAGATGGATCGATACATTTTGCTTGTATCGATACAT
          1 TCTAG-AAACCCAGATGGATCAATACATTTTGCTTATATCAATACAT

                    
    1010422 TCTAGAAA
          1 TCTAGAAA

    1010430 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:1010430 original size:47 final size:48

Alignment explanation


    Indices: 1010315--1010462  Score: 140
    Period size: 48  Copynumber: 3.1  Consensus size: 48

    1010305 CATTAGTGAG

                    *   *                 *      *          
    1010315 TGTATCGACACAATCTAG-AAACCCAGATGTATCAATGCATTATTCAT
          1 TGTATCGATACATTCTAGAAAACCCAGATGGATCAATACATTATTCAT

             *    *               *           *              
    1010362 TATATCAATACATTCTAGAAAATCCAGATGGATCGATACATT-TTGC-T
          1 TGTATCGATACATTCTAGAAAACCCAGATGGATCAATACATTATT-CAT

                                    *     **          **     
    1010409 TGTATCGATACATTCTAGAAAAACTCAGATATATCAATACATCGTTCAT
          1 TGTATCGATACATTCTAG-AAAACCCAGATGGATCAATACATTATTCAT

                 
    1010458 TGTAT
          1 TGTAT

    1010463 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.