Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1647

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: 7321
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:736 original size:48 final size:50

Alignment explanation


    Indices: 644--813  Score: 133
    Period size: 48  Copynumber: 3.5  Consensus size: 50

        634 TAATGTTGAT

                     *                     *                  
        644 GCCATGTCCTAGACATGGTCTTACACT-GACTATCGAAATAGAGGCCGAC
          1 GCCATGTCCCAGACATGGTCTTACACTAGACCATCGAAATAGAGGCCGAC

                    **                      *        *        *
        693 GCCAT-TCTGAGACATGGTCTTACACTAG-CCCTC-AGAATCGAGGCCGAT
          1 GCCATGTCCCAGACATGGTCTTACACTAGACCATCGA-AATAGAGGCCGAC

              *                   *          *    *             *
        741 GCTATGTCCCAGACATGGTCTTGCACTA-ACACCTC--TATACGTA--CCGAT
          1 GCCATGTCCCAGACATGGTCTTACACTAGAC-CATCGAAATA-G-AGGCCGAC

                                     
        789 GCCATGTCCCAGACATGGTCTTACA
          1 GCCATGTCCCAGACATGGTCTTACA

        814 TTGACACTTC


Statistics
Matches: 100,  Mismatches: 14, Indels: 15
        0.78            0.11        0.12

Matches are distributed among these distances:
  47    1  0.01
  48   67  0.67
  49   27  0.27
  50    5  0.05

ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24


Consensus pattern (50 bp):   
GCCATGTCCCAGACATGGTCTTACACTAGACCATCGAAATAGAGGCCGAC

Found at i:887 original size:46 final size:46

Alignment explanation


    Indices: 833--997  Score: 162
    Period size: 46  Copynumber: 3.6  Consensus size: 46

        823 CTCACAGCCA

                                              *            
        833 ATGCATGTCCTAGACATGTCTTACACTGGCT-TAGATATCGAGGCTG
          1 ATGCATGTCCTAGACATGTCTTACACTGGCTCT-CATATCGAGGCTG

                                        *        *  * *  * 
        879 ATGCATGT-CTAAGACATGTC-T-CACTAGCTCTCATCTCAACGCCG
          1 ATGCATGTCCT-AGACATGTCTTACACTGGCTCTCATATCGAGGCTG

                       *                               *      
        923 ATGCCATGTCCCAGACATGTTCTTACACTGGCTCTCATAAT-GTGG-TCG
          1 ATG-CATGTCCTAGACATG-TCTTACACTGGCTCTCAT-ATCGAGGCT-G

                                       
        971 ATGCATGTCCTAGACATGTCTTACACT
          1 ATGCATGTCCTAGACATGTCTTACACT

        998 AGCGCACAAA


Statistics
Matches: 96,  Mismatches: 14, Indels: 18
        0.75            0.11        0.14

Matches are distributed among these distances:
  44   18  0.19
  45   16  0.17
  46   29  0.30
  47   15  0.16
  48   17  0.18
  49    1  0.01

ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30


Consensus pattern (46 bp):   
ATGCATGTCCTAGACATGTCTTACACTGGCTCTCATATCGAGGCTG

Found at i:3595 original size:15 final size:15

Alignment explanation


    Indices: 3575--3606  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3565 GCAACCACTT

                           
       3575 AAGCCATTTGTTCAC
          1 AAGCCATTTGTTCAC

                           
       3590 AAGCCATTTGTTCAC
          1 AAGCCATTTGTTCAC

              
       3605 AA
          1 AA

       3607 ATGAGAACCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31


Consensus pattern (15 bp):   
AAGCCATTTGTTCAC

Found at i:6359 original size:21 final size:20

Alignment explanation


    Indices: 6330--6375  Score: 51
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       6320 CGAAATGCAA

                                  
       6330 TCAACCTAACATGA-ATTAAAT
          1 TCAACCTAA-A-GAGATTAAAT

                *               
       6351 TCAAGCTAAAGAGATTAAAT
          1 TCAACCTAAAGAGATTAAAT

                  
       6371 T-AACC
          1 TCAACC

       6376 ATTCCAACAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  19    5  0.23
  20    9  0.41
  21    8  0.36

ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26


Consensus pattern (20 bp):   
TCAACCTAAAGAGATTAAAT
Done.