Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00487.N1

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: 3099
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Found at i:1471 original size:136 final size:137

Alignment explanation


    Indices: 1226--1500  Score: 507
    Period size: 136  Copynumber: 2.0  Consensus size: 137

       1216 GAGTAGTCTC

                                                                             
       1226 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                                                *          * 
       1291 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
         66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       1356 ACTGTTA
        131 ACTGTTA

                                    *                                        
       1363 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

             *                                                               
       1427 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       1492 ACTGTTA
        131 ACTGTTA

              
       1499 CC
          1 CC

       1501 TGAATAGGCT


Statistics
Matches: 134,  Mismatches: 4, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 136  114  0.85
 137   20  0.15

ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32


Consensus pattern (137 bp):   
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA

Found at i:1993 original size:40 final size:40

Alignment explanation


    Indices: 1947--2085  Score: 120
    Period size: 40  Copynumber: 3.2  Consensus size: 40

       1937 TCAACCCTTA

                                                    
       1947 CCCAAACCCCAAATACCCATCTAAACTAACCCAACAGAAG
          1 CCCAAACCCCAAATACCCATCTAAACTAACCCAACAGAAG

                              *            *               **  
       1987 CCCAAACCCCTTACAA-AACCAT-TAACCCATTAAGCCCAAATATCACCAG
          1 CCCAAACCCC--A-AATACCCATCTAA---ACTAA-CCC--A-A-CAGAAG

                                              *     
       2036 CCCAAACCCCAAATACCCATCTAAACTAACCCAATAGAAG
          1 CCCAAACCCCAAATACCCATCTAAACTAACCCAACAGAAG

                      
       2076 CCCAAACCCC
          1 CCCAAACCCC

       2086 TTACAACCCA


Statistics
Matches: 77,  Mismatches: 9, Indels: 26
        0.69            0.08        0.23

Matches are distributed among these distances:
  40   23  0.30
  41    4  0.05
  42    7  0.09
  43    2  0.03
  44    7  0.09
  45    7  0.09
  46    2  0.03
  47    7  0.09
  48    4  0.05
  49   14  0.18

ACGTcount: A:0.42, C:0.41, G:0.04, T:0.12


Consensus pattern (40 bp):   
CCCAAACCCCAAATACCCATCTAAACTAACCCAACAGAAG
Done.