Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00702.F3

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: 1938
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:276 original size:20 final size:20

Alignment explanation


    Indices: 235--276  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        225 TTCTACAAAA

                         *   *  
        235 AAAGAAAGAATTAGTTATTT
          1 AAAGAAAGAATTAATTACTT

                  *             
        255 AAAGAAGGAATTAATTACTT
          1 AAAGAAAGAATTAATTACTT

              
        275 AA
          1 AA

        277 TGATGAAAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31


Consensus pattern (20 bp):   
AAAGAAAGAATTAATTACTT

Found at i:1088 original size:87 final size:86

Alignment explanation


    Indices: 924--1269  Score: 428
    Period size: 87  Copynumber: 4.0  Consensus size: 86

        914 CTGTTAATCT

                *                       *                 *                  
        924 GATTCCCATTTTTGAAATGATTTTCTTCATGGC--GTGCATAACTTGCATCATGTTTATAAATTT
          1 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTG-ATAA-TTACATCATGTTTATAAATTT

              *  *              *  
        987 ACAAATGAGGCCAAGCCCGAGAG
         64 ACGAACGAGGCCAAGCCCGAAAG

                *    *                                                      *
       1010 GAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTT
          1 G-ATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTA

            *    *  *               
       1075 TGAACAAGCCCAAGCCTC-AAACG
         65 CGAACGAGGCCAAGCC-CGAAA-G

                                                 **                          
       1098 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTTTTAATTACATCATGTTTATAAATTTAC
          1 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTAC

                 *               
       1163 GAACGGGGCCAAGCCCGAAAG
         66 GAACGAGGCCAAGCCCGAAAG

                                        *        * *                         
       1184 GTATTTCCATTTTTGAAATGATTTTCTTTGTGGCATGCGTTAATTACATCATGTTTATAAATTTA
          1 G-ATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTA

             *  *   *            
       1249 CAAATGAGCCCAAGCCCGAAA
         65 CGAACGAGGCCAAGCCCGAAA

       1270 CACTGTTGCC


Statistics
Matches: 225,  Mismatches: 28, Indels: 13
        0.85            0.11        0.05

Matches are distributed among these distances:
  86    4  0.02
  87  211  0.94
  88    7  0.03
  89    3  0.01

ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Consensus pattern (86 bp):   
GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTAC
GAACGAGGCCAAGCCCGAAAG

Found at i:1219 original size:174 final size:174

Alignment explanation


    Indices: 924--1247  Score: 488
    Period size: 174  Copynumber: 1.9  Consensus size: 174

        914 CTGTTAATCT

                                             *          *                    
        924 GATTCCCATTTTTGAAATGATTTTCTTCATGGCGTGCATAACTTGCATCATGTTTATAAATTTAC
          1 GATTCCCATTTTTGAAATGATTTTCTTCATGGCATGCATAACTTACATCATGTTTATAAATTTAC

               *              *                                       *      
        989 AAATGAGGCCAAGCCCGAGAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGTGATAAT
         66 AAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAAT

                                                        
       1054 TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG
        131 TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG

                *                       *        **                          
       1098 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTTTTAA-TTACATCATGTTTATAAATTTA
          1 GATTCCCATTTTTGAAATGATTTTCTTCATGGCATG-CATAACTTACATCATGTTTATAAATTTA

             *    *                *  *    *                  *          *   
       1162 CGAACGGGGCCAAGCCCGAAAGGTATTTCCATTTTTGAAATGATTTTCTTTGTGGCATGCGTTAA
         65 CAAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAA

                                 
       1227 TTACATCATGTTTATAAATTT
        130 TTACATCATGTTTATAAATTT

       1248 ACAAATGAGC


Statistics
Matches: 133,  Mismatches: 16, Indels: 2
        0.88            0.11        0.01

Matches are distributed among these distances:
 174  130  0.98
 175    3  0.02

ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38


Consensus pattern (174 bp):   
GATTCCCATTTTTGAAATGATTTTCTTCATGGCATGCATAACTTACATCATGTTTATAAATTTAC
AAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAAT
TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG

Found at i:1881 original size:89 final size:89

Alignment explanation


    Indices: 1774--1936  Score: 290
    Period size: 89  Copynumber: 1.8  Consensus size: 89

       1764 CACCTACAAA

                                                *         *                  
       1774 TCCTACCTGTGCCTGTATGTATTTAAGGTTAACAGGTATTTTGAATTAGTATTAACTATAAATAG
          1 TCCTACCTGTGCCTGTATGTATTTAAGGTTAACAGGCATTTTGAATCAGTATTAACTATAAATAG

            *                       
       1839 TTCATTTTTAATTATTTATATTTG
         66 ATCATTTTTAATTATTTATATTTG

                 *                                                           
       1863 TCCTAGCTGTGCCTGTATGTATTTAAGGTTAACAGGCATTTTGAATCAGTATTAACTATAAATAG
          1 TCCTACCTGTGCCTGTATGTATTTAAGGTTAACAGGCATTTTGAATCAGTATTAACTATAAATAG

                     
       1928 ATCATTTTT
         66 ATCATTTTT

       1937 TG


Statistics
Matches: 70,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  89   70  1.00

ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44


Consensus pattern (89 bp):   
TCCTACCTGTGCCTGTATGTATTTAAGGTTAACAGGCATTTTGAATCAGTATTAACTATAAATAG
ATCATTTTTAATTATTTATATTTG
Done.