Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00035.M1

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: 5000
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33


Found at i:4350 original size:132 final size:131

Alignment explanation


    Indices: 4199--4461  Score: 370
    Period size: 132  Copynumber: 2.0  Consensus size: 131

       4189 TTTTTGTGTA

                                                                             
       4199 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GCCATAGATGAG
          1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGCCATAGATGAG

                                                                             
       4263 CTAGATACAAATTGTAACATAGTGTTT-CTGATTCAGC-TGTAACCATGGATGTAACATAAATGC
         66 CTAGATACAAATTGTAACATAG-GTTTGCTGA-TC--CTTGTAACCATGGATGTAACATAAATGC

                 
       4326 TCCCC
        127 TCCCC

                                             *        *   *        *         
       4331 AGCACTTGTTCATGCTTGTATATACTTGTAATCGATATGTTAGTTTGTAATAGGGGCATAGATGA
          1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GGCCATAGATGA

               *   * *                                 * *           *       
       4396 GCTTGATGCGAATTGTAACATAGGTTTGCTGATCCTTGTAACCGTTGATGTAACATACATGCTCC
         65 GCTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCC

             
       4461 C
        130 C

       4462 TTTTTCTGTA


Statistics
Matches: 117,  Mismatches: 10, Indels: 8
        0.87            0.07        0.06

Matches are distributed among these distances:
 131    1  0.01
 132   76  0.65
 133    6  0.05
 134   34  0.29

ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35


Consensus pattern (131 bp):   
AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGCCATAGATGAG
CTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCCC
C

Found at i:4858 original size:135 final size:133

Alignment explanation


    Indices: 4664--4905  Score: 396
    Period size: 135  Copynumber: 1.8  Consensus size: 133

       4654 TCGAAGTAAT

                    * *                                       *              
       4664 ATACATGCTCTCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATATTTGTAATATATATG
          1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG

                                *                                            
       4729 TTAGCATAGTAGTCATAGATGAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
         66 TTAGC--A-TAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA

                  
       4794 CCATTG
        128 CCATTG

                                                                        *    
       4800 ATACATGCGCCCCAGTTTCTGTGTAAGCAC-TGTTCATGCTTTGTATATACTTGTAATATGTATG
          1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG

                         *                            
       4864 TTAGCATAGTCATTGATAAGCTATATGCAAATTGTAACATAG
         66 TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAG

       4906 GATTGCCGAT


Statistics
Matches: 100,  Mismatches: 6, Indels: 4
        0.91            0.05        0.04

Matches are distributed among these distances:
 132   34  0.34
 133    1  0.01
 135   37  0.37
 136   28  0.28

ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37


Consensus pattern (133 bp):   
ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAACCA
TTG
Done.