Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00588.F1

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: 2797
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26


Found at i:694 original size:159 final size:159

Alignment explanation


    Indices: 531--1191  Score: 1095
    Period size: 159  Copynumber: 4.2  Consensus size: 159

        521 CTTTTGGGAA

                                                                             
        531 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

            * *         *                                                    
        596 GTTAAACTCTCAGCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

             *  *  *                     
        661 CAAATTCTGTGCCGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                                                                             
        690 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

                                  *                                          
        755 CTCAAACTCTCACCATACTGGGAAATTTCAATCGAATGT---A-G-CAG-GTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                                         
        814 CGAACTCAGTGCCGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                                                                             
        843 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *                          *            *                     
        908 CTCGAACTCTCACCATACTGGGCAATTTCATTCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                *                        
        973 CGAATTCAGTGCCGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                             *                                               
       1002 CATCCTCAACCAACAAGTCAACCTCAATTGAATGAAACACGTCAGAACCAGA--CTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *        *                *          *              *         
       1065 CTCGAACTCTCAGCATACTGGGCAATTTCGATCGAATGTACCAGGTCAGAGTCAAGCAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                        *                
       1130 CGAACTCAGTGCAGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

            *                                
       1159 TATCCTCAACCAACAAGCCAACCTCAATTGAAT
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAAT

       1192 CACGGATACT


Statistics
Matches: 474,  Mismatches: 22, Indels: 14
        0.93            0.04        0.03

Matches are distributed among these distances:
 153  142  0.30
 154    3  0.01
 155    1  0.00
 156    2  0.00
 157  129  0.27
 158    3  0.01
 159  194  0.41

ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22


Consensus pattern (159 bp):   
CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA
CGAACTCAGTGCCGAGTGACAGCTTGGTG

Found at i:958 original size:312 final size:314

Alignment explanation


    Indices: 531--1191  Score: 1114
    Period size: 312  Copynumber: 2.1  Consensus size: 314

        521 CTTTTGGGAA

                                                                             
        531 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

            * *         *                              *                     
        596 GTTAAACTCTCAGCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA

                   *                                                         
        661 CAAATTCTGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA
        131 CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA

                                                                             
        726 ACACGTCAGAACCAGACTCTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA
        196 ACACGTCAGAACCAGA--CTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA

                                                   *                
        791 TGT-A-G-CAG-GTCAAACAGATCTAACGAACTCAGTGCCGAGTGACAGCTTGGTG
        259 TGTCAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG

                                                                             
        843 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *                          *                                  
        908 CTCGAACTCTCACCATACTGGGCAATTTCATTCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA

             *                                            *                  
        973 CGAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGTCAACCTCAATTGAATGAA
        131 CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA

                                          *        *         *      *        
       1038 ACACGTCAGAACCAGACTGATTCATCACTCGAACTCTCAGCATACTGGGCAATTTCGATCGAATG
        196 ACACGTCAGAACCAGACTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAATG

                             *                                      
       1103 TACCAGGTCAGAGTCAAGCAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG
        261 T--CAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG

            *                                
       1159 TATCCTCAACCAACAAGCCAACCTCAATTGAAT
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAAT

       1192 CACGGATACT


Statistics
Matches: 327,  Mismatches: 16, Indels: 8
        0.93            0.05        0.02

Matches are distributed among these distances:
 310   46  0.14
 312  202  0.62
 313    1  0.00
 314    1  0.00
 315    3  0.01
 316   74  0.23

ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22


Consensus pattern (314 bp):   
CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA
ACACGTCAGAACCAGACTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAATG
TCAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG
Done.