Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga02g00100.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: 3842
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:1443 original size:139 final size:142

Alignment explanation


    Indices: 1183--1633  Score: 519
    Period size: 139  Copynumber: 3.2  Consensus size: 142

       1173 CAATGGCAGA

                          *                                    **          * 
       1183 AAGGGCGCAAAGCCAAGCTAGAACCCCTAA-ATTGTCTTGCATTCGAAAGAGGT-TTT-TTGTAT
          1 AAGGGCGCAAAGCCGAGCTAGAA-CCCTAATATTGTCTTGCATTCG-AAGATTTCTTTCTTGTGT

            * *           *           *            *             *           
       1245 GTGTTTCTC-TGTCGAAAGGGTT-TAAGACATTTTTGTAGTAGAGCTAAATTCTCTAGGCAATGG
         64 CTCTTTCTCAT-TCAAAAGGGTTCT-GGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGG

              *             
       1308 CAGAACTAGTGTTGTT
        127 CACAACTAGTGTTGTT

              *  *        *        * *                                       
       1324 AAAGGTGCAAAGCCAAGCTAGAATCTTAATATTGTCTTGCATTCG-A-A-TT-TTTC-TGTGTCT
          1 AAGGGCGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAGATTTCTTTCTTGTGTCT

                                        *             *                      
       1384 CTCTCTCTCATTCAAAAGGGTTC-GTGATATTTTTGTACTAGCGCTAAATTCACTAGGCAATGGC
         66 CT-T-TCTCATTCAAAAGGGTTCTG-GACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGGC

                           
       1448 ACAACTAGTGTTGTT
        128 ACAACTAGTGTTGTT

                                                       *                     
       1463 AAGGGCGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTTGAAAGGATTTCTTTCTTGTGT
          1 AAGGGCGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCG-AA-GATTTCTTTCTTGTGT

            * *          *                          *           *         *  
       1528 GTGTTTCTCATTCGAAAGGGTTCTGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTCA
         64 CTCTTTCTCATTCAAAAGGGTTCTGGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCA

                          
       1593 CAACTAGTGTTGTT
        129 CAACTAGTGTTGTT

                                       
       1607 AAGGGCGCAAAGCCGAGCTAGAACCCT
          1 AAGGGCGCAAAGCCGAGCTAGAACCCT

       1634 TACATTGTTT


Statistics
Matches: 266,  Mismatches: 29, Indels: 27
        0.83            0.09        0.08

Matches are distributed among these distances:
 137   10  0.04
 138    2  0.01
 139  103  0.39
 140    5  0.02
 141   37  0.14
 143    1  0.00
 144   95  0.36
 145    6  0.02
 146    7  0.03

ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33


Consensus pattern (142 bp):   
AAGGGCGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAGATTTCTTTCTTGTGTCT
CTTTCTCATTCAAAAGGGTTCTGGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACA
ACTAGTGTTGTT

Found at i:1589 original size:144 final size:142

Alignment explanation


    Indices: 1183--1689  Score: 577
    Period size: 144  Copynumber: 3.6  Consensus size: 142

       1173 CAATGGCAGA

                                                               **         *  
       1183 AAGGGCGCAAAGCCAAGCTAGAACCCCTAA-ATTGTCTTGCATTCGAAAGAGGTTTT-TTGTATG
          1 AAGGGCGCAAAGCCAAGCTAGAA-CCCTAATATTGTCTTGCATTCGAAAGATTTTTTCTTGTGTG

                                     *            *                          
       1246 TGTTTCTC-TGTCGAAAGGGTT-TAAGACATTTTTGTAGTAGAGCTAAATTC-TCTAGGCAATGG
         65 TGTTTCTCAT-TCGAAAGGGTTCT-GGACATTTTTGTACTAGAGCTAAATTCAT-TAGGCAATGG

              *             
       1308 CAGAACTAGTGTTGTT
        127 CACAACTAGTGTTGTT

              *  *                 * *                                     * 
       1324 AAAGGTGCAAAGCCAAGCTAGAATCTTAATATTGTCTTGCATTCG--A-A-TTTTTC-TGTGTCT
          1 AAGGGCGCAAAGCCAAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGATTTTTTCTTGTGTGT

            *            *              *             *          *           
       1384 CTCTCTCTCATTCAAAAGGGTTC-GTGATATTTTTGTACTAGCGCTAAATTCACTAGGCAATGGC
         66 GT-T-TCTCATTCGAAAGGGTTCTG-GACATTTTTGTACTAGAGCTAAATTCATTAGGCAATGGC

                           
       1448 ACAACTAGTGTTGTT
        128 ACAACTAGTGTTGTT

                          *                            *                     
       1463 AAGGGCGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTTGAAAGGATTTCTTTCTTGTGT
          1 AAGGGCGCAAAGCCAAGCTAGAACCCTAATATTGTCTTGCATTCGAAA-GATTT-TTTCTTGTGT

                                                    *                     *  
       1528 GTGTTTCTCATTCGAAAGGGTTCTGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTCA
         64 GTGTTTCTCATTCGAAAGGGTTCTGGACATTTTTGTACTAGAGCTAAATTCATTAGGCAATGGCA

                          
       1593 CAACTAGTGTTGTT
        129 CAACTAGTGTTGTT

                          *            * *     *   *   *      *           *  
       1607 AAGGGCGCAAAGCCGAGCTAGAACCCTTACATTGTTTTGGATTTGAAAGGGTTTTTTCTTTTATG
          1 AAGGGCGCAAAGCCAAGCTAGAACCCTAATATTGTCTTGCATTCGAAA-GATTTTTTC--TTGTG

                              
       1672 TGTGTTTCTCATTCGAAA
         63 TGTGTTTCTCATTCGAAA

       1690 TGTTTCGAAA


Statistics
Matches: 313,  Mismatches: 35, Indels: 32
        0.82            0.09        0.08

Matches are distributed among these distances:
 137   10  0.03
 138    2  0.01
 139  102  0.33
 140    5  0.02
 141   37  0.12
 143    5  0.02
 144  117  0.37
 145   28  0.09
 146    7  0.02

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (142 bp):   
AAGGGCGCAAAGCCAAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGATTTTTTCTTGTGTGT
GTTTCTCATTCGAAAGGGTTCTGGACATTTTTGTACTAGAGCTAAATTCATTAGGCAATGGCACA
ACTAGTGTTGTT
Done.