Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g02401.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: 4713
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:3254 original size:210 final size:210

Alignment explanation


    Indices: 2864--3461  Score: 803
    Period size: 210  Copynumber: 2.8  Consensus size: 210

       2854 TTGAAAAATG

                 *    *    *                       *                  **     
       2864 TTCCACTAACGGGACAATGTT-ATTCTCTTGAAAAGCTTCGCATTTCATCATGTGAAAGTTTAAG
          1 TTCCAATAACCGGACGATGTTCA-TCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAG

                            *                             *       *  *    *  
       2928 CAAGATCGGAGACGGACTATCTACCTCCACTTGTCTCAAAGAATTATATCTATATGAGTGT-TTT
         65 CAAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATAAGATTGTCCTT

                                                         *            *    * 
       2992 AATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAATATCTGTCAATTCTAA-GTT
        130 -ATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT-AAATGGT

              *               
       3056 GCTACGAATTGGAAGTAC
        193 GCAACGAATTGGAAGTAC

                                                          ****  *            
       3074 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGC
          1 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC

                 *     *        *                                            
       3139 AAGATTGGAGATGGATTATCAACCTCCACTTGTCTCAAAGAATTAGATCT-TGAAGATTGTCCTT
         66 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTAT-AAGATTGTCCTT

                         *  *                                                
       3203 ATTTAAGTTCGATTCCTAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGC
        130 ATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGC

                            
       3268 AACGAATTGGAAGTAC
        195 AACGAATTGGAAGTAC

                          *       * *         *                       *      
       3284 TTCCAATAACCGGAGGATGTTCTTTTCTTGAAAATCTTAGCATTTCATCATGTGAAAAGTTAAGC
          1 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC

                                                           *                 
       3349 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATT-GTGTCTA-AAGAATTGTCCT
         66 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAG-ATCTATAAG-ATTGTCCT

            *                                  *              
       3412 AATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCATCTCTTCAAAATCT
        129 TATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCT

       3462 ATCAGTTGAT


Statistics
Matches: 338,  Mismatches: 43, Indels: 14
        0.86            0.11        0.04

Matches are distributed among these distances:
 209    7  0.02
 210  328  0.97
 211    3  0.01

ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Consensus pattern (210 bp):   
TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC
AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATAAGATTGTCCTTA
TTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGCA
ACGAATTGGAAGTAC

Found at i:3404 original size:14 final size:15

Alignment explanation


    Indices: 3379--3408  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       3369 TACCTCCACT

                           
       3379 TGTCTCAAAGAATTG
          1 TGTCTCAAAGAATTG

                           
       3394 TGTCT-AAAGAATTG
          1 TGTCTCAAAGAATTG

             
       3408 T
          1 T

       3409 CCTAATTTAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   10  0.67
  15    5  0.33

ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37


Consensus pattern (15 bp):   
TGTCTCAAAGAATTG

Found at i:4112 original size:144 final size:144

Alignment explanation


    Indices: 3855--4117  Score: 332
    Period size: 144  Copynumber: 1.8  Consensus size: 144

       3845 TTGGTTGGGA

                                          **  **      *              *       
       3855 AAAGCTAAAGAGTCTTCCTCACCAACTTCAGTTCTTCACTGCTCTCGAAGAATTGACGATGGAAG
          1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATGGAAG

                     *            *     * *    **      *     *               
       3920 GGTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGAAAACTTTCTTCTCTAAAGCGTCTAAGT
         66 GGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAACTCTCTTCCCTAAAGCGTCTAAGT

                          
       3985 TTGAGTGGTTTTGG
        131 TTGAGTGGTTTTGG

                                                         *     *            *
       3999 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTTGAAGAGTTGACAATGTG-C
          1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATG-GAA

                    *                                               
       4063 GGGTTTCATGAAATAGAAGCCTTGCCAGACTCGTT-CAAAAATCTCTCTTCCCTAA
         65 GGGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAA-CTCTCTTCCCTAA

       4118 GGTGTCTGCG


Statistics
Matches: 99,  Mismatches: 18, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 143    4  0.04
 144   94  0.95
 145    1  0.01

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Consensus pattern (144 bp):   
AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATGGAAG
GGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAACTCTCTTCCCTAAAGCGTCTAAGT
TTGAGTGGTTTTGG
Done.