Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00911.F4

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, 640

Length: 1067
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43


Found at i:443 original size:164 final size:152

Alignment explanation


    Indices: 161--462  Score: 379
    Period size: 164  Copynumber: 1.9  Consensus size: 152

        151 TCAAATCTCT

                                             *      *                        
        161 TTTTTAATCCTTCTTGCATGTATATATATCGATGCAGTATTACTTGTTACTGAATTTTTTGAATT
          1 TTTTTAATCCTTCTTGCATGTATATATATCGATACAGTATCACTTGTTACTGAATTTTTTGAATT

                          *                       *     *                    
        226 TTGTGTTGTGGCTATGGAATTTATATGCGTTTCGAACTTTTTAGGTAGGTATTTTGGTTGATGAT
         66 TTGTGTTGTGGCTACGGAATTTATATGCGTTTCGAACTCTTTAGATAGGTA-TTTGGTTGAT--T

              *                      
        291 TTTTTTTCTATCAAAATAGCGACTG
        128 TTATTTTCTATCAAAATAGCGACTG

                            *                   *              *       *     
        316 TTTTTAATCCTTCTTGTATGTATATATATATCGATATAGTATCACTTGTTATTGAGTTTTTTTGC
          1 TTTTTAATCCTTCTTGCATG--TATATATATCGATACAGTATCACTTGTTACTGA----ATTT--

                                             *       *             *         
        381 TTTCGAATTTTGTGTTGTGGCTACGGAATTTATTTGCGTTTTGAACTCTTTAGATCGGTATTTGG
         58 TTT-GAATTTTGTGTTGTGGCTACGGAATTTATATGCGTTTCGAACTCTTTAGATAGGTATTTGG

                             
        446 TTGATTTTATTTTCTAT
        122 TTGATTTTATTTTCTAT

        463 TTACTTGCTG


Statistics
Matches: 125,  Mismatches: 13, Indels: 12
        0.83            0.09        0.08

Matches are distributed among these distances:
 155   19  0.15
 157   29  0.23
 161   14  0.11
 163   13  0.10
 164   50  0.40

ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51


Consensus pattern (152 bp):   
TTTTTAATCCTTCTTGCATGTATATATATCGATACAGTATCACTTGTTACTGAATTTTTTGAATT
TTGTGTTGTGGCTACGGAATTTATATGCGTTTCGAACTCTTTAGATAGGTATTTGGTTGATTTTA
TTTTCTATCAAAATAGCGACTG

Found at i:703 original size:187 final size:191

Alignment explanation


    Indices: 304--703  Score: 499
    Period size: 188  Copynumber: 2.1  Consensus size: 191

        294 TTTTCTATCA

                                   *    *                              *   **
        304 AAATAGCGACTGTTTTTAATCCTTCTTGTATGTATATATATATCGATATAGTATCACTTGTTATT
          1 AAATAGCGACTGTTTTTAATCCTGCTTGCATG-ATATATATATCGATATAGTATCACTTCTTACC

                   *                                     *                   
        369 GAGTTTTTTTGCTTTCGAATTTTGTGTTGTGGCTACGGAATTTATTTGCGTTTTGAACTCTTTAG
         65 GAG---TGTT-CTTTCGAATTTTGTGTTGTGGCTACGGAATTTATCTGCGTTTTGAACTCTTTAG

                        *                *    **                          *  
        434 ATCGGTATTTGGTTGATTTTATTTTCTATTTACTTGCTGGATTCGAGAAAGTGGAAAGAAAATAT
        126 ATCGGTATTTGGATGATTTTATTTTC-ATCTACTCACTGGATTCGAGAAAGTGGAAAGAAAAGAT

              
        499 CG
        190 CG

                                                       *                     
        501 AAATAGCGACTGTTTTTAATCCTGCTTGCATG-TATATATATCTATATAGTATCACTTCTTACCG
          1 AAATAGCGACTGTTTTTAATCCTGCTTGCATGATATATATATCGATATAGTATCACTTCTTACCG

                                          *   *        *          *          
        565 AG-GTT-TTT-GAATTTTGTGTTGTGGCTATGGATTTTATCTGTGTTTTGAACTTTTTAGATCGG
         66 AGTGTTCTTTCGAATTTTGTGTTGTGGCTACGGAATTTATCTGCGTTTTGAACTCTTTAGATCGG

                                                    *                       
        627 TATTTAGTTGATGATTTTATTTTC-TCT-C-CACTGGATTTGAGAAAGTGGAAAGAAAAGATCG
        131 TATTT-G--GATGATTTTATTTTCATCTACTCACTGGATTCGAGAAAGTGGAAAGAAAAGATCG

                  *         
        688 AAATAGTGACTGTTTT
          1 AAATAGCGACTGTTTT

        704 CATAGTTTCT


Statistics
Matches: 181,  Mismatches: 19, Indels: 16
        0.84            0.09        0.07

Matches are distributed among these distances:
 187   44  0.24
 188   55  0.30
 189    6  0.03
 191   16  0.09
 195   30  0.17
 197   30  0.17

ACGTcount: A:0.25, C:0.11, G:0.20, T:0.45


Consensus pattern (191 bp):   
AAATAGCGACTGTTTTTAATCCTGCTTGCATGATATATATATCGATATAGTATCACTTCTTACCG
AGTGTTCTTTCGAATTTTGTGTTGTGGCTACGGAATTTATCTGCGTTTTGAACTCTTTAGATCGG
TATTTGGATGATTTTATTTTCATCTACTCACTGGATTCGAGAAAGTGGAAAGAAAAGATCG
Done.