Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00172.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, 658

Length: 1097
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28


Found at i:268 original size:18 final size:17

Alignment explanation


    Indices: 245--300  Score: 53
    Period size: 18  Copynumber: 3.3  Consensus size: 17

        235 ACCCGAAATA

                              
        245 CCTAAAATGCCTGAGTTG
          1 CCTAAAAT-CCTGAGTTG

                   *   *      
        263 CCTAAAGTTCCGGAGTTG
          1 CCTAAA-ATCCTGAGTTG

                         *   
        281 CC-AAAA-CCTGAATTG
          1 CCTAAAATCCTGAGTTG

                 
        296 CCTAA
          1 CCTAA

        301 GATTCCCGAG


Statistics
Matches: 31,  Mismatches: 5, Indels: 6
        0.74            0.12        0.14

Matches are distributed among these distances:
  15    9  0.29
  16    2  0.06
  17    3  0.10
  18   16  0.52
  19    1  0.03

ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25


Consensus pattern (17 bp):   
CCTAAAATCCTGAGTTG

Found at i:312 original size:51 final size:50

Alignment explanation


    Indices: 230--412  Score: 195
    Period size: 51  Copynumber: 3.6  Consensus size: 50

        220 GCCAGAAATT

                    *   *       *  *  *              *  *      
        230 CCAAAACCCGAAATACCTAAAATGCCTGAGTTGCCTAAAGTTCCGGAGTTG
          1 CCAAAACCTGAATTACCTAAGATTCCCGAGTT-CCTAAAGTGCCAGAGTTG

                          *                 *                  
        281 CCAAAACCTGAATTGCCTAAGATTCCCGAGTTTCTGAAAGTGCCAGAGTTG
          1 CCAAAACCTGAATTACCTAAGATTCCCGAGTTCCT-AAAGTGCCAGAGTTG

                                 *    *        *         *     
        332 CCAAAACCTGAATTACCTAAGGTTCCTGAGTTTCCAAAAGTGCCAAAGTTG
          1 CCAAAACCTGAATTACCTAAGATTCCCGAG-TTCCTAAAGTGCCAGAGTTG

                 *        *      *        
        383 CCAAAGCCTGAATTTCCTAAGGTTCCCGAG
          1 CCAAAACCTGAATTACCTAAGATTCCCGAG

        413 ATGAAAAAAC


Statistics
Matches: 112,  Mismatches: 18, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  50    2  0.02
  51  107  0.96
  52    3  0.03

ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24


Consensus pattern (50 bp):   
CCAAAACCTGAATTACCTAAGATTCCCGAGTTCCTAAAGTGCCAGAGTTG

Found at i:745 original size:33 final size:33

Alignment explanation


    Indices: 686--773  Score: 106
    Period size: 33  Copynumber: 2.7  Consensus size: 33

        676 TGAATTACCA

                    *   *  *     *           
        686 AAAATTCCCGAGTTAACAAAATCAGAATT-GCC
          1 AAAATTCCTGAGGTACCAAAACCAGAATTGGCC

                              *               
        718 TAAAATTCCTGAGGTACCGAAACCAGAATTGGCC
          1 -AAAATTCCTGAGGTACCAAAACCAGAATTGGCC

               *                  
        752 AAAGTTCCTGAGGTACCAAAAC
          1 AAAATTCCTGAGGTACCAAAAC

        774 TTGAATTACC


Statistics
Matches: 47,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  33   44  0.94
  34    3  0.06

ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20


Consensus pattern (33 bp):   
AAAATTCCTGAGGTACCAAAACCAGAATTGGCC

Found at i:747 original size:84 final size:84

Alignment explanation


    Indices: 514--772  Score: 284
    Period size: 84  Copynumber: 3.1  Consensus size: 84

        504 AATTTGAAGC

                                     *    *              *                   
        514 ACCAAAAATTCCCGAGTTACCAAAGCCAGAGTTGCCTAAAGTTCCCGAGGTGCCCAAGCCTGAAT
          1 ACCAAAAATTCCCGAGTTACCAAAGTCAGAATTGCCTAAAGTTCCAGAGGTGCCCAAGCCTGAAT

             *     *     *     
        579 TACCCAAGGCTCCCGAGTT
         66 TGCCCAAAGCTCCTGAGTT

            *      *    *        * *  **                          *          
        598 GCCAAAAGTTCCAGAGTTACCGACGTTGGAATTGCCTAAAGTTCCAGAGGTGCCTAAGCCTGAAT
          1 ACCAAAAATTCCCGAGTTACCAAAGTCAGAATTGCCTAAAGTTCCAGAGGTGCCCAAGCCTGAAT

                            *  
        663 TGCCCAAAGCTCCTGAATT
         66 TGCCCAAAGCTCCTGAGTT

                               *    *               *    *     *  *  *  *    
        682 ACCAAAAATTCCCGAGTTAACAAAATCAGAATTGCCTAAAATTCCTGAGGTACCGAAACCAGAAT
          1 ACCAAAAATTCCCGAGTTACCAAAGTCAGAATTGCCTAAAGTTCCAGAGGTGCCCAAGCCTGAAT

              *      *       * 
        747 TGGCCAAAGTTCCTGAGGT
         66 TGCCCAAAGCTCCTGAGTT

                   
        766 ACCAAAA
          1 ACCAAAA

        773 CTTGAATTAC


Statistics
Matches: 141,  Mismatches: 34, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  84  141  1.00

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


Consensus pattern (84 bp):   
ACCAAAAATTCCCGAGTTACCAAAGTCAGAATTGCCTAAAGTTCCAGAGGTGCCCAAGCCTGAAT
TGCCCAAAGCTCCTGAGTT

Found at i:789 original size:33 final size:33

Alignment explanation


    Indices: 677--792  Score: 103
    Period size: 33  Copynumber: 3.5  Consensus size: 33

        667 CAAAGCTCCT

                        *    *   *  *         
        677 GAATTACCAAAAATTCCCGAGTTAACAAAA-TCA
          1 GAATTACCAAAAGTTCCTGAGGTACCAAAACT-A

                 *                     *    * 
        710 GAATTGCCTAAAA-TTCCTGAGGTACCGAAACCA
          1 GAATTACC-AAAAGTTCCTGAGGTACCAAAACTA

                  *                          *
        743 GAATTGGCC-AAAGTTCCTGAGGTACCAAAACTT
          1 GAATT-ACCAAAAGTTCCTGAGGTACCAAAACTA

                             
        776 GAATTACCAAAAGTTCC
          1 GAATTACCAAAAGTTCC

        793 CGAATTGCCA


Statistics
Matches: 68,  Mismatches: 10, Indels: 10
        0.77            0.11        0.11

Matches are distributed among these distances:
  32    5  0.07
  33   56  0.82
  34    7  0.10

ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22


Consensus pattern (33 bp):   
GAATTACCAAAAGTTCCTGAGGTACCAAAACTA
Done.