Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01959.N1

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, 535

Length: 892
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33


Found at i:337 original size:28 final size:26

Alignment explanation


    Indices: 295--369  Score: 78
    Period size: 26  Copynumber: 2.8  Consensus size: 26

        285 AAAAGTAGCT

                    * *               * 
        295 AAATTACTATAATACCCCTATGTATGGA
          1 AAATTACTGTTATACCCCTA-G-ATGCA

                           *     *    
        323 AAATTACTGTTATACACCTAGGTGCA
          1 AAATTACTGTTATACCCCTAGATGCA

                   *             
        349 AAATTACCGTTATACCCCTAG
          1 AAATTACTGTTATACCCCTAG

        370 GGTTAATTTT


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  26   22  0.55
  27    1  0.03
  28   17  0.43

ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31


Consensus pattern (26 bp):   
AAATTACTGTTATACCCCTAGATGCA

Found at i:511 original size:27 final size:27

Alignment explanation


    Indices: 473--588  Score: 178
    Period size: 27  Copynumber: 4.3  Consensus size: 27

        463 GAGGAAGCGT

                            *          
        473 TCTGGTGGCTCTGCCAAAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                                       
        500 TCTGGTGGCTCTGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                              *       *
        527 TCTGGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                             * *        
        554 TCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

                   
        582 TCTGGTG
          1 TCTGGTG

        589 ACTTTGTCAC


Statistics
Matches: 81,  Mismatches: 7, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  27   74  0.91
  28    7  0.09

ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:558 original size:54 final size:55

Alignment explanation


    Indices: 473--612  Score: 194
    Period size: 54  Copynumber: 2.6  Consensus size: 55

        463 GAGGAAGCGT

                            * *       *                            
        473 TCTGGTGGCTCTGCCAAAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                                                        * *        
        527 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                   *  *  *                  
        582 TCTGGTGACTTTGTCACAT-TATCTGTTCTGG
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG

        613 CAGCCATGTT


Statistics
Matches: 77,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  54   60  0.78
  55   17  0.22

ACGTcount: A:0.18, C:0.24, G:0.23, T:0.36


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

Found at i:602 original size:27 final size:28

Alignment explanation


    Indices: 473--612  Score: 166
    Period size: 27  Copynumber: 5.2  Consensus size: 28

        463 GAGGAAGCGT

                            *  *        
        473 TCTGGTGGCTCTGCCAAAAATATCTG-A
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                               *        
        500 TCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                                         
        527 TCTGGTGGCTCTGCCAC-ATATATCTGT-
          1 TCTGGTGGCTCTGCCACAAT-TATCTGTA

                             *          
        554 TCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                   *  *  *              
        582 TCTGGTGACTTTGTCAC-ATTATCTGT-
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                 
        608 TCTGG
          1 TCTGG

        613 CAGCCATGTT


Statistics
Matches: 104,  Mismatches: 5, Indels: 9
        0.88            0.04        0.08

Matches are distributed among these distances:
  26    6  0.06
  27   82  0.79
  28   16  0.15

ACGTcount: A:0.18, C:0.24, G:0.23, T:0.36


Consensus pattern (28 bp):   
TCTGGTGGCTCTGCCACAATTATCTGTA

Found at i:698 original size:19 final size:22

Alignment explanation


    Indices: 674--713  Score: 59
    Period size: 19  Copynumber: 2.0  Consensus size: 22

        664 CTCCCCACAC

                                  
        674 GGTGTA-A-GGTTGG-TATGGG
          1 GGTGTATACGGTTGGATATGGG

                                 
        693 GGTGTATACGGTTGGATATGG
          1 GGTGTATACGGTTGGATATGG

        714 TTGGGTTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    6  0.33
  20    1  0.06
  21    6  0.33
  22    5  0.28

ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33


Consensus pattern (22 bp):   
GGTGTATACGGTTGGATATGGG

Done.