Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00244.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, 1000

Length: 3884
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:2056 original size:72 final size:72

Alignment explanation


    Indices: 1934--2203  Score: 325
    Period size: 72  Copynumber: 3.8  Consensus size: 72

       1924 CACTTTGGAC

                               *                  *   *                      
       1934 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAG-CG
          1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG

                     
       1998 -TTTGCTAT
         66 TTTTG--AT

                *      *     *           *            *                *   * 
       2006 GCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAACTAAGAGG
          1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG

                   
       2071 TTTTGAT
         66 TTTTGAT

                               *    *                                        
       2078 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
          1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAGAC

                     
       2141 AGTTTTGAT
         65 -GTTTTGAT

             *                                     *  *            
       2150 GTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
          1 GCATCTTATAACAATTTGAA-TGGCCCAATTCCAAATTGCTTAGGCAATATGAGT

       2204 GCTCTGATTT


Statistics
Matches: 171,  Mismatches: 21, Indels: 12
        0.84            0.10        0.06

Matches are distributed among these distances:
  71    4  0.02
  72  160  0.94
  73    3  0.02
  74    4  0.02

ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35


Consensus pattern (72 bp):   
GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
TTTTGAT

Found at i:2197 original size:144 final size:143

Alignment explanation


    Indices: 1934--2203  Score: 368
    Period size: 144  Copynumber: 1.9  Consensus size: 143

       1924 CACTTTGGAC

                                                  *   *                      
       1934 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCGT
          1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT

                       *      *                              *               
       1999 TTGCTATGCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAAC
         66 TTGC-ATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAAC

                          
       2064 TAAGAGGTTTTGAT
        130 TAAGAGGTTTTGAT

                                    *                                        
       2078 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
          1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAG-C

                       *                            *        *  *            
       2141 AGTTTTG-ATGTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
         64 -G-TTTGCATGCATCTTATAACAATTTCAA-TGGCCCAATACCAAATTGCTTAGGCAATATGAGT

       2204 GCTCTGATTT


Statistics
Matches: 111,  Mismatches: 10, Indels: 10
        0.85            0.08        0.08

Matches are distributed among these distances:
 143    4  0.04
 144  102  0.92
 145    1  0.01
 146    4  0.04

ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35


Consensus pattern (143 bp):   
GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT
TTGCATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAACT
AAGAGGTTTTGAT

Found at i:3608 original size:17 final size:17

Alignment explanation


    Indices: 3586--3621  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3576 AGCTGGACAT

                    *        
       3586 GGAATGTCTAGTCAGGA
          1 GGAATGTCCAGTCAGGA

                             
       3603 GGAATGTCCAGTCAGGA
          1 GGAATGTCCAGTCAGGA

              
       3620 GG
          1 GG

       3622 TACGTTATCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.28, C:0.14, G:0.39, T:0.19


Consensus pattern (17 bp):   
GGAATGTCCAGTCAGGA
Done.