Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00120.M5

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: 5628
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32


Found at i:1144 original size:78 final size:78

Alignment explanation


    Indices: 1055--1289  Score: 380
    Period size: 78  Copynumber: 3.0  Consensus size: 78

       1045 GTCAGGCAGA

                                    *    **                                  
       1055 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       1120 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

                                                              *              
       1133 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       1198 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

            *                              *           *             *  *    
       1211 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

             *           
       1276 CAGCTTTCTGGAC
         66 CGGCTTTCTGGAC

             
       1289 G
          1 G

       1290 GCATGTCCGT


Statistics
Matches: 145,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  78  145  1.00

ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23


Consensus pattern (78 bp):   
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC

Found at i:2395 original size:192 final size:189

Alignment explanation


    Indices: 2068--2443  Score: 515
    Period size: 192  Copynumber: 2.0  Consensus size: 189

       2058 AGTTTTTTGG

                                                                    *        
       2068 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
          1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA

                          * *                  *      *                      
       2133 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
         66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA

                    *  **                                                 
       2198 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
        131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC

                                    *                                        
       2260 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
          1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT

                       *       *           *          *            *         
       2323 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
         64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT

                                      *       **       *             
       2387 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTTCATAGTAGAAGCTTCTTTATT
        128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT

       2444 ATATATAATC


Statistics
Matches: 163,  Mismatches: 18, Indels: 9
        0.86            0.09        0.05

Matches are distributed among these distances:
 189   14  0.09
 190   27  0.17
 191   33  0.20
 192   79  0.48
 193   10  0.06

ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47


Consensus pattern (189 bp):   
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC
Done.