Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g00852.M1

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: 5505
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:5141 original size:18 final size:18

Alignment explanation


    Indices: 5120--5178  Score: 57
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       5110 TAAGAAGATG

                              
       5120 AAGTATGCCTTGAAGGCT
          1 AAGTATGCCTTGAAGGCT

                *   * *    * *
       5138 AAGTGT-CATAGAAGACG
          1 AAGTATGCCTTGAAGGCT

               *              
       5155 AAGCATGCCTTGAAGGCT
          1 AAGTATGCCTTGAAGGCT

                  
       5173 AAGTAT
          1 AAGTAT

       5179 TTGAGAAGAT


Statistics
Matches: 28,  Mismatches: 12, Indels: 2
        0.67            0.29        0.05

Matches are distributed among these distances:
  17   11  0.39
  18   17  0.61

ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24


Consensus pattern (18 bp):   
AAGTATGCCTTGAAGGCT

Found at i:5163 original size:35 final size:35

Alignment explanation


    Indices: 5112--5242  Score: 158
    Period size: 35  Copynumber: 3.7  Consensus size: 35

       5102 CCTGTTTCTA

                  *                            
       5112 AGAAGATGAAGTATGCCTTGAAGGCTAAGTGTCAT
          1 AGAAGACGAAGTATGCCTTGAAGGCTAAGTGTCAT

                       *                  *  * 
       5147 AGAAGACGAAGCATGCCTTGAAGGCTAAGTAT-TT
          1 AGAAGACGAAGTATGCCTTGAAGGCTAAGTGTCAT

                   *     *      *           *    
       5181 GAGAAGATGAAGTTTGCCTTAAAGGCTAAGTGCCGA-
          1 -AGAAGACGAAGTATGCCTTGAAGGCTAAGTGTC-AT

                                      
       5217 AGAAGACGAAGTATGCCTTGAAGGCT
          1 AGAAGACGAAGTATGCCTTGAAGGCT

       5243 GTGTCTAAGA


Statistics
Matches: 79,  Mismatches: 14, Indels: 6
        0.80            0.14        0.06

Matches are distributed among these distances:
  34    1  0.01
  35   78  0.99

ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23


Consensus pattern (35 bp):   
AGAAGACGAAGTATGCCTTGAAGGCTAAGTGTCAT

Found at i:5192 original size:70 final size:70

Alignment explanation


    Indices: 5112--5242  Score: 210
    Period size: 70  Copynumber: 1.9  Consensus size: 70

       5102 CCTGTTTCTA

                               *           *                                 
       5112 AGAAGATGAAGTATGCCTTGAAGGCTAAGTGTC-ATAGAAGACGAAGCATGCCTTGAAGGCTAAG
          1 AGAAGATGAAGTATGCCTTAAAGGCTAAGTGCCGA-AGAAGACGAAGCATGCCTTGAAGGCTAAG

                  
       5176 TATTTG
         65 TATTTG

                        *                                 *              
       5182 AGAAGATGAAGTTTGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGTATGCCTTGAAGGCT
          1 AGAAGATGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGCATGCCTTGAAGGCT

       5243 GTGTCTAAGA


Statistics
Matches: 56,  Mismatches: 4, Indels: 2
        0.90            0.06        0.03

Matches are distributed among these distances:
  70   55  0.98
  71    1  0.02

ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23


Consensus pattern (70 bp):   
AGAAGATGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGCATGCCTTGAAGGCTAAGT
ATTTG

Found at i:5306 original size:103 final size:104

Alignment explanation


    Indices: 5111--5314  Score: 236
    Period size: 103  Copynumber: 2.0  Consensus size: 104

       5101 GCCTGTTTCT

                   *                                              *          
       5111 AAGAAGATGAAGTATGCCTTGAAGGCTAAGTGTCATAGAAGACGAAGCATGCCTTGAAGGCTAAG
          1 AAGAAGACGAAGTATGCCTTGAAGGCT-AGTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAG

                              **  *     *           
       5176 TATTTGAGAAGATGAAGTTTGCCTTAAAGGCTAAGTGCCG
         65 TATTTGAGAAGATGAAGTACGCATTAAAAGCTAAGTGCCG

                                                    *       *   *    *   *   
       5216 AAGAAGACGAAGTATGCCTTGAAGGCT-GTGTC-TAAGAATA-GCAAGTATGTCTCGTAGGTTAA
          1 AAGAAGACGAAGTATGCCTTGAAGGCTAGTGTCAT-AGAAGACG-AAGCATGCCTCGAAGGCTAA

              *                                   
       5278 GTGTTTGAGAAG-TAGAAGTACGCATTAAAAGCTAAGT
         64 GTATTTGAGAAGAT-GAAGTACGCATTAAAAGCTAAGT

       5315 TCCTGGAAAT


Statistics
Matches: 84,  Mismatches: 12, Indels: 8
        0.81            0.12        0.08

Matches are distributed among these distances:
 102    3  0.04
 103   55  0.65
 105   26  0.31

ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25


Consensus pattern (104 bp):   
AAGAAGACGAAGTATGCCTTGAAGGCTAGTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAGT
ATTTGAGAAGATGAAGTACGCATTAAAAGCTAAGTGCCG
Done.