Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g03236.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, 1000

Length: 3497
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31


Found at i:486 original size:46 final size:46

Alignment explanation


    Indices: 430--605  Score: 189
    Period size: 46  Copynumber: 3.8  Consensus size: 46

        420 TGGTTGAGCA

                 *     *              *                   
        430 TCCGAACTCGTCGAGTTGAGTCCGAGATCACTTATGGATGCGAATG
          1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

             *                            * *        *       
        476 TTCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
          1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G

                        *                                 * 
        521 CATCCGAGCTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

            *                                    
        569 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG

        606 GCGGGTTACA


Statistics
Matches: 106,  Mismatches: 15, Indels: 18
        0.76            0.11        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    5  0.05
  45    3  0.03
  46   60  0.57
  47   27  0.25
  48    3  0.03
  50    4  0.04
  51    2  0.02

ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28


Consensus pattern (46 bp):   
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

Found at i:586 original size:93 final size:93

Alignment explanation


    Indices: 427--597  Score: 281
    Period size: 93  Copynumber: 1.8  Consensus size: 93

        417 GGATGGTTGA

                                                           * **              
        427 GCATCCGAACTCGTCGAGTTGAGTCCGAGATCACTTATGGATGCGAATGTTCGAGCTCGTTGAGT
          1 GCATCCGAACTCGTCGAGTTGAGTCCGAGATCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT

                                        
        492 TGAGTCCGAGTTCGTGAGATGTAACTAG
         66 TGAGTCCGAGTTCGTGAGATGTAACTAG

                    *                     *                                  
        520 GCATCCGAGCTCGAT-GAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
          1 GCATCCGAACTCG-TCGAGTTGAGTCCGAGATCACTTATGGATGCGAACGCCCGAGCTCGTTGAG

                          
        584 TTGAGTCCGAGTTC
         65 TTGAGTCCGAGTTC

        598 ACTTATGGGC


Statistics
Matches: 72,  Mismatches: 5, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  93   71  0.99
  94    1  0.01

ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27


Consensus pattern (93 bp):   
GCATCCGAACTCGTCGAGTTGAGTCCGAGATCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG

Found at i:3228 original size:46 final size:45

Alignment explanation


    Indices: 3126--3292  Score: 185
    Period size: 46  Copynumber: 3.6  Consensus size: 45

       3116 GAGATTTGTG

                               *  *              * *    *  
       3126 TGCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGA
          1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA

             *  *                                         
       3173 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
          1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA

                      *                   *                
       3219 TAGCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-
          1 T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA

               *                         
       3264 TGCTAGTGTAAGACATGTCTGGGACATGC
          1 TGCCAGTGTAAGACATGTCTGGGACATGC

       3293 GTCAGCACGG


Statistics
Matches: 104,  Mismatches: 13, Indels: 8
        0.83            0.10        0.06

Matches are distributed among these distances:
  44   26  0.25
  45    3  0.03
  46   52  0.50
  47   12  0.12
  48   11  0.11

ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23


Consensus pattern (45 bp):   
TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA

Found at i:3287 original size:44 final size:44

Alignment explanation


    Indices: 3175--3335  Score: 184
    Period size: 46  Copynumber: 3.6  Consensus size: 44

       3165 TGAGACGAGG

                                        *                 
       3175 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAT
          1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-T

               *     *                                   
       3220 AGCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
          1 -GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT

                                           *          *    
       3265 GCTAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGT
          1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTAC-G--AGATGT

                          *           
       3311 G-TCAGTGTAAGACCTGTCTGGGACA
          1 GCT-AGTGTAAGACATGTCTGGGACA

       3336 CGGCATCGAC


Statistics
Matches: 102,  Mismatches: 8, Indels: 10
        0.85            0.07        0.08

Matches are distributed among these distances:
  43    2  0.02
  44   32  0.31
  45    4  0.04
  46   64  0.63

ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24


Consensus pattern (44 bp):   
GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT

Done.