Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00184.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, 946

Length: 1577
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32


Found at i:206 original size:26 final size:26

Alignment explanation


    Indices: 175--301  Score: 227
    Period size: 26  Copynumber: 4.9  Consensus size: 26

        165 TGATATCCAT

                          *    *      
        175 GTTAGGTAAATGTTCCATGGTAATGG
          1 GTTAGGTAAATGTTTCATGATAATGG

                                    * 
        201 GTTAGGTAAATGTTTCATGATAATAG
          1 GTTAGGTAAATGTTTCATGATAATGG

                                      
        227 GTTAGGTAAATGTTTCATGATAATGG
          1 GTTAGGTAAATGTTTCATGATAATGG

                                      
        253 GTTAGGTAAATGTTTCATGATAATGG
          1 GTTAGGTAAATGTTTCATGATAATGG

                                   
        279 GTTAGGTAAATGTTTCATGATAA
          1 GTTAGGTAAATGTTTCATGATAA

        302 GAATTTCATG


Statistics
Matches: 97,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   97  1.00

ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38


Consensus pattern (26 bp):   
GTTAGGTAAATGTTTCATGATAATGG

Found at i:1047 original size:27 final size:27

Alignment explanation


    Indices: 1006--1145  Score: 165
    Period size: 27  Copynumber: 5.2  Consensus size: 27

        996 GAGGAAGCGT

                      *                
       1006 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                                       
       1033 TCTGGTGGCTCTGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                        *     *       *
       1060 TCTGGTGGCTCTACCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                            ** *        
       1087 TCTGGTGGCTCTGCCATGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

                   *     *     *      *
       1115 TCTGGTGACTCTGTCAC-ATTATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                 
       1141 TCTGG
          1 TCTGG

       1146 CAGCCATGCT


Statistics
Matches: 98,  Mismatches: 14, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  26    5  0.05
  27   79  0.81
  28   14  0.14

ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:1091 original size:54 final size:55

Alignment explanation


    Indices: 1006--1145  Score: 185
    Period size: 54  Copynumber: 2.6  Consensus size: 55

        996 GAGGAAGCGT

                      *       *       *                            
       1006 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                        *                              ** *        
       1060 TCTGGTGGCTCTACCACATATATCTGTTCTGGTGGCTCTGCCATGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                   *     *                  
       1115 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG

       1146 CAGCCATGCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
  54   58  0.77
  55   17  0.23

ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

Found at i:1231 original size:19 final size:22

Alignment explanation


    Indices: 1207--1246  Score: 59
    Period size: 19  Copynumber: 2.0  Consensus size: 22

       1197 CTCCCCACAC

                                  
       1207 GGTGTA-A-GGTTGG-TATGGG
          1 GGTGTATACGGTTGGATATGGG

                                 
       1226 GGTGTATACGGTTGGATATGG
          1 GGTGTATACGGTTGGATATGG

       1247 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.