Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00444.P3

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: 6133
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30


Found at i:1132 original size:34 final size:35

Alignment explanation


    Indices: 1083--1169  Score: 99
    Period size: 34  Copynumber: 2.5  Consensus size: 35

       1073 GTGTATGGAA

                                                
       1083 TTAGGGTTTATGGTTTAGAATTTAGATTTA-A-GGT
          1 TTAGGGTTTATGGTTTAGAATTTAG-TTTATAGGGT

                *    *        *                
       1117 TTAGTGTTTTTGGTTTAGGATTTAGTTTATAGGGT
          1 TTAGGGTTTATGGTTTAGAATTTAGTTTATAGGGT

               *               
       1152 TTAAGGTTTAAT-GTTTAG
          1 TTAGGGTTT-ATGGTTTAG

       1170 GGCATTGGGT


Statistics
Matches: 44,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  33    4  0.09
  34   23  0.52
  35   16  0.36
  36    1  0.02

ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51


Consensus pattern (35 bp):   
TTAGGGTTTATGGTTTAGAATTTAGTTTATAGGGT

Found at i:1181 original size:14 final size:14

Alignment explanation


    Indices: 1164--1214  Score: 66
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       1154 AAGGTTTAAT

                    *     
       1164 GTTTAGGGCATTGG
          1 GTTTAGGGTATTGG

                 *        
       1178 GTTTAAGGTATTGG
          1 GTTTAGGGTATTGG

             *          * 
       1192 GCTTAGGGTATTAG
          1 GTTTAGGGTATTGG

                     
       1206 GTTTAGGGT
          1 GTTTAGGGT

       1215 TTAGTCTATT


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  14   31  1.00

ACGTcount: A:0.18, C:0.04, G:0.39, T:0.39


Consensus pattern (14 bp):   
GTTTAGGGTATTGG

Found at i:1217 original size:7 final size:7

Alignment explanation


    Indices: 1083--1218  Score: 57
    Period size: 7  Copynumber: 19.6  Consensus size: 7

       1073 GTGTATGGAA

                   
       1083 TTAGGGT
          1 TTAGGGT

               *   
       1090 TTATGGT
          1 TTAGGGT

                ** 
       1097 TTAGAAT
          1 TTAGGGT

                 * 
       1104 TTA-GAT
          1 TTAGGGT

               *   
       1110 TTAAGGT
          1 TTAGGGT

                *  
       1117 TTAGTGT
          1 TTAGGGT

              **   
       1124 TTTTGGT
          1 TTAGGGT

                 * 
       1131 TTAGGAT
          1 TTAGGGT

                 * 
       1138 TTA-GTT
          1 TTAGGGT

                    
       1144 TATAGGGT
          1 T-TAGGGT

               *   
       1152 TTAAGGT
          1 TTAGGGT

               **  
       1159 TTAATGT
          1 TTAGGGT

                   *
       1166 TTAGGGCA
          1 TTAGGG-T

                   
       1174 TT-GGGT
          1 TTAGGGT

               *   
       1180 TTAAGGT
          1 TTAGGGT

                   *
       1187 ATT-GGGC
          1 -TTAGGGT

                   
       1194 TTAGGGT
          1 TTAGGGT

                    
       1201 ATTA-GGT
          1 -TTAGGGT

                   
       1208 TTAGGGT
          1 TTAGGGT

                
       1215 TTAG
          1 TTAG

       1219 TCTATTGGTT


Statistics
Matches: 94,  Mismatches: 26, Indels: 18
        0.68            0.19        0.13

Matches are distributed among these distances:
   6   15  0.16
   7   69  0.73
   8   10  0.11

ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46


Consensus pattern (7 bp):   
TTAGGGT

Found at i:5895 original size:21 final size:21

Alignment explanation


    Indices: 5854--5926  Score: 85
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       5844 TAGAGCGGAT

                *                 
       5854 GCAGTAGC-AAGGAAGGCAGCG
          1 GCAGCAGCGAAGG-AGGCAGCG

                   *  *     *    
       5875 GCAGCAGGGAGGGAGGTAGCG
          1 GCAGCAGCGAAGGAGGCAGCG

                               * 
       5896 GCAGCAGCGAAGGAGGCAGAG
          1 GCAGCAGCGAAGGAGGCAGCG

                      
       5917 GCAGCAGCGA
          1 GCAGCAGCGA

       5927 TGGTAGCAGA


Statistics
Matches: 43,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  21   40  0.93
  22    3  0.07

ACGTcount: A:0.30, C:0.19, G:0.48, T:0.03


Consensus pattern (21 bp):   
GCAGCAGCGAAGGAGGCAGCG

Done.