Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01198.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, 1000

Length: 2019
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32


Found at i:89 original size:26 final size:26

Alignment explanation


    Indices: 60--169  Score: 166
    Period size: 26  Copynumber: 4.2  Consensus size: 26

         50 TGATACAAAT

                                      
         60 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                     *          *     
         86 TGATAATGGATTAGGTAAATATTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                                   *  
        112 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                     *    *        *  
        138 TGATAATGGTTTAGATAAATGTTTCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                  
        164 TGATAA
          1 TGATAA

        170 GAATTTCATG


Statistics
Matches: 77,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   77  1.00

ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37


Consensus pattern (26 bp):   
TGATAATGGGTTAGGTAAATGTTCCA

Found at i:145 original size:13 final size:13

Alignment explanation


    Indices: 129--169  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        119 GGGTTAGGTA

                         
        129 AATGTTTCATGAT
          1 AATGTTTCATGAT

                          
        142 AATGGTTT-A-GAT
          1 AAT-GTTTCATGAT

                          
        154 AAATGTTTCATGAT
          1 -AATGTTTCATGAT

              
        168 AA
          1 AA

        170 GAATTTCATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 8
        0.75            0.00        0.25

Matches are distributed among these distances:
  12    7  0.29
  13   10  0.42
  14    7  0.29

ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41


Consensus pattern (13 bp):   
AATGTTTCATGAT

Found at i:168 original size:14 final size:14

Alignment explanation


    Indices: 127--169  Score: 56
    Period size: 14  Copynumber: 3.2  Consensus size: 14

        117 ATGGGTTAGG

                          
        127 TAAATGTTTCATGA
          1 TAAATGTTTCATGA

                           
        141 T-AATGGTTT-A-GA
          1 TAAAT-GTTTCATGA

                          
        153 TAAATGTTTCATGA
          1 TAAATGTTTCATGA

               
        167 TAA
          1 TAA

        170 GAATTTCATG


Statistics
Matches: 25,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
  12    7  0.28
  13    8  0.32
  14   10  0.40

ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42


Consensus pattern (14 bp):   
TAAATGTTTCATGA

Found at i:1281 original size:136 final size:136

Alignment explanation


    Indices: 1037--1321  Score: 534
    Period size: 136  Copynumber: 2.1  Consensus size: 136

       1027 GAGTAGTCTC

                      *                                                      
       1037 CCCAAATGGGTTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
          1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT

                                                               *             
       1102 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATCA
         66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATCA

                  
       1167 CTGTTA
        131 CTGTTA

                                                                             
       1173 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
          1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT

                                                                             
       1238 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATCA
         66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATCA

                  
       1303 CTGTTA
        131 CTGTTA

              **         
       1309 CCTGAATGGGCTT
          1 CCCAAATGGGCTT

       1322 AGGCCCAATA


Statistics
Matches: 145,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 136  145  1.00

ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33


Consensus pattern (136 bp):   
CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATCA
CTGTTA
Done.