Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01219.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: 2226
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27


Found at i:1207 original size:3 final size:3

Alignment explanation


    Indices: 1199--1246  Score: 69
    Period size: 3  Copynumber: 16.0  Consensus size: 3

       1189 CGCAGCAACT

                            *   *   *                                      
       1199 GCA GCA GCA GCA ACA ACA CCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
          1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA

       1247 AAGGCAAAAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   42  1.00

ACGTcount: A:0.38, C:0.35, G:0.27, T:0.00


Consensus pattern (3 bp):   
GCA

Found at i:1210 original size:15 final size:15

Alignment explanation


    Indices: 1190--1246  Score: 69
    Period size: 15  Copynumber: 3.8  Consensus size: 15

       1180 AGCAACAAAC

                    *      
       1190 GCAGCAACTGCAGCA
          1 GCAGCAACAGCAGCA

                     *  *  
       1205 GCAGCAACAACACCA
          1 GCAGCAACAGCAGCA

                  *        
       1220 GCAGCAGCAGCAGCA
          1 GCAGCAACAGCAGCA

                  *     
       1235 GCAGCAGCAGCA
          1 GCAGCAACAGCA

       1247 AAGGCAAAAA


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   36  1.00

ACGTcount: A:0.37, C:0.35, G:0.26, T:0.02


Consensus pattern (15 bp):   
GCAGCAACAGCAGCA

Found at i:1214 original size:27 final size:27

Alignment explanation


    Indices: 1179--1237  Score: 84
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       1169 ACCATCTCCT

                                *       
       1179 CAGCAACAA-ACGCAGCAACTGCAGCAG
          1 CAGCAACAACAC-CAGCAACAGCAGCAG

                             *         
       1206 CAGCAACAACACCAGCAGCAGCAGCAG
          1 CAGCAACAACACCAGCAACAGCAGCAG

                 
       1233 CAGCA
          1 CAGCA

       1238 GCAGCAGCAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   27  0.93
  28    2  0.07

ACGTcount: A:0.41, C:0.36, G:0.22, T:0.02


Consensus pattern (27 bp):   
CAGCAACAACACCAGCAACAGCAGCAG

Found at i:1760 original size:6 final size:6

Alignment explanation


    Indices: 1749--1796  Score: 87
    Period size: 6  Copynumber: 8.0  Consensus size: 6

       1739 GTGCATGCAC

                                                 *                 
       1749 ATACAT ATACAT ATACAT ATACAT ATACAT ATTCAT ATACAT ATACAT
          1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT

       1797 GTATTGATTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   6   40  1.00

ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35


Consensus pattern (6 bp):   
ATACAT

Done.