Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01740.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, 825

Length: 1375
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23


Found at i:808 original size:24 final size:24

Alignment explanation


    Indices: 781--857  Score: 68
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        771 CAAGTCAATG

                       *            
        781 GAGAGGGAAAAACCAAGAAAGCAT
          1 GAGAGGGAAAAGCCAAGAAAGCAT

                 *       *     *     *
        805 GAGAGAGAAGAAGTCAAGTCAA-C-G
          1 GAGAGGGAA-AAGCCAAG-AAAGCAT

                *                   
        829 GAGAAGGAAAAGCCAAGAAAGCAT
          1 GAGAGGGAAAAGCCAAGAAAGCAT

                 
        853 GAGAG
          1 GAGAG

        858 AGAAGAAGAT


Statistics
Matches: 38,  Mismatches: 11, Indels: 8
        0.67            0.19        0.14

Matches are distributed among these distances:
  22    2  0.05
  23    8  0.21
  24   19  0.50
  25    7  0.18
  26    2  0.05

ACGTcount: A:0.51, C:0.12, G:0.32, T:0.05


Consensus pattern (24 bp):   
GAGAGGGAAAAGCCAAGAAAGCAT

Found at i:838 original size:48 final size:48

Alignment explanation


    Indices: 768--865  Score: 169
    Period size: 48  Copynumber: 2.0  Consensus size: 48

        758 AATTTGTTTC

                       *     *                              
        768 AGTCAAGTCAATGGAGAGGGAAAAACCAAGAAAGCATGAGAGAGAAGA
          1 AGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAAGA

                                    *                       
        816 AGTCAAGTCAACGGAGAAGGAAAAGCCAAGAAAGCATGAGAGAGAAGA
          1 AGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAAGA

              
        864 AG
          1 AG

        866 ATCCAGATGA


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  48   47  1.00

ACGTcount: A:0.50, C:0.11, G:0.32, T:0.07


Consensus pattern (48 bp):   
AGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAAGA

Found at i:858 original size:26 final size:26

Alignment explanation


    Indices: 781--858  Score: 60
    Period size: 23  Copynumber: 3.2  Consensus size: 26

        771 CAAGTCAATG

                *      *              
        781 GAGAGGGAAAAACCAAGAAAGCATGA
          1 GAGAAGGAAAAGCCAAGAAAGCATGA

                         *     *        
        807 GAG-A-GAAGAAGTCAAGTCAA-C--G-
          1 GAGAAGGAA-AAGCCAAG-AAAGCATGA

                                      
        829 GAGAAGGAAAAGCCAAGAAAGCATGA
          1 GAGAAGGAAAAGCCAAGAAAGCATGA

                
        855 GAGA
          1 GAGA

        859 GAAGAAGATC


Statistics
Matches: 38,  Mismatches: 6, Indels: 16
        0.63            0.10        0.27

Matches are distributed among these distances:
  22    5  0.13
  23   10  0.26
  24    6  0.16
  25    8  0.21
  26    9  0.24

ACGTcount: A:0.51, C:0.12, G:0.32, T:0.05


Consensus pattern (26 bp):   
GAGAAGGAAAAGCCAAGAAAGCATGA

Found at i:1163 original size:5 final size:5

Alignment explanation


    Indices: 1153--1179  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

       1143 GAGTTGAGCT

                                            
       1153 GACCA GACCA GACCA GACCA GACCA GA
          1 GACCA GACCA GACCA GACCA GACCA GA

       1180 GCGGGGTTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.41, C:0.37, G:0.22, T:0.00


Consensus pattern (5 bp):   
GACCA

Done.