Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g02560.R1

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, 914

Length: 1524
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28


Found at i:917 original size:24 final size:24

Alignment explanation


    Indices: 885--937  Score: 106
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        875 GAATTGGGAA

                                    
        885 ACAATGATGCCAGAGAAAATCAAG
          1 ACAATGATGCCAGAGAAAATCAAG

                                    
        909 ACAATGATGCCAGAGAAAATCAAG
          1 ACAATGATGCCAGAGAAAATCAAG

                 
        933 ACAAT
          1 ACAAT

        938 ATGAAGCTGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.51, C:0.17, G:0.19, T:0.13


Consensus pattern (24 bp):   
ACAATGATGCCAGAGAAAATCAAG

Found at i:1229 original size:42 final size:42

Alignment explanation


    Indices: 1182--1315  Score: 180
    Period size: 42  Copynumber: 3.2  Consensus size: 42

       1172 AGGAAAGGCG

                                        *            *
       1182 AACTGAAGGTGGAGAAGGGAGAAGCTGATTTAAAAGAAAACA
          1 AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC

                          *    *                      
       1224 AACTGAAGGTGGAGCAGGGCGAAGCTGAGTTAAAAGAAAACC
          1 AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC

                    *            *           *         
       1266 AACTGAAGCTGGAGAA-GGACAAAGCTGAGTTAGAAGAAAACC
          1 AACTGAAGGTGGAGAAGGGA-GAAGCTGAGTTAAAAGAAAACC

            *       
       1308 TACTGAAG
          1 AACTGAAG

       1316 CTAAAAACGT


Statistics
Matches: 81,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  41    2  0.02
  42   79  0.98

ACGTcount: A:0.44, C:0.12, G:0.31, T:0.13


Consensus pattern (42 bp):   
AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC

Found at i:1486 original size:76 final size:78

Alignment explanation


    Indices: 1376--1524  Score: 212
    Period size: 76  Copynumber: 1.9  Consensus size: 78

       1366 ATACATTCTC

                    *                                      *                 
       1376 AATGGTTTGTTGAGGATGTTGATGAACTGAAGATACAAACAGTATGTGTTTATGT-GATGGTTCT
          1 AATGGTTTATTGAGGATGTTGATGAACTGAAGATACAAACAGTATGTATTTATGTCGATGGTTCT

                         
       1440 GTGTTTGAATCTT
         66 GTGTTTGAATCTT

                                *    *           *     *                    *
       1453 AATGGTTTATTG-GGATGTTTATGAGCTGAAGATACAGACAGTTTGTATTTATGTGCGATGGTTT
          1 AATGGTTTATTGAGGATGTTGATGAACTGAAGATACAAACAGTATGTATTTATGT-CGATGGTTC

                    
       1517 TGTGTTTG
         65 TGTGTTTG


Statistics
Matches: 63,  Mismatches: 7, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  76   37  0.59
  77   11  0.17
  78   15  0.24

ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42


Consensus pattern (78 bp):   
AATGGTTTATTGAGGATGTTGATGAACTGAAGATACAAACAGTATGTATTTATGTCGATGGTTCT
GTGTTTGAATCTT
Done.