Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g00870.C1

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: 5270
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28


Found at i:1222 original size:39 final size:39

Alignment explanation


    Indices: 1166--1250  Score: 136
    Period size: 39  Copynumber: 2.2  Consensus size: 39

       1156 AAACACACTG

                                                    
       1166 AAGCTTGCAACTCCAAAGCAAGT-AAGGGAAAAGAAACCA
          1 AAGCTTGCAACTCCAAAGCAAGTCAA-GGAAAAGAAACCA

             *                 *                   
       1205 AGGCTTGCAACTCCAAAGCTAGTCAAGGAAAAGAAACCA
          1 AAGCTTGCAACTCCAAAGCAAGTCAAGGAAAAGAAACCA

                   
       1244 AAGCTTG
          1 AAGCTTG

       1251 TAGCTGCGAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  39   40  0.95
  40    2  0.05

ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13


Consensus pattern (39 bp):   
AAGCTTGCAACTCCAAAGCAAGTCAAGGAAAAGAAACCA

Found at i:2207 original size:87 final size:87

Alignment explanation


    Indices: 2079--2301  Score: 297
    Period size: 87  Copynumber: 2.6  Consensus size: 87

       2069 ATTGATCAAA

                 *            *  *          *   *                            
       2079 CAGTGGGGGAGATCGAAGAATGGGAAACTGATGCTCTGATTACTGGCAAAAATAACCTTCGTGTC
          1 CAGTGAGGGAGATCGAAGTATTGGAAACTGATACTCCGATTACTGGCAAAAATAACCTTCGTGTC

                                   
       2144 ACT-GATAAGATGGATATATCAG
         66 ACTGGA-AAGATGGATATATCAG

                         *                                  ***        *     
       2166 CAGTGAGGGAGATTGAAGTATTGGAAACTGATACTCCGATTACTGGCACTGATAACCTTTGTGTC
          1 CAGTGAGGGAGATCGAAGTATTGGAAACTGATACTCCGATTACTGGCAAAAATAACCTTCGTGTC

                           *      
       2231 ACTGGAAAGATGGATCTATCAG
         66 ACTGGAAAGATGGATATATCAG

              *           *                                   
       2253 CAATGAGGGAGATCAAAGTATTGGAAACTGATA-TCCTGATTACTGGCAA
          1 CAGTGAGGGAGATCGAAGTATTGGAAACTGATACTCC-GATTACTGGCAA

       2302 GAGAAAGCGT


Statistics
Matches: 119,  Mismatches: 15, Indels: 4
        0.86            0.11        0.03

Matches are distributed among these distances:
  86    3  0.03
  87  114  0.96
  88    2  0.02

ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26


Consensus pattern (87 bp):   
CAGTGAGGGAGATCGAAGTATTGGAAACTGATACTCCGATTACTGGCAAAAATAACCTTCGTGTC
ACTGGAAAGATGGATATATCAG

Found at i:5238 original size:62 final size:62

Alignment explanation


    Indices: 5139--5256  Score: 173
    Period size: 62  Copynumber: 1.9  Consensus size: 62

       5129 GAATATATGT

                           *          *                                   
       5139 TCGACATGTATTTAGTTCCTTGATAGGCACGTAGTAAGTATTTAAAACAATTTATTTGACAA
          1 TCGACATGTATTTAGATCCTTGATAGACACGTAGTAAGTATTTAAAACAATTTATTTGACAA

                         *    *          *  *                *      
       5201 TCGACATGTATTTTGATCTTTGATAGACATGTGGTAAGTATTTAAAACAGTTTATT
          1 TCGACATGTATTTAGATCCTTGATAGACACGTAGTAAGTATTTAAAACAATTTATT

       5257 GTTTTTTCTG


Statistics
Matches: 49,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  62   49  1.00

ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40


Consensus pattern (62 bp):   
TCGACATGTATTTAGATCCTTGATAGACACGTAGTAAGTATTTAAAACAATTTATTTGACAA
Done.