Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02253.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: 2037
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27


Found at i:484 original size:54 final size:54

Alignment explanation


    Indices: 425--593  Score: 207
    Period size: 54  Copynumber: 3.1  Consensus size: 54

        415 GAAGCTCGGC

                                    *                               
        425 ATGAAGCTCATCATGC-AGAAGA-AAAAGTTGCAGATGCGATGGAGCATGGAAGAG
          1 ATGAAGCTCATCATGCGA-AAGATGAAA-TTGCAGATGCGATGGAGCATGGAAGAG

            *             *            *         *   *     *      
        479 GTGAAGCTCATCATACGAAAGATGAAACTGCAGATGCAATGCAGCATAGAAGAG
          1 ATGAAGCTCATCATGCGAAAGATGAAATTGCAGATGCGATGGAGCATGGAAGAG

                   *                               *           *  
        533 ATGAAGCCCATCATGCGAAAGATGAAATTGCAGATGCGAAGGAGCATGGAACAG
          1 ATGAAGCTCATCATGCGAAAGATGAAATTGCAGATGCGATGGAGCATGGAAGAG

              *    
        587 ATAAAGC
          1 ATGAAGC

        594 AGCAGATACA


Statistics
Matches: 96,  Mismatches: 17, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
  54   92  0.96
  55    4  0.04

ACGTcount: A:0.40, C:0.15, G:0.28, T:0.16


Consensus pattern (54 bp):   
ATGAAGCTCATCATGCGAAAGATGAAATTGCAGATGCGATGGAGCATGGAAGAG

Found at i:1002 original size:39 final size:39

Alignment explanation


    Indices: 948--1027  Score: 142
    Period size: 39  Copynumber: 2.1  Consensus size: 39

        938 CATATGCATC

                                     *             
        948 TGGTGATAAGATCATGAGTGAAGATTTTATGGCTAAGTT
          1 TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

                            *                      
        987 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTT
          1 TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

              
       1026 TG
          1 TG

       1028 AGGCTTTGAC


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35


Consensus pattern (39 bp):   
TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

Found at i:1204 original size:180 final size:177

Alignment explanation


    Indices: 987--1312  Score: 474
    Period size: 180  Copynumber: 1.8  Consensus size: 177

        977 TGGCTAAGTT

                          * *             *           *                      
        987 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTTTGAGGCTTTGACAGAGAAGGCT-TCC
          1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGG-TGTCC

                        *   *             *      *                       *   
       1051 CATATTATAGCTGATGGTGTAGCTAGGATCCTTAAAGGTAAGGCTGCAGAATCAATCTCGCGTGG
         65 CATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGG

                                                               
       1116 AAGAAATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC
        130 -AG--ATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC

                                                                    *     *  
       1167 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGACGGTGTGCC
          1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGGTGTCCC

              *                         *                      *             
       1232 ATGTTATAGCTAATGATGTAGCTAGGATTATTAAAGATAAGGCTGCAGAATTAATCTCGCATGGA
         66 ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA

                       *    
       1297 GATGAAGTTTCGCATG
        131 GATGAAGTTTCCCATG

       1313 CCACATATGC


Statistics
Matches: 130,  Mismatches: 15, Indels: 5
        0.87            0.10        0.03

Matches are distributed among these distances:
 177   14  0.11
 179    3  0.02
 180  113  0.87

ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29


Consensus pattern (177 bp):   
TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGGTGTCCC
ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA
GATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC
Done.