Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00841.F6

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: 4383
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31


Found at i:863 original size:31 final size:31

Alignment explanation


    Indices: 808--885  Score: 88
    Period size: 31  Copynumber: 2.5  Consensus size: 31

        798 TTTTCCTTAA

                     *                    * 
        808 TGGCTTGGATAAGCCTT--GATGCAATCGAGT
          1 TGGCTT-GAGAAGCCTTGAGATGCAATCGAAT

                     *                **   
        838 TGGCTTGAGTAGCCTTGAGATGCAATTTAAT
          1 TGGCTTGAGAAGCCTTGAGATGCAATCGAAT

                             
        869 TGGCTTGAGAAGCCTTG
          1 TGGCTTGAGAAGCCTTG

        886 TGGCAAATGA


Statistics
Matches: 40,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  29    8  0.20
  30    6  0.15
  31   26  0.65

ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32


Consensus pattern (31 bp):   
TGGCTTGAGAAGCCTTGAGATGCAATCGAAT

Found at i:3166 original size:164 final size:166

Alignment explanation


    Indices: 2880--3204  Score: 451
    Period size: 164  Copynumber: 2.0  Consensus size: 166

       2870 TTGCTGGCTA

                                             * **                 **         
       2880 TGTTAACTTTCTCATAATTGCATTAGTGTACAAGTTTGTTGCTTGTGGGGAGTTTTTAACATAAT
          1 TGTTAAC-TTCTCATAATTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAAT

               *            *     *                                          
       2945 TATTTAGTTGTTGAAATTGTGACTAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTT
         65 TATGTAGTTGTTGAAAATGTGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTT

                         *                       
       3010 ACCAATGTATCTGGCTGAGAAATTCTCAACCGGAATC
        130 ACCAATGTATCTGACTGAGAAATTCTCAACCGGAATC

                        *                                                 *  
       3047 TGTTAAC-TCTCTTAATTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAG-TCATAACATGCA-
          1 TGTTAACTTCTCATAATTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACAT-AAT

                                                       *                *    
       3109 TATGTAGTTGTTGAAAATGCTGAAT-ATTAGGCTTTTGAAGAATATTGACTTATGTTTCTTGATT
         65 TATGTAGTTGTTGAAAATG-TGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATT

               *     *                 *    
       3173 TACTAATGTGTCTGACTGAGAAATTCTTAACC
        129 TACCAATGTATCTGACTGAGAAATTCTCAACC

       3205 AAAATGTGCT


Statistics
Matches: 140,  Mismatches: 16, Indels: 7
        0.86            0.10        0.04

Matches are distributed among these distances:
 164   89  0.64
 165   44  0.31
 167    7  0.05

ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40


Consensus pattern (166 bp):   
TGTTAACTTCTCATAATTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAATT
ATGTAGTTGTTGAAAATGTGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTA
CCAATGTATCTGACTGAGAAATTCTCAACCGGAATC
Done.