Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00208.F2

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: 2995
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:591 original size:72 final size:72

Alignment explanation


    Indices: 486--680  Score: 241
    Period size: 72  Copynumber: 2.7  Consensus size: 72

        476 CTTGAAGAGT

                                 **    *                 *            *      
        486 TTGAAACTGTTGGACCTATC-ACATAATCAAATTACTGGTCCTATTCCTTCTACCCTGTGCAACT
          1 TTGAAACTGTTGGACCTATCTGGA-AACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACT

                    
        550 TAACAAAC
         65 TAACAAAC

                   *                          *   *               *          
        558 TTGAAACAGTTGGACCTATCTGGAAACCAAATTATTGGCCCTATCCCTTCTACCTTGGGCAACTT
          1 TTGAAACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACTT

               *   
        623 AACCAAC
         66 AACAAAC

                   *     *              *                       
        630 TT-AGAATTGTTGAACCTATCTGGAAACGAAATTACTGGTCCTATCCCTTCT
          1 TTGA-AACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCT

        681 GCCTTGGGTA


Statistics
Matches: 105,  Mismatches: 16, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  71    1  0.01
  72  103  0.98
  73    1  0.01

ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31


Consensus pattern (72 bp):   
TTGAAACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACTT
AACAAAC

Found at i:686 original size:72 final size:72

Alignment explanation


    Indices: 513--700  Score: 243
    Period size: 72  Copynumber: 2.6  Consensus size: 72

        503 ATCACATAAT

                             *         *  *          *               *       
        513 CAAATTACTGGTCCTATTCCTTCTACCCTGTGCAACTTAACAAACTTGAAACAGTTGGACCTATC
          1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGAAACAGTTGAACCTATC

                   
        578 TGGAAAC
         66 TGGAAAC

                   *   *                                        **           
        585 CAAATTATTGGCCCTATCCCTTCTACCTTGGGCAACTTAACCAACTT-AGAATTGTTGAACCTAT
          1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGA-AACAGTTGAACCTAT

                    
        649 CTGGAAAC
         65 CTGGAAAC

            *                       *       *  *        
        657 GAAATTACTGGTCCTATCCCTTCTGCCTTGGGTAAATTAACCAA
          1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAA

        701 TTTAAAAGAG


Statistics
Matches: 100,  Mismatches: 15, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  71    1  0.01
  72   99  0.99

ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30


Consensus pattern (72 bp):   
CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGAAACAGTTGAACCTATC
TGGAAAC

Found at i:1156 original size:144 final size:144

Alignment explanation


    Indices: 896--1174  Score: 332
    Period size: 144  Copynumber: 1.9  Consensus size: 144

        886 CAATCCCTCA

                                         *       *       *     *             
        896 TGAAATTGGAAACTTAAAGAATTTGGTTGCATTGAATTTAAGTAACAACAATCTCAAGCATCGGA
          1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA

             *        *       *                                            * 
        961 TTCCTCAATCCCTAACTACTTTATCCAAATTGAGCTACTTGTACTTGGATTCAAAT-TTTCTACA
         66 TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTT-TAAA

                           
       1025 AGGTCCAATTCCTAG
        130 AGGTCCAATTCCTAG

                           *         *                                  * ** 
       1040 TGAAATTGGAAACTTGAAGAATTTGTTTGAATTGAATCTAAGTAAAAACAAGCTCAATG-GTTTG
          1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAA-GCATCGG

                            *          * *         *     *                   
       1104 ATCCCTTC-ATCACTAGCTAATTTATCTAGATTGAGCTATTTGTTCCTT-GATTCAAATCTTTTA
         65 ATCCC-TCAATCACTAACTAATTTATCCAAATTGAGCTACTTG-TACTTGGATTCAAATCTTTTA

                    
       1167 AAAGGTCC
        128 AAAGGTCC

       1175 CTTACCATCT


Statistics
Matches: 113,  Mismatches: 18, Indels: 8
        0.81            0.13        0.06

Matches are distributed among these distances:
 144  103  0.91
 145   10  0.09

ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Consensus pattern (144 bp):   
TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA
TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTTTAAAA
GGTCCAATTCCTAG

Done.