Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03668.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: 3059
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:600 original size:191 final size:194

Alignment explanation


    Indices: 235--608  Score: 560
    Period size: 191  Copynumber: 1.9  Consensus size: 194

        225 TGGAAAGGGA

                                                                             
        235 AATTGGAGAGAAAAGGGAGTAACTTGCACAGACTTACTGGAAAGGGGAACCGACGGACAACCCAA
          1 AATTGGAGAG-AAAGGGAGTAACTTGCACAGACTTACTGGAAAGGGGAACCGACGGACAACCCAA

            *     *                                  *                       
        300 GATTTATCTTGCCTTGCTACCAGATACTCAAATCGTGAAATGTCACAATTGAGCCATCACAGAGC
         65 AATTTACCTTGCCTTGCTACCAGATAC-C--ATCGTGAAATATCACAATTGAGCCATCACAGAGC

                      *                          *                           
        365 TACTGATCCATTGGGCAAATTTGGGACCAAAAGAAGCCACATGGGAGGATTTTCGGTTCTATAGG
        127 TACTGATCCAGTGGGCAAATTTGGGACCAAAAGAAGCAACATGGGAGGATTTTCGGTTCTATAGG

               
        430 CTC
        192 CTC

                                    *  *              *      *               
        433 AATTGGAGAG-AAGGGAGTAACTTTCAGAGACTTACTGGAAATGGGAACTGACGGACAACCCAAA
          1 AATTGGAGAGAAAGGGAGTAACTTGCACAGACTTACTGGAAAGGGGAACCGACGGACAACCCAAA

                           *                                                 
        497 ATTTACCTTGCCTTGGTACCAGATA-C-TCGTGAAATATCACAATTGAGCCATCATGCA-A-CTA
         66 ATTTACCTTGCCTTGCTACCAGATACCATCGTGAAATATCACAATTGAGCCATCA--CAGAGCTA

            *                                                  
        558 TTGATCCAGTGGGCAAATTTGGGACCAAAAGAAGCAACATGGGAGGATTTT
        129 CTGATCCAGTGGGCAAATTTGGGACCAAAAGAAGCAACATGGGAGGATTTT

        609 GCTCAATTTT


Statistics
Matches: 163,  Mismatches: 11, Indels: 11
        0.88            0.06        0.06

Matches are distributed among these distances:
 191   77  0.47
 192    1  0.01
 193    2  0.01
 194    1  0.01
 196   72  0.44
 198   10  0.06

ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23


Consensus pattern (194 bp):   
AATTGGAGAGAAAGGGAGTAACTTGCACAGACTTACTGGAAAGGGGAACCGACGGACAACCCAAA
ATTTACCTTGCCTTGCTACCAGATACCATCGTGAAATATCACAATTGAGCCATCACAGAGCTACT
GATCCAGTGGGCAAATTTGGGACCAAAAGAAGCAACATGGGAGGATTTTCGGTTCTATAGGCTC

Found at i:840 original size:78 final size:78

Alignment explanation


    Indices: 711--870  Score: 320
    Period size: 78  Copynumber: 2.1  Consensus size: 78

        701 GAAATAAAAC

                                                                             
        711 CTAATTTTGACCTAGACCCTAAATTGATTTAGCAGACTCAAATGAGAAAAAGGCTAAAAGAAATT
          1 CTAATTTTGACCTAGACCCTAAATTGATTTAGCAGACTCAAATGAGAAAAAGGCTAAAAGAAATT

                         
        776 GGACCAAAGAAGA
         66 GGACCAAAGAAGA

                                                                             
        789 CTAATTTTGACCTAGACCCTAAATTGATTTAGCAGACTCAAATGAGAAAAAGGCTAAAAGAAATT
          1 CTAATTTTGACCTAGACCCTAAATTGATTTAGCAGACTCAAATGAGAAAAAGGCTAAAAGAAATT

                         
        854 GGACCAAAGAAGA
         66 GGACCAAAGAAGA

                
        867 CTAA
          1 CTAA

        871 CGATGCCCAA


Statistics
Matches: 82,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  78   82  1.00

ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22


Consensus pattern (78 bp):   
CTAATTTTGACCTAGACCCTAAATTGATTTAGCAGACTCAAATGAGAAAAAGGCTAAAAGAAATT
GGACCAAAGAAGA
Done.