Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g04035.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: 5725
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Found at i:2984 original size:201 final size:201

Alignment explanation


    Indices: 2632--3036  Score: 632
    Period size: 201  Copynumber: 2.0  Consensus size: 201

       2622 GAAATTACTA

                  *         *        *  *       *                            
       2632 AGAATGGCTCTCGTCTTTGTTGCTATCCGAAATTGAGAATTCTTAAGATAGACGATTGCAGAAGT
          1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATAGACGATTGCAGAAGT

                           *   *                           *                 
       2697 TTAAAATATGTTTGTTCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATCTGTCAAAATAAG
         66 TTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAAG

                                                            * *              
       2762 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGGTGTTGTGG
        131 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTGG

                  
       2827 TTCCTC
        196 TTCCTC

                                    *                   *         *       *  
       2833 AGAATGACTCTCGTCTCTGTTGCTGCCCCAAATTGAAAATTCTTGAGATAGGA-TATTGCAGTAG
          1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATA-GACGATTGCAGAAG

                                      *                                      
       2897 TTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA
         65 TTTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA

              **                                                             
       2962 GTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG
        130 GTAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG

               *   
       3027 GTTTCTC
        195 GTTCCTC

               
       3034 AGA
          1 AGA

       3037 GGTTTAAAAT


Statistics
Matches: 185,  Mismatches: 18, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 201  183  0.99
 202    2  0.01

ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Consensus pattern (201 bp):   
AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATAGACGATTGCAGAAGT
TTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAAG
TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTGG
TTCCTC

Found at i:3152 original size:142 final size:142

Alignment explanation


    Indices: 2896--3178  Score: 494
    Period size: 142  Copynumber: 2.0  Consensus size: 142

       2886 TATTGCAGTA

                             *         *                                     
       2896 GTTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
          1 GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA

                *                                                            
       2961 AGTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
         66 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT

                *       
       3026 GGTTTCTCAGAG
        131 GGTTCCTCAGAG

                                 *                           *               
       3038 GTTTAAAATATGTTTGTCCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATCTGTCAAAATA
          1 GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA

                                                              * *            
       3103 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGGTGTTGT
         66 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT

                       
       3168 GGTTCCTCAGA
        131 GGTTCCTCAGA

       3179 TCCATTGCTG


Statistics
Matches: 133,  Mismatches: 8, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 142  133  1.00

ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30


Consensus pattern (142 bp):   
GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
GGTTCCTCAGAG
Done.