Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3320

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, 460

Length: 767
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32


Found at i:272 original size:125 final size:125

Alignment explanation


    Indices: 50--306  Score: 453
    Period size: 125  Copynumber: 2.1  Consensus size: 125

         40 TCCCGGGAAA

                            * *  *                                           
         50 AGAAATTGTGAAATCATGGCCTCGTGGACGCGATTTCGCTACAGTGGTCATGTAAGAAATAAATT
          1 AGAAATTGTGAAATCACGCCCCCGTGGACGCGATTTCGCTACAGTGGTCATGTAAGAAATAAATT

                                                                        
        115 TTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACAATGATGCTATATTGGGC
         66 TTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACAATGATGCTATATTGGGC

                           *                                       *         
        175 AGAAATTGTGAAATCGCGCCCCCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAAT-AAT
          1 AGAAATTGTGAAATCACGCCCCCGTGGACGCGATTTCGCTACAG-TGGTCATGTAAGAAATAAAT

                                                                         
        239 TTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACAATGATGCTATATTGGGC
         65 TTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACAATGATGCTATATTGGGC

                   
        300 AGAAATT
          1 AGAAATT

        307 CGTAAAAGAA


Statistics
Matches: 126,  Mismatches: 5, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
 125  111  0.88
 126   15  0.12

ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32


Consensus pattern (125 bp):   
AGAAATTGTGAAATCACGCCCCCGTGGACGCGATTTCGCTACAGTGGTCATGTAAGAAATAAATT
TTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACAATGATGCTATATTGGGC

Found at i:348 original size:125 final size:124

Alignment explanation


    Indices: 86--400  Score: 345
    Period size: 125  Copynumber: 2.5  Consensus size: 124

         76 GACGCGATTT

                    *          *                                             
         86 CGCTAC-AGTGGTCATGTAAGAAATAAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCG
          1 CGCTACAATTGGTCATGTAGGAAAT-AATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCG

                                                   * *  *     ** *      *
        150 CTGATACAATGATGCTATATTGGGCAGAAATTGTGAAATCGCGCCCCCGTGGACGCGATTT
         65 CTGATACAATGATGCTATATTGGGCAGAAATTGTGAAATAGAGCACCCGTAAAAGC-ATTG

                   *                                                         
        211 CGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGC
          1 CGCTACAATTGGTCATGTAGGAAATAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGC

                                                       ** **       *       
        276 TGATACAATGATGCTATATTGGGCAGAAATTCGT-AAA-AGAATTAGGCGTAAAATC-TTCGG
         66 TGATACAATGATGCTATATTGGGCAGAAATT-GTGAAATAG-AGCACCCGTAAAAGCATT--G

                                        *                   *        * *     
        336 CGCT-CAAATTGGTCATGTAGGAAATATTTTTTTTTGACG-TTTCTGAACAAATAGTGTCAAATC
          1 CGCTAC-AATTGGTCATGTAGGAAATA-ATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATC

              
        399 GC
         64 GC

        401 GCCCTCGTGG


Statistics
Matches: 163,  Mismatches: 20, Indels: 14
        0.83            0.10        0.07

Matches are distributed among these distances:
 123    2  0.01
 124    2  0.01
 125  131  0.80
 126   28  0.17

ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32


Consensus pattern (124 bp):   
CGCTACAATTGGTCATGTAGGAAATAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGC
TGATACAATGATGCTATATTGGGCAGAAATTGTGAAATAGAGCACCCGTAAAAGCATTG
Done.