Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: LOC111286030

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: 2622
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35


Found at i:297 original size:120 final size:122

Alignment explanation


    Indices: 156--419  Score: 333
    Period size: 124  Copynumber: 2.2  Consensus size: 122

        146 TCTCTCAACC

                    *                                       *      *   *     
        156 GTTGGTTTTAAATA-AAAAAAC-AATAAGTTGAAGA-TC-T-CTTGGATTTCAAATTTCTTCAGA
          1 GTTGGTTTGAAA-AGAAAAAACAAATAAGTTGAAGACTCATGCTTGGACTTC-AACTTCAT-AGA

                *                 *                                      
        216 GACTTTTAGATAGACACCTTATGGTGCTTT-CGTTGCTAACTTCTTTCTCTCGAAATTTCA
         63 GACTCTTAGATAGAC-CCTTATCGTGCTTTCCGTTGCTAACTTCTTTCTCTCGAAATTTCA

                                       *               *                     
        276 GTTGGTTTGAAAAGAAAAAACAAATAATTTGAAGACCTCTATGTTTGGACTTCAACTTCATAGAG
          1 GTTGGTTTGAAAAGAAAAAACAAATAAGTTGAAGA-CTC-ATGCTTGGACTTCAACTTCATAGAG

                      *                       *  *                     
        341 ACTCTTAGATGGACCCTTATCGTGCTTTCCGTTGTTACCTTCTTTCTCTCGAAATTTCA
         64 ACTCTTAGATAGACCCTTATCGTGCTTTCCGTTGCTAACTTCTTTCTCTCGAAATTTCA

                                
        400 GTTGGTTTGAAAAGAAAAAA
          1 GTTGGTTTGAAAAGAAAAAA

        420 ACAACAATAT


Statistics
Matches: 125,  Mismatches: 11, Indels: 12
        0.84            0.07        0.08

Matches are distributed among these distances:
 119    1  0.01
 120   18  0.14
 121   12  0.10
 123   15  0.12
 124   64  0.51
 125    7  0.06
 126    8  0.06

ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Consensus pattern (122 bp):   
GTTGGTTTGAAAAGAAAAAACAAATAAGTTGAAGACTCATGCTTGGACTTCAACTTCATAGAGAC
TCTTAGATAGACCCTTATCGTGCTTTCCGTTGCTAACTTCTTTCTCTCGAAATTTCA

Found at i:374 original size:124 final size:124

Alignment explanation


    Indices: 213--454  Score: 362
    Period size: 124  Copynumber: 2.0  Consensus size: 124

        203 AAATTTCTTC

                   *                 *                                       
        213 AGAGACTTTTAGATAGACACCTTATGGTGCTTTCGTTGCTAACTTCTTTCTCTCGAAATTTCAGT
          1 AGAGACTCTTAGATAGACACCTTATCGTGCTTTCGTTGCTAACTTCTTTCTCTCGAAATTTCAGT

                                   *   *    *           *               
        278 TGGTTTGAAAAG-AAAAAACAAATAATTTGAAGACCTCTATGTTTGGACTTCAACTTCAT
         66 TGGTTTGAAAAGAAAAAAAC-AACAATATGAAAACCTCTATGTTCGGACTTCAACTTCAT

                          *                        *  *                      
        337 AGAGACTCTTAGATGGAC-CCTTATCGTGCTTTCCGTTGTTACCTTCTTTCTCTCGAAATTTCAG
          1 AGAGACTCTTAGATAGACACCTTATCGTGCTTT-CGTTGCTAACTTCTTTCTCTCGAAATTTCAG

                                               *                  
        401 TTGGTTTGAAAAGAAAAAAACAACAATATGAAAACGTCTATGTTCGGACTTCAA
         65 TTGGTTTGAAAAGAAAAAAACAACAATATGAAAACCTCTATGTTCGGACTTCAA

        455 ATAGAGACTT


Statistics
Matches: 106,  Mismatches: 10, Indels: 4
        0.88            0.08        0.03

Matches are distributed among these distances:
 123   13  0.12
 124   86  0.81
 125    7  0.07

ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35


Consensus pattern (124 bp):   
AGAGACTCTTAGATAGACACCTTATCGTGCTTTCGTTGCTAACTTCTTTCTCTCGAAATTTCAGT
TGGTTTGAAAAGAAAAAAACAACAATATGAAAACCTCTATGTTCGGACTTCAACTTCAT
Done.