Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01090.N6

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: 1854
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33


Found at i:179 original size:37 final size:37

Alignment explanation


    Indices: 138--215  Score: 88
    Period size: 37  Copynumber: 2.1  Consensus size: 37

        128 TTAAGCATTT

                               *               *   
        138 TTCTCCATGTCTTTCA-GTTTGA-AAACTAAGACGTTTC
          1 TTCTCC-TGTCTTTCATG-CTGAGAAACTAAGACGCTTC

                   * *                           
        175 TTCTCCTTTTTTTCATGCTGAGAAACTAAGACGCTTC
          1 TTCTCCTGTCTTTCATGCTGAGAAACTAAGACGCTTC

                
        212 TTCT
          1 TTCT

        216 TCTTTTCTTT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  36   10  0.29
  37   25  0.71

ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42


Consensus pattern (37 bp):   
TTCTCCTGTCTTTCATGCTGAGAAACTAAGACGCTTC

Found at i:221 original size:37 final size:37

Alignment explanation


    Indices: 159--260  Score: 116
    Period size: 38  Copynumber: 2.7  Consensus size: 37

        149 TTTCAGTTTG

                        *       *                 
        159 AAAACTAAGACGTTTCTTCTCCTTTT-TTTCATGCTGA
          1 AAAACTAAGACGCTTCTTCTTCTTTTCTTTCATGCT-A

            *                             *      
        196 GAAACTAAGACGCTTCTTCTTCTTTTCTTTTATGCTA
          1 AAAACTAAGACGCTTCTTCTTCTTTTCTTTCATGCTA

                  *   *            *    
        233 AAAATCGAAGGCGCTTCTTCTTCATTTC
          1 AAAA-CTAAGACGCTTCTTCTTCTTTTC

        261 ACGCCGAACG


Statistics
Matches: 55,  Mismatches: 8, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  37   27  0.49
  38   28  0.51

ACGTcount: A:0.24, C:0.23, G:0.12, T:0.42


Consensus pattern (37 bp):   
AAAACTAAGACGCTTCTTCTTCTTTTCTTTCATGCTA

Found at i:1830 original size:40 final size:40

Alignment explanation


    Indices: 1758--1854  Score: 117
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       1748 CGGATATAAC

                   *                                 
       1758 GACTCGCTCAAATGCCTTCGGGACGAAGCCC-GGTTATAGT
          1 GACTCGCACAAATGCCTTCGGGACGAAGCCCGGGTT-TAGT

                     *               *               
       1798 GACTCGCACGAATGCCTTCGGGACTTAA-CCCGGGTTTAGT
          1 GACTCGCACAAATGCCTTCGGGAC-GAAGCCCGGGTTTAGT

            *   *            
       1838 AACTTGCACAAATGCCT
          1 GACTCGCACAAATGCCT


Statistics
Matches: 49,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
  40   43  0.88
  41    6  0.12

ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24


Consensus pattern (40 bp):   
GACTCGCACAAATGCCTTCGGGACGAAGCCCGGGTTTAGT
Done.