Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01090.N4

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: 1708
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32


Found at i:55 original size:37 final size:38

Alignment explanation


    Indices: 14--107  Score: 111
    Period size: 37  Copynumber: 2.5  Consensus size: 38

          4 TTCAGTTTGA

                       *                          
         14 AAACTAAGACGTTTCTTCTCCTTTT-TTTCATGCTGAG
          1 AAACTAAGACGCTTCTTCTCCTTTTCTTTCATGCTGAG

                               *         *       *
         51 AAACTAAGACGCTTCTTCTTCTTTTCTTTTATGCT-AA
          1 AAACTAAGACGCTTCTTCTCCTTTTCTTTCATGCTGAG

                 *   *          
         88 AAATCGAAGGCGCTTCTTCT
          1 AAA-CTAAGACGCTTCTTCT

        108 TCATTTCACG


Statistics
Matches: 49,  Mismatches: 6, Indels: 3
        0.84            0.10        0.05

Matches are distributed among these distances:
  37   27  0.55
  38   22  0.45

ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41


Consensus pattern (38 bp):   
AAACTAAGACGCTTCTTCTCCTTTTCTTTCATGCTGAG

Found at i:102 original size:38 final size:38

Alignment explanation


    Indices: 13--114  Score: 109
    Period size: 38  Copynumber: 2.7  Consensus size: 38

          3 TTTCAGTTTG

                 *      *       *                 
         13 AAAACTAAGACGTTTCTTCTCCTTTT-TTTCATGCTGA
          1 AAAACGAAGACGCTTCTTCTTCTTTTCTTTCATGCTGA

            *    *                        *       
         50 GAAACTAAGACGCTTCTTCTTCTTTTCTTTTATGCT-A
          1 AAAACGAAGACGCTTCTTCTTCTTTTCTTTCATGCTGA

                      *            *    
         87 AAAATCGAAGGCGCTTCTTCTTCATTTC
          1 AAAA-CGAAGACGCTTCTTCTTCTTTTC

        115 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 (38 bp):   
AAAACGAAGACGCTTCTTCTTCTTTTCTTTCATGCTGA

Found at i:1684 original size:40 final size:40

Alignment explanation


    Indices: 1612--1708  Score: 117
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       1602 CGGATATAAC

                   *                                 
       1612 GACTCGCTCAAATGCCTTCGGGACGAAGCCC-GGTTATAGT
          1 GACTCGCACAAATGCCTTCGGGACGAAGCCCGGGTT-TAGT

                     *               *               
       1652 GACTCGCACGAATGCCTTCGGGACTTAA-CCCGGGTTTAGT
          1 GACTCGCACAAATGCCTTCGGGAC-GAAGCCCGGGTTTAGT

            *   *            
       1692 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.