Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008548.1 Hibiscus syriacus cultivar Beakdansim tig00111440_pilon, whole genome shotgun sequence

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: 1170587
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 7 of 7

Found at i:1167789 original size:21 final size:20

Alignment explanation


    Indices: 1167763--1167804  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

    1167753 TGCAGAGATT

                         *       
    1167763 TCATCCTCAAACGGCTAGAAA
          1 TCATCC-CAAACGACTAGAAA

                   *            
    1167784 TCATCCCTAACGACTAGAAA
          1 TCATCCCAAACGACTAGAAA

             
    1167804 T
          1 T

    1167805 GGCTACAACT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   13  0.68
  21    6  0.32

ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21


Consensus pattern (20 bp):   
TCATCCCAAACGACTAGAAA

Found at i:1168356 original size:44 final size:44

Alignment explanation


    Indices: 1168287--1168384  Score: 142
    Period size: 44  Copynumber: 2.2  Consensus size: 44

    1168277 AACAGTGATA

                  *   *                                 
    1168287 GTATCGATACTACCTAGAGAATATCGATACTTCTCTTAACTTTG
          1 GTATCGGTACCACCTAGAGAATATCGATACTTCTCTTAACTTTG

                            *   *        *        *     
    1168331 GTATCGGTACCACCTATAGAGTATCGATATTTCTCTTACCTTTG
          1 GTATCGGTACCACCTAGAGAATATCGATACTTCTCTTAACTTTG

                      
    1168375 GTATCGGTAC
          1 GTATCGGTAC

    1168385 AACGTGAACA


Statistics
Matches: 48,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  44   48  1.00

ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37


Consensus pattern (44 bp):   
GTATCGGTACCACCTAGAGAATATCGATACTTCTCTTAACTTTG

Found at i:1168400 original size:44 final size:44

Alignment explanation


    Indices: 1168287--1168405  Score: 132
    Period size: 44  Copynumber: 2.7  Consensus size: 44

    1168277 AACAGTGATA

                  *   *     * *          *              
    1168287 GTATCGATACTACCTAGAGAATATCGATACTTCTCTTAACTTTG
          1 GTATCGGTACAACCTATACAATATCGATATTTCTCTTAACTTTG

                      *       * *                 *     
    1168331 GTATCGGTACCACCTATAGAGTATCGATATTTCTCTTACCTTTG
          1 GTATCGGTACAACCTATACAATATCGATATTTCTCTTAACTTTG

                         *                  
    1168375 GTATCGGTACAACGTGA-ACAATATCGATATT
          1 GTATCGGTACAACCT-ATACAATATCGATATT

    1168406 GTTCATGCAG


Statistics
Matches: 64,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  44   63  0.98
  45    1  0.02

ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35


Consensus pattern (44 bp):   
GTATCGGTACAACCTATACAATATCGATATTTCTCTTAACTTTG

Done.