Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005222.1 Hibiscus syriacus cultivar Beakdansim tig00011823_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: 38158
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:3164 original size:17 final size:17

Alignment explanation


    Indices: 3142--3211  Score: 104
    Period size: 17  Copynumber: 4.1  Consensus size: 17

       3132 AATTAAGAGT

                     *       
       3142 TAGTTTAATAAATGAAC
          1 TAGTTTAATTAATGAAC

                  *   *  *   
       3159 TAGTTTGATTTATTAAC
          1 TAGTTTAATTAATGAAC

                             
       3176 TAGTTTAATTAATGAAC
          1 TAGTTTAATTAATGAAC

                             
       3193 TAGTTTAATTAATGAAC
          1 TAGTTTAATTAATGAAC

              
       3210 TA
          1 TA

       3212 ACTTTATTAA


Statistics
Matches: 46,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  17   46  1.00

ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43


Consensus pattern (17 bp):   
TAGTTTAATTAATGAAC

Found at i:3220 original size:17 final size:17

Alignment explanation


    Indices: 3145--3221  Score: 75
    Period size: 17  Copynumber: 4.5  Consensus size: 17

       3135 TAAGAGTTAG

                  *         *
       3145 TTTAATAAATGAACTAG
          1 TTTAATTAATGAACTAC

               *   *  *     *
       3162 TTTGATTTATTAACTAG
          1 TTTAATTAATGAACTAC

                            *
       3179 TTTAATTAATGAACTAG
          1 TTTAATTAATGAACTAC

                              
       3196 TTTAATTAATGAACTAAC
          1 TTTAATTAATGAACT-AC

                     
       3214 TTT-ATTAA
          1 TTTAATTAA

       3222 ATTAATAGAT


Statistics
Matches: 51,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  17   47  0.92
  18    4  0.08

ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44


Consensus pattern (17 bp):   
TTTAATTAATGAACTAC

Found at i:3221 original size:34 final size:34

Alignment explanation


    Indices: 3145--3221  Score: 93
    Period size: 34  Copynumber: 2.3  Consensus size: 34

       3135 TAAGAGTTAG

                  *             *   *  *     *
       3145 TTTAATAAATGAACTAGTTTGATTTATTAACTAG
          1 TTTAATTAATGAACTAGTTTAATTAATGAACTAC

                                               
       3179 TTTAATTAATGAACTAGTTTAATTAATGAACTAAC
          1 TTTAATTAATGAACTAGTTTAATTAATGAACT-AC

                     
       3214 TTT-ATTAA
          1 TTTAATTAA

       3222 ATTAATAGAT


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  34   33  0.89
  35    4  0.11

ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44


Consensus pattern (34 bp):   
TTTAATTAATGAACTAGTTTAATTAATGAACTAC

Found at i:5404 original size:2 final size:2

Alignment explanation


    Indices: 5390--5427  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       5380 CGGATTCAAA

                     *                                                
       5390 AT AT AT TT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5428 ATAAAAAATC


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6176 original size:15 final size:15

Alignment explanation


    Indices: 6152--6204  Score: 54
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       6142 TAAAACAAGA

                 *         
       6152 AGAAAATTAAATGCT
          1 AGAAATTTAAATGCT

                       *    
       6167 AGAAATTTAAAGGACT
          1 AGAAATTTAAATG-CT

                          * 
       6183 -GAAATTTATAATGTT
          1 AGAAATTTA-AATGCT

                   
       6198 AGAAATT
          1 AGAAATT

       6205 AAAAGACGCA


Statistics
Matches: 31,  Mismatches: 4, Indels: 5
        0.77            0.10        0.12

Matches are distributed among these distances:
  15   20  0.65
  16   11  0.35

ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32


Consensus pattern (15 bp):   
AGAAATTTAAATGCT
Done.