Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003634.1 Hibiscus syriacus cultivar Beakdansim tig00007694_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: 40837
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:1129 original size:2 final size:2

Alignment explanation


    Indices: 1124--1157  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       1114 AACACACACA

                                                    *           
       1124 CT CT CT CT C- CT CT CT CT CT CT CT CT CG CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

       1158 CAAATTATTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.00, C:0.53, G:0.03, T:0.44


Consensus pattern (2 bp):   
CT

Found at i:5134 original size:22 final size:22

Alignment explanation


    Indices: 5106--5148  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5096 ATACATTTAT

                                   
       5106 TCGTTAG-TTTTACCGAATTGGC
          1 TCGTTAGCTTTT-CCGAATTGGC

                         *       
       5128 TCGTTAGCTTTTCTGAATTGG
          1 TCGTTAGCTTTTCCGAATTGG

       5149 ATAGTTGGTG


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

Matches are distributed among these distances:
  22   15  0.79
  23    4  0.21

ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44


Consensus pattern (22 bp):   
TCGTTAGCTTTTCCGAATTGGC

Found at i:16454 original size:3 final size:3

Alignment explanation


    Indices: 16446--16471  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      16436 CTCCGAAATT

                                              
      16446 TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT

      16472 TTTGTATTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:29320 original size:21 final size:21

Alignment explanation


    Indices: 29286--29333  Score: 60
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      29276 AGTGTTATTT

                 *   *    *      
      29286 AAAATATTATTTTTTTTACCG
          1 AAAATGTTAATTTTGTTACCG

                                *
      29307 AAAATGTTAATTTTGTTACCT
          1 AAAATGTTAATTTTGTTACCG

                  
      29328 AAAATG
          1 AAAATG

      29334 AATATTTCAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46


Consensus pattern (21 bp):   
AAAATGTTAATTTTGTTACCG

Found at i:29971 original size:25 final size:24

Alignment explanation


    Indices: 29935--29982  Score: 69
    Period size: 25  Copynumber: 2.0  Consensus size: 24

      29925 TATCTTTCTT

                                    
      29935 AATTTTAAATTTAAATATTTAATA
          1 AATTTTAAATTTAAATATTTAATA

                    *    *          
      29959 AATTATTATATTTTAATATTTAAT
          1 AATT-TTAAATTTAAATATTTAAT

      29983 CTTACTTCCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    4  0.19
  25   17  0.81

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (24 bp):   
AATTTTAAATTTAAATATTTAATA

Found at i:33072 original size:18 final size:18

Alignment explanation


    Indices: 33049--33084  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      33039 TTAAGAAAAT

                              
      33049 TCGCATACAATCAACTTC
          1 TCGCATACAATCAACTTC

                              
      33067 TCGCATACAATCAACTTC
          1 TCGCATACAATCAACTTC

      33085 ACAGAAATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28


Consensus pattern (18 bp):   
TCGCATACAATCAACTTC

Found at i:38228 original size:2 final size:2

Alignment explanation


    Indices: 38173--38212  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      38163 TTTCTCTCCT

                                                       *               
      38173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      38213 CGTTTGTATG


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:40194 original size:27 final size:27

Alignment explanation


    Indices: 40164--40221  Score: 64
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      40154 CATTTAGCAA

                     *                  
      40164 TCTAAAGTTTTTTAGTTA-ATTTAAGTG
          1 TCTAAAGTTATTT-GTTACATTTAAGTG

                 *                  *   
      40191 TCTAACGTTATTTGTTATCATTTAGGTG
          1 TCTAAAGTTATTTGTTA-CATTTAAGTG

               
      40219 TCT
          1 TCT

      40222 TGATCGTAAC


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  26    4  0.15
  27   11  0.42
  28   11  0.42

ACGTcount: A:0.24, C:0.09, G:0.16, T:0.52


Consensus pattern (27 bp):   
TCTAAAGTTATTTGTTACATTTAAGTG
Done.