Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003550.1 Hibiscus syriacus cultivar Beakdansim tig00007491_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: 31775
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:8487 original size:45 final size:45

Alignment explanation


    Indices: 8437--8535  Score: 146
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       8427 CAAACATCGA

                                     *                   
       8437 ATGCATTTTATGCATCGACGCAC-ATACCATGCATCGATGCACTC
          1 ATGCATTTTATGCATCGACGCACAAGACCATGCATCGATGCACTC

                     *         *                          
       8481 AGTGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
          1 A-TGCATTTTATGCATCGACGCACAAGACCATGCATCGATGCACTC

                *    
       8527 ATGCTTTTT
          1 ATGCATTTT

       8536 CAAAACATCG


Statistics
Matches: 48,  Mismatches: 5, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  44    1  0.02
  45   26  0.54
  46   21  0.44

ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29


Consensus pattern (45 bp):   
ATGCATTTTATGCATCGACGCACAAGACCATGCATCGATGCACTC

Found at i:11339 original size:18 final size:17

Alignment explanation


    Indices: 11309--11349  Score: 64
    Period size: 18  Copynumber: 2.4  Consensus size: 17

      11299 AACTGGTGAC

                             
      11309 TTTTATTCTTTGATTTG
          1 TTTTATTCTTTGATTTG

                              
      11326 TTTTATTACTTTGATTTG
          1 TTTTATT-CTTTGATTTG

            *     
      11344 GTTTAT
          1 TTTTAT

      11350 CTCGATATTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  17    7  0.32
  18   15  0.68

ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68


Consensus pattern (17 bp):   
TTTTATTCTTTGATTTG

Found at i:11838 original size:24 final size:24

Alignment explanation


    Indices: 11793--11841  Score: 64
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11783 GCTGCTACGC

                  *         *       
      11793 TCCCGATCTCGATCTCGATCCCGT
          1 TCCCGACCTCGATCTCCATCCCGT

                                     
      11817 TCCCGACCTCGATC-CCATTCCCGT
          1 TCCCGACCTCGATCTCCA-TCCCGT

             
      11841 T
          1 T

      11842 GCCTTGATCC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  23    2  0.09
  24   20  0.91

ACGTcount: A:0.12, C:0.45, G:0.14, T:0.29


Consensus pattern (24 bp):   
TCCCGACCTCGATCTCCATCCCGT

Found at i:25262 original size:15 final size:15

Alignment explanation


    Indices: 25244--25273  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      25234 CAATCTCTTT

                           
      25244 TTCGTTATCTAAACC
          1 TTCGTTATCTAAACC

                           
      25259 TTCGTTATCTAAACC
          1 TTCGTTATCTAAACC

      25274 AAATGTGTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40


Consensus pattern (15 bp):   
TTCGTTATCTAAACC

Found at i:29339 original size:20 final size:22

Alignment explanation


    Indices: 29310--29360  Score: 61
    Period size: 20  Copynumber: 2.4  Consensus size: 22

      29300 CAGACCCCGT

                 *                
      29310 GGGGGTATCGATTCCC-T-AAA
          1 GGGGGAATCGATTCCCATCAAA

                      *            
      29330 GGGGGAATCGGTTCCCATTCAAA
          1 GGGGGAATCGATTCCCA-TCAAA

                    
      29353 GGGGGAAT
          1 GGGGGAAT

      29361 ATGTTCCCCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  20   14  0.54
  22    1  0.04
  23   11  0.42

ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22


Consensus pattern (22 bp):   
GGGGGAATCGATTCCCATCAAA

Found at i:29379 original size:24 final size:23

Alignment explanation


    Indices: 29327--29379  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      29317 TCGATTCCCT

                       *           
      29327 AAAGGGGGAATCGGTTCCCATTC
          1 AAAGGGGGAATAGGTTCCCATTC

                        *      *   
      29350 AAAGGGGGAATATGTTCCCCTTC
          1 AAAGGGGGAATAGGTTCCCATTC

                   
      29373 AAGAGGG
          1 AA-AGGG

      29380 TATCGATTCC


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  23   22  0.85
  24    4  0.15

ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21


Consensus pattern (23 bp):   
AAAGGGGGAATAGGTTCCCATTC
Done.