Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007899.1 Hibiscus syriacus cultivar Beakdansim tig00110289_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: 52871
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:14837 original size:39 final size:39

Alignment explanation


    Indices: 14783--14863  Score: 135
    Period size: 39  Copynumber: 2.1  Consensus size: 39

      14773 GAAGGGTTCT

                   *                               
      14783 TCTTCCTTAACCATCACTCACAAGTAAATGGTGAAAGCC
          1 TCTTCCTCAACCATCACTCACAAGTAAATGGTGAAAGCC

                     *                *            
      14822 TCTTCCTCAGCCATCACTCACAAGTACATGGTGAAAGCC
          1 TCTTCCTCAACCATCACTCACAAGTAAATGGTGAAAGCC

               
      14861 TCT
          1 TCT

      14864 GTCATTTTAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.30, C:0.31, G:0.14, T:0.26


Consensus pattern (39 bp):   
TCTTCCTCAACCATCACTCACAAGTAAATGGTGAAAGCC

Found at i:18318 original size:37 final size:37

Alignment explanation


    Indices: 18265--18336  Score: 99
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      18255 ACAATTTATA

                       *       **                
      18265 TTTTATTATAGTTATGTATCGCATTTTAGCCCTAAAT
          1 TTTTATTATAGGTATGTATAACATTTTAGCCCTAAAT

                     *                  *      
      18302 TTTTATTATGGGTATGTATAACATTTTATCCCTAA
          1 TTTTATTATAGGTATGTATAACATTTTAGCCCTAA

      18337 TTCATTCCAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  37   30  1.00

ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49


Consensus pattern (37 bp):   
TTTTATTATAGGTATGTATAACATTTTAGCCCTAAAT

Found at i:19324 original size:60 final size:60

Alignment explanation


    Indices: 19178--19324  Score: 163
    Period size: 60  Copynumber: 2.5  Consensus size: 60

      19168 GAACATACGA

                  *  *                               *              *   
      19178 ATAGTCAAGTGACCATTTTGTAACTTTTAATAGTCGGAAGATTCAACAAAGCAACATCCT
          1 ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAGCAACACCCT

                 *      **                         *       *      *      
      19238 ATAGTTGAGGGATAATTTTGTAACTTTTAATAGTC-GAGGGACTCAATAAAGCATCACCCT
          1 ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGGA-AGACTCAACAAAGCAACACCCT

                   *                    
      19298 ATAGTCGGGGGACCATTTATGT-ACTTT
          1 ATAGTCGAGGGACCATTT-TGTAACTTT

      19325 ACCCAAAATA


Statistics
Matches: 71,  Mismatches: 14, Indels: 4
        0.80            0.16        0.04

Matches are distributed among these distances:
  59    2  0.03
  60   66  0.93
  61    3  0.04

ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Consensus pattern (60 bp):   
ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAGCAACACCCT

Found at i:38409 original size:17 final size:17

Alignment explanation


    Indices: 38387--38425  Score: 78
    Period size: 17  Copynumber: 2.3  Consensus size: 17

      38377 AACGATCAAC

                             
      38387 GGTCAACGGTCGGGTCG
          1 GGTCAACGGTCGGGTCG

                             
      38404 GGTCAACGGTCGGGTCG
          1 GGTCAACGGTCGGGTCG

                 
      38421 GGTCA
          1 GGTCA

      38426 GTCGGGTGGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18


Consensus pattern (17 bp):   
GGTCAACGGTCGGGTCG

Found at i:50515 original size:16 final size:17

Alignment explanation


    Indices: 50490--50523  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

      50480 GTGTGGTGCA

                 *           
      50490 TTATGTGTATG-TTGTT
          1 TTATGAGTATGCTTGTT

                             
      50506 TTATGAGTATGCTTGTT
          1 TTATGAGTATGCTTGTT

             
      50523 T
          1 T

      50524 GATTATCTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16   10  0.62
  17    6  0.38

ACGTcount: A:0.15, C:0.03, G:0.24, T:0.59


Consensus pattern (17 bp):   
TTATGAGTATGCTTGTT

Done.