Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008152.1 Hibiscus syriacus cultivar Beakdansim tig00110718_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: 877984
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


File 5 of 5

Found at i:865311 original size:43 final size:42

Alignment explanation


    Indices: 865261--865396  Score: 123
    Period size: 43  Copynumber: 3.4  Consensus size: 42

     865251 TTTGTGCATA

                                                       
     865261 GAGTATCGATACCCCTTATACAGGTATCGATACCCCCTTGAAT
          1 GAGTATCGATACCCCTTATA-AGGTATCGATACCCCCTTGAAT

                                                  *      
     865304 -AGGTATCGATACCCCTTGA-ATAGGTATCGAT----CTTTGAAT
          1 GA-GTATCGATACCCCTT-ATA-AGGTATCGATACCCCCTTGAAT

                                         *              
     865343 GAGTATCGATACCCCCCTTAT--GGTATCAATACCCCCTT--AT
          1 GAGTATCGATA--CCCCTTATAAGGTATCGATACCCCCTTGAAT

                           
     865383 G-GTATCGATACCCC
          1 GAGTATCGATACCCC

     865397 CTGTCAGGTT


Statistics
Matches: 79,  Mismatches: 4, Indels: 26
        0.72            0.04        0.24

Matches are distributed among these distances:
  37    4  0.05
  38    8  0.10
  39   25  0.32
  40    5  0.06
  41    6  0.08
  42    4  0.05
  43   26  0.33
  44    1  0.01

ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29


Consensus pattern (42 bp):   
GAGTATCGATACCCCTTATAAGGTATCGATACCCCCTTGAAT

Found at i:865374 original size:20 final size:20

Alignment explanation


    Indices: 865345--865397  Score: 90
    Period size: 19  Copynumber: 2.7  Consensus size: 20

     865335 CTTTGAATGA

                                
     865345 GTATCGATACCCCCCTTATG
          1 GTATCGATACCCCCCTTATG

                 *              
     865365 GTATCAATA-CCCCCTTATG
          1 GTATCGATACCCCCCTTATG

                          
     865384 GTATCGATACCCCC
          1 GTATCGATACCCCC

     865398 TGTCAGGTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  19   18  0.60
  20   12  0.40

ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28


Consensus pattern (20 bp):   
GTATCGATACCCCCCTTATG

Found at i:867990 original size:22 final size:19

Alignment explanation


    Indices: 867936--868070  Score: 105
    Period size: 18  Copynumber: 6.8  Consensus size: 19

     867926 GAATGCTCGG

                          *    
     867936 ATGGTACCGATACCTCCAT
          1 ATGGTACCGATACCCCCAT

                  *   *        
     867955 A-GGTATCGACACCCCCAT
          1 ATGGTACCGATACCCCCAT

                                  
     867973 GCAATGGTACCGATACCCCCAT
          1 ---ATGGTACCGATACCCCCAT

                  *   *        
     867995 A-GGTATCGACACCCCCAT
          1 ATGGTACCGATACCCCCAT

                                  
     868013 GCAATGGTACCGATACCCCCAT
          1 ---ATGGTACCGATACCCCCAT

                  *         *  
     868035 A-GGTATCGATACCCCTAT
          1 ATGGTACCGATACCCCCAT

                              
     868053 GCAATGGTACCGATACCC
          1 ---ATGGTACCGATACCC

     868071 TCAGGCATAT


Statistics
Matches: 92,  Mismatches: 12, Indels: 21
        0.74            0.10        0.17

Matches are distributed among these distances:
  18   44  0.48
  19    3  0.03
  21    3  0.03
  22   42  0.46

ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20


Consensus pattern (19 bp):   
ATGGTACCGATACCCCCAT

Found at i:867995 original size:40 final size:40

Alignment explanation


    Indices: 867936--868070  Score: 243
    Period size: 40  Copynumber: 3.4  Consensus size: 40

     867926 GAATGCTCGG

                          *                         
     867936 ATGGTACCGATACCTCCATAGGTATCGACACCCCCATGCA
          1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA

                                                    
     867976 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
          1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA

                                        *     *     
     868016 ATGGTACCGATACCCCCATAGGTATCGATACCCCTATGCA
          1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA

                           
     868056 ATGGTACCGATACCC
          1 ATGGTACCGATACCC

     868071 TCAGGCATAT


Statistics
Matches: 92,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  40   92  1.00

ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20


Consensus pattern (40 bp):   
ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA

Found at i:872227 original size:57 final size:59

Alignment explanation


    Indices: 872105--872234  Score: 162
    Period size: 59  Copynumber: 2.3  Consensus size: 59

     872095 ATATTTGAAC

                   **                                             *    
     872105 TTCATCCTTAAACTATGACTATCATTCTAAATTAGTCCTCAAATTTTGAACATTTCAAT
          1 TTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCTCAAATTTTGAACATTCCAAT

                                   *          *                          
     872164 TTCATCCCCAAACTATGACCT-TTATTC-AAATTGGTCC-CAAACTTTT-AACATTCCAAT
          1 TTCATCCCCAAACTATGA-CTATCATTCTAAATTAGTCCTCAAA-TTTTGAACATTCCAAT

                           
     872221 TTCAT-CCCAAACTA
          1 TTCATCCCCAAACTA

     872235 AATATATATA


Statistics
Matches: 64,  Mismatches: 5, Indels: 7
        0.84            0.07        0.09

Matches are distributed among these distances:
  56    9  0.14
  57   19  0.30
  58   13  0.20
  59   21  0.33
  60    2  0.03

ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37


Consensus pattern (59 bp):   
TTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCTCAAATTTTGAACATTCCAAT

Done.