Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009152.1 Hibiscus syriacus cultivar Beakdansim tig00112678_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: 885575
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


File 4 of 4

Found at i:837671 original size:8 final size:8

Alignment explanation


    Indices: 837652--837690  Score: 50
    Period size: 8  Copynumber: 5.4  Consensus size: 8

     837642 GTCAACGCCA

                    
     837652 GTCAAC-G
          1 GTCAACGG

                    
     837659 GTCAACGG
          1 GTCAACGG

                    
     837667 GTCAACGG
          1 GTCAACGG

                    
     837675 GTCAA---
          1 GTCAACGG

                    
     837680 GTCAACGG
          1 GTCAACGG

               
     837688 GTC
          1 GTC

     837691 GGGTCGGGTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 7
        0.80            0.00        0.20

Matches are distributed among these distances:
   5    5  0.18
   7    6  0.21
   8   17  0.61

ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15


Consensus pattern (8 bp):   
GTCAACGG

Found at i:837698 original size:23 final size:23

Alignment explanation


    Indices: 837672--837717  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

     837662 AACGGGTCAA

                      *            
     837672 CGGGTCAAGTCAACGGGTCGGGT
          1 CGGGTCAAGTAAACGGGTCGGGT

                  **               
     837695 CGGGTCGGGTAAACGGGTCGGGT
          1 CGGGTCAAGTAAACGGGTCGGGT

     837718 AAACGGGTCG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17


Consensus pattern (23 bp):   
CGGGTCAAGTAAACGGGTCGGGT

Found at i:837710 original size:36 final size:36

Alignment explanation


    Indices: 837664--837733  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

     837654 CAACGGTCAA

                 *            *                 
     837664 CGGGTCAACGGGTCAAGTCAACGGGTCGGGTCGGGT
          1 CGGGTAAACGGGTCAAGTAAACGGGTCGGGTCGGGT

                          **                  
     837700 CGGGTAAACGGGTCGGGTAAACGGGTCGGGTCGG
          1 CGGGTAAACGGGTCAAGTAAACGGGTCGGGTCGG

     837734 ATTGTGACCG


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.17, C:0.20, G:0.47, T:0.16


Consensus pattern (36 bp):   
CGGGTAAACGGGTCAAGTAAACGGGTCGGGTCGGGT

Found at i:837713 original size:13 final size:13

Alignment explanation


    Indices: 837664--837730  Score: 77
    Period size: 13  Copynumber: 5.4  Consensus size: 13

     837654 CAACGGTCAA

                 *       
     837664 CGGGTCAACGGGT
          1 CGGGTAAACGGGT

             **  *       
     837677 CAAGTCAACGGGT
          1 CGGGTAAACGGGT

                         
     837690 CGGGT---CGGGT
          1 CGGGTAAACGGGT

                         
     837700 CGGGTAAACGGGT
          1 CGGGTAAACGGGT

                         
     837713 CGGGTAAACGGGT
          1 CGGGTAAACGGGT

                 
     837726 CGGGT
          1 CGGGT

     837731 CGGATTGTGA


Statistics
Matches: 47,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
  10   10  0.21
  13   37  0.79

ACGTcount: A:0.18, C:0.19, G:0.46, T:0.16


Consensus pattern (13 bp):   
CGGGTAAACGGGT

Found at i:842768 original size:21 final size:20

Alignment explanation


    Indices: 842744--842783  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 20

     842734 TCAACCACCT

                  *              
     842744 AATATATAATAAATTTATATA
          1 AATATAAAAT-AATTTATATA

                      *        
     842765 AATATAAAATCATTTATAT
          1 AATATAAAATAATTTATAT

     842784 CGGTATGAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    8  0.47
  21    9  0.53

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (20 bp):   
AATATAAAATAATTTATATA

Found at i:870763 original size:24 final size:20

Alignment explanation


    Indices: 870703--870769  Score: 82
    Period size: 21  Copynumber: 3.1  Consensus size: 20

     870693 AATTCTAGAA

                                
     870703 CCCC-AGGGGGGAATCGGTT
          1 CCCCTAGGGGGGAATCGGTT

                                 
     870722 CCCCTAGGCGGGGAATCGGTT
          1 CCCCTAGG-GGGGAATCGGTT

                                    
     870743 CCCCTTCAAAGGGGGGAATCGGTT
          1 CCCC-T---AGGGGGGAATCGGTT

               
     870767 CCC
          1 CCC

     870770 TCATGAGGGT


Statistics
Matches: 42,  Mismatches: 0, Indels: 7
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    4  0.10
  20    3  0.07
  21   16  0.38
  22    1  0.02
  24   15  0.36
  25    3  0.07

ACGTcount: A:0.16, C:0.30, G:0.36, T:0.18


Consensus pattern (20 bp):   
CCCCTAGGGGGGAATCGGTT

Done.