Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016584.1 Corchorus olitorius cultivar O-4 contig16617, 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: 5992
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37


Found at i:5688 original size:21 final size:22

Alignment explanation


    Indices: 5663--5703  Score: 75
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       5653 CCATACATGA

                                  
       5663 TTTGGGATTTGA-CCATTACAC
          1 TTTGGGATTTGATCCATTACAC

                                
       5684 TTTGGGATTTGATCCATTAC
          1 TTTGGGATTTGATCCATTAC

       5704 TAGTAGGGGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   12  0.63
  22    7  0.37

ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41


Consensus pattern (22 bp):   
TTTGGGATTTGATCCATTACAC

Found at i:5788 original size:87 final size:86

Alignment explanation


    Indices: 5615--5935  Score: 459
    Period size: 87  Copynumber: 3.7  Consensus size: 86

       5605 TAGCCCCAAA

                                  *         *                                
       5615 ACTAGTAGGGGTTTGCCTAATCTTGCTTTACAGTTTCACCATACATGATTTGGGATTTGACCATT
          1 ACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT

             *                     
       5680 ACACTTTGGGATTTGAT-CCATT
         66 AGA-TTTGGG-TTTGATCCCATT

                                 *                 *              *          
       5702 ACTAGTAGGGGTTTGCCTAATTATGCTTTA-AATTTCACTATACATGATTTGGGGTTTGACCATT
          1 ACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT

                                   
       5766 ATGATTTGGCGTTTGATCCCATT
         66 A-GATTTGG-GTTTGATCCCATT

                   *       *                                                 
       5789 ACTAGTAAGGGTTTGTCTAATCATGCTTTA-AATTTCACCATACATGATTTGGGATTTGACCATT
          1 ACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT

                               *   
       5853 ACGATTTGAGGTTTGATCCAATT
         66 A-GATTTG-GGTTTGATCCCATT

                    *                        *                    *     
       5876 ACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACCATACATGATTTGGGGTTTGA
          1 ACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGA

       5936 TCTCATTACT


Statistics
Matches: 211,  Mismatches: 18, Indels: 9
        0.89            0.08        0.04

Matches are distributed among these distances:
  86   43  0.20
  87  140  0.66
  88   28  0.13

ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39


Consensus pattern (86 bp):   
ACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT
AGATTTGGGTTTGATCCCATT

Found at i:5867 original size:21 final size:23

Alignment explanation


    Indices: 5834--5877  Score: 58
    Period size: 21  Copynumber: 2.0  Consensus size: 23

       5824 CACCATACAT

                                   
       5834 GATTTGGGATTTGA-CC-ATTAC
          1 GATTTGGGATTTGATCCAATTAC

                                    
       5855 GATTTGAGG-TTTGATCCAATTAC
          1 GATTTG-GGATTTGATCCAATTAC

       5878 TAGTAGAGGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  21   11  0.55
  22    4  0.20
  23    5  0.25

ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39


Consensus pattern (23 bp):   
GATTTGGGATTTGATCCAATTAC

Found at i:5905 original size:174 final size:175

Alignment explanation


    Indices: 5615--5935  Score: 515
    Period size: 174  Copynumber: 1.8  Consensus size: 175

       5605 TAGCCCCAAA

                   *              *         *                                
       5615 ACTAGTAGGGGTTTGCCTAATCTTGCTTTACAGTTTCACCATACATGATTTGGGATTTGACCATT
          1 ACTAGTAAGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT

                                          *            *           *     *   
       5680 ACACTTTGGGATTTGATCCATTACTAGTAGGGGTTTGCCTAATTATGCTTTA-AATTTCACTATA
         66 ACACTTTGGGATTTGATCCATTACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACCATA

                                                         
       5744 CATGATTTGGGGTTTGACCATTATGATTTGGCGTTTGATCCCATT
        131 CATGATTTGGGGTTTGACCATTATGATTTGGCGTTTGATCCCATT

                           *                                                 
       5789 ACTAGTAAGGGTTTGTCTAATCATGCTTTA-AATTTCACCATACATGATTTGGGATTTGACCATT
          1 ACTAGTAAGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT

                                                                             
       5853 ACGA-TTTGAGG-TTTGATCCAATTACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACC
         66 AC-ACTTTG-GGATTTGATCC-ATTACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACC

                                
       5916 ATACATGATTTGGGGTTTGA
        128 ATACATGATTTGGGGTTTGA

       5936 TCTCATTACT


Statistics
Matches: 135,  Mismatches: 8, Indels: 7
        0.90            0.05        0.05

Matches are distributed among these distances:
 173   47  0.35
 174   61  0.45
 175   27  0.20

ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39


Consensus pattern (175 bp):   
ACTAGTAAGGGTTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGATTTGACCATT
ACACTTTGGGATTTGATCCATTACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACCATA
CATGATTTGGGGTTTGACCATTATGATTTGGCGTTTGATCCCATT

Found at i:5963 original size:67 final size:66

Alignment explanation


    Indices: 5855--5992  Score: 215
    Period size: 67  Copynumber: 2.1  Consensus size: 66

       5845 TGACCATTAC

                                                                             
       5855 GATTTGAGGTTTGATCCAATTACTAGTAGAGGTTTGCCTAATCATGCTTTACAACTTCACCATAC
          1 GATTTGAGGTTTGATCCAATTACTAGTAGAGGTTTGCCTAATCATGCTTTA-AACTTCACCATAC

              
       5920 AT
         65 AT

                  *                       *                       *     *    
       5922 GATTTGGGGTTTGATCTC-ATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACTATAC
          1 GATTTGAGGTTTGATC-CAATTACTAGTAGAGGTTTGCCTAATCATGCTTTAAACTTCACCATAC

              
       5986 AT
         65 AT

                 
       5988 GATTT
          1 GATTT


Statistics
Matches: 66,  Mismatches: 4, Indels: 3
        0.90            0.05        0.04

Matches are distributed among these distances:
  66   18  0.27
  67   47  0.71
  68    1  0.02

ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39


Consensus pattern (66 bp):   
GATTTGAGGTTTGATCCAATTACTAGTAGAGGTTTGCCTAATCATGCTTTAAACTTCACCATACA
T
Done.