Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000995.1 Corchorus capsularis cultivar CVL-1 contig00995, 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, 643

Length: 1073
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34


Found at i:156 original size:29 final size:29

Alignment explanation


    Indices: 74--165  Score: 67
    Period size: 29  Copynumber: 3.1  Consensus size: 29

         64 TTAGTCTCAG

                                          * 
         74 TTGATCCAGGGAGATCTTTCTTTAGACTTCCA
          1 TTGATCCAGGGAGATCTTTCTTTAG--TT-AA

            *   *      * *  **           
        106 GTGACCCAGGGCGGTCCATCTTTAGTTAA
          1 TTGATCCAGGGAGATCTTTCTTTAGTTAA

                       *          *   *  
        135 TTGATCCAGGGTGATCTTTCTTCAGTAAA
          1 TTGATCCAGGGAGATCTTTCTTTAGTTAA

              
        164 TT
          1 TT

        166 TCGGCTAATC


Statistics
Matches: 45,  Mismatches: 15, Indels: 3
        0.71            0.24        0.05

Matches are distributed among these distances:
  29   24  0.53
  30    2  0.04
  32   19  0.42

ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36


Consensus pattern (29 bp):   
TTGATCCAGGGAGATCTTTCTTTAGTTAA

Found at i:237 original size:35 final size:35

Alignment explanation


    Indices: 142--225  Score: 168
    Period size: 35  Copynumber: 2.4  Consensus size: 35

        132 TAATTGATCC

                                               
        142 AGGGTGATCTTTCTTCAGTAAATTTCGGCTAATCT
          1 AGGGTGATCTTTCTTCAGTAAATTTCGGCTAATCT

                                               
        177 AGGGTGATCTTTCTTCAGTAAATTTCGGCTAATCT
          1 AGGGTGATCTTTCTTCAGTAAATTTCGGCTAATCT

                          
        212 AGGGTGATCTTTCT
          1 AGGGTGATCTTTCT

        226 ATAGCAAATT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   49  1.00

ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40


Consensus pattern (35 bp):   
AGGGTGATCTTTCTTCAGTAAATTTCGGCTAATCT

Found at i:597 original size:16 final size:16

Alignment explanation


    Indices: 561--682  Score: 187
    Period size: 16  Copynumber: 7.8  Consensus size: 16

        551 ATTGGGCGGG

                           *
        561 TTCGGGTTCGGGTA-C
          1 TTCGGGTTCGGGTATT

                            
        576 TTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

                            
        592 TTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

                             
        608 TTCGGGTTCGGG-ATTT
          1 TTCGGGTTCGGGTA-TT

                         *  
        624 TTCGGGTTCGGGTTTT
          1 TTCGGGTTCGGGTATT

                            
        640 TTCGGGTTCGGGTA-T
          1 TTCGGGTTCGGGTATT

                            
        655 TTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

               *        
        671 TTCAGGTTCGGG
          1 TTCGGGTTCGGG

        683 CTCGGATCGG


Statistics
Matches: 99,  Mismatches: 4, Indels: 7
        0.90            0.04        0.06

Matches are distributed among these distances:
  15   30  0.30
  16   69  0.70

ACGTcount: A:0.06, C:0.14, G:0.39, T:0.42


Consensus pattern (16 bp):   
TTCGGGTTCGGGTATT

Found at i:617 original size:32 final size:32

Alignment explanation


    Indices: 561--682  Score: 187
    Period size: 31  Copynumber: 3.9  Consensus size: 32

        551 ATTGGGCGGG

                           *                
        561 TTCGGGTTCGGGTA-CTTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATTTTCGGGTTCGGGTATT

                                             
        592 TTCGGGTTCGGGTATTTTCGGGTTCGGG-ATTT
          1 TTCGGGTTCGGGTATTTTCGGGTTCGGGTA-TT

                         *                  
        624 TTCGGGTTCGGGTTTTTTCGGGTTCGGGTA-T
          1 TTCGGGTTCGGGTATTTTCGGGTTCGGGTATT

                               *        
        655 TTCGGGTTCGGGTATTTTCAGGTTCGGG
          1 TTCGGGTTCGGGTATTTTCGGGTTCGGG

        683 CTCGGATCGG


Statistics
Matches: 84,  Mismatches: 4, Indels: 6
        0.89            0.04        0.06

Matches are distributed among these distances:
  31   42  0.50
  32   41  0.49
  33    1  0.01

ACGTcount: A:0.06, C:0.14, G:0.39, T:0.42


Consensus pattern (32 bp):   
TTCGGGTTCGGGTATTTTCGGGTTCGGGTATT

Found at i:693 original size:48 final size:48

Alignment explanation


    Indices: 593--700  Score: 139
    Period size: 47  Copynumber: 2.2  Consensus size: 48

        583 TCGGGTATTT

                                              *         ****
        593 TCGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCGGGTTCGGGTTTTT
          1 TCGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCAGGTTCGGGTCGGA

                                                              
        641 TCGGGTTCGGGTA-TTTCGGGTTCGGG-TATTTTCAGGTTCGGGCTCGGA
          1 TCGGGTTCGGGTATTTTCGGGTTCGGGAT-TTTTCAGGTTCGGG-TCGGA

                        
        689 TCGGGTTCGGGT
          1 TCGGGTTCGGGT

        701 CCGGGTCGGG


Statistics
Matches: 53,  Mismatches: 5, Indels: 4
        0.85            0.08        0.06

Matches are distributed among these distances:
  46    1  0.02
  47   26  0.49
  48   26  0.49

ACGTcount: A:0.06, C:0.15, G:0.40, T:0.40


Consensus pattern (48 bp):   
TCGGGTTCGGGTATTTTCGGGTTCGGGATTTTTCAGGTTCGGGTCGGA
Done.