Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007199.1 Corchorus capsularis cultivar CVL-1 contig07220, 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: 44163
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:78 original size:26 final size:26

Alignment explanation


    Indices: 45--97  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

         35 CATTTTACTG

                       *          *    
         45 TTACTATTTT-ACTCTCTTGAATTTAA
          1 TTACTATTTTCGCTCT-TTGAACTTAA

                                      
         71 TTACTATTTTCGCTCTTTGAACTTAA
          1 TTACTATTTTCGCTCTTTGAACTTAA

             
         97 T
          1 T

         98 CACCATTTGC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26   20  0.83
  27    4  0.17

ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53


Consensus pattern (26 bp):   
TTACTATTTTCGCTCTTTGAACTTAA

Found at i:120 original size:32 final size:33

Alignment explanation


    Indices: 84--147  Score: 94
    Period size: 32  Copynumber: 2.0  Consensus size: 33

         74 CTATTTTCGC

                                   *         
         84 TCTTTGAACTTAATCACCA-TTTGCCATTTTAT
          1 TCTTTGAACTTAATCACCATTTTACCATTTTAT

                    *     *                 
        116 TCTTTGAATTTAATTACCATTTTACCATTTTA
          1 TCTTTGAACTTAATCACCATTTTACCATTTTA

        148 CCCTTTACTG


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  32   17  0.61
  33   11  0.39

ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50


Consensus pattern (33 bp):   
TCTTTGAACTTAATCACCATTTTACCATTTTAT

Found at i:283 original size:41 final size:41

Alignment explanation


    Indices: 197--335  Score: 226
    Period size: 41  Copynumber: 3.4  Consensus size: 41

        187 TCTTTACCGA

                     *              *                
        197 TTTACTGATCACTTCTTTTACTTTTACTC-TTAATTACCAT
          1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACCAT

                                                     
        237 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACCAT
          1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACCAT

                                                   *  
        278 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTGAT
          1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTAC-CAT

                            
        320 TTCTACTGATTACTTC
          1 TT-TACTGATTACTTC

        336 ATTAATCCAT


Statistics
Matches: 93,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  40   27  0.29
  41   49  0.53
  42    4  0.04
  43   13  0.14

ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53


Consensus pattern (41 bp):   
TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACCAT

Found at i:9528 original size:21 final size:21

Alignment explanation


    Indices: 9479--9532  Score: 56
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       9469 AGCACTGGAG

                        *        
       9479 CACATGGGGCGCGAGGCAAAC
          1 CACATGGGGCGCCAGGCAAAC

              **             **  
       9500 CAGGTGGGGCGCCAGGCTTAC
          1 CACATGGGGCGCCAGGCAAAC

                         
       9521 CACAT-GGGCGCC
          1 CACATGGGGCGCC

       9533 CAGCGCCAGT


Statistics
Matches: 26,  Mismatches: 7, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  20    7  0.27
  21   19  0.73

ACGTcount: A:0.20, C:0.31, G:0.39, T:0.09


Consensus pattern (21 bp):   
CACATGGGGCGCCAGGCAAAC

Found at i:29172 original size:14 final size:15

Alignment explanation


    Indices: 29143--29177  Score: 54
    Period size: 14  Copynumber: 2.4  Consensus size: 15

      29133 AACCCTAAAC

                           
      29143 ACATTAAACAATTAG
          1 ACATTAAACAATTAG

                  *        
      29158 ACATTACAC-ATTAG
          1 ACATTAAACAATTAG

                  
      29172 ACATTA
          1 ACATTA

      29178 TATATTCTCT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   11  0.58
  15    8  0.42

ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29


Consensus pattern (15 bp):   
ACATTAAACAATTAG

Found at i:31683 original size:21 final size:21

Alignment explanation


    Indices: 31658--31725  Score: 61
    Period size: 21  Copynumber: 3.3  Consensus size: 21

      31648 TATAATTACA

                               * 
      31658 AACATAACAACTAACAAAGCC
          1 AACATAACAACTAACAAAGAC

                     *            
      31679 AACATAA-AGCTACACAAA-AC
          1 AACATAACAACTA-ACAAAGAC

                  *            * 
      31699 AA-ATACCAACTAACAAAGTC
          1 AACATAACAACTAACAAAGAC

             *     
      31719 ATCATAA
          1 AACATAA

      31726 AGATGCACAA


Statistics
Matches: 36,  Mismatches: 7, Indels: 8
        0.71            0.14        0.16

Matches are distributed among these distances:
  19    8  0.22
  20   13  0.36
  21   15  0.42

ACGTcount: A:0.57, C:0.25, G:0.04, T:0.13


Consensus pattern (21 bp):   
AACATAACAACTAACAAAGAC
Done.