Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012799.1 Corchorus capsularis cultivar CVL-1 contig12820, 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: 18613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:494 original size:20 final size:21

Alignment explanation


    Indices: 469--507  Score: 71
    Period size: 20  Copynumber: 1.9  Consensus size: 21

        459 TTTAGAAGCA

                                 
        469 ATTAATTAAAAA-CATTAAAC
          1 ATTAATTAAAAACCATTAAAC

                               
        489 ATTAATTAAAAACCATTAA
          1 ATTAATTAAAAACCATTAA

        508 GGAAGGGAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20   12  0.67
  21    6  0.33

ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31


Consensus pattern (21 bp):   
ATTAATTAAAAACCATTAAAC

Found at i:600 original size:74 final size:74

Alignment explanation


    Indices: 514--670  Score: 271
    Period size: 74  Copynumber: 2.1  Consensus size: 74

        504 TTAAGGAAGG

                *                  *                *                        
        514 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTT
          1 GAAAAGTGTAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT

                      
        579 TAGTCATCC-
         66 TAGTCA-CCT

                                                                             
        588 GAAAAGTGTAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
          1 GAAAAGTGTAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT

                     
        653 TAGTCACCT
         66 TAGTCACCT

                     
        662 GAAAAGTGT
          1 GAAAAGTGT

        671 GAAAAGACCA


Statistics
Matches: 79,  Mismatches: 3, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  73    2  0.03
  74   77  0.97

ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21


Consensus pattern (74 bp):   
GAAAAGTGTAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
TAGTCACCT

Found at i:1175 original size:27 final size:29

Alignment explanation


    Indices: 1137--1195  Score: 86
    Period size: 27  Copynumber: 2.1  Consensus size: 29

       1127 TGTACGGAGT

                        *  *             
       1137 ATATATTATATTGTAGGGAGTA-ATTA-A
          1 ATATATTATATTATACGGAGTATATTATA

                                         
       1164 ATATATTATATTATACGGAGTATATTATA
          1 ATATATTATATTATACGGAGTATATTATA

               
       1193 ATA
          1 ATA

       1196 ATGATGATAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   20  0.71
  28    4  0.14
  29    4  0.14

ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42


Consensus pattern (29 bp):   
ATATATTATATTATACGGAGTATATTATA

Found at i:3286 original size:37 final size:37

Alignment explanation


    Indices: 3239--3327  Score: 106
    Period size: 37  Copynumber: 2.4  Consensus size: 37

       3229 CACTCTTCAT

                 *              *        *       
       3239 CGCAGGGCTCTCCTTACCGCTGTAGCACCGTCTTTAC
          1 CGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTAC

                        *    *        *          
       3276 CGCAGAGCTCTCTTTACTGCGGTAGCGCCCTCTTTAC
          1 CGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTAC

                *     *    
       3313 CGCAAAGCTCCCCTT
          1 CGCAGAGCTCTCCTT

       3328 GGCCATACTC


Statistics
Matches: 43,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  37   43  1.00

ACGTcount: A:0.15, C:0.38, G:0.20, T:0.27


Consensus pattern (37 bp):   
CGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTAC

Found at i:17805 original size:81 final size:79

Alignment explanation


    Indices: 17712--17864  Score: 252
    Period size: 81  Copynumber: 1.9  Consensus size: 79

      17702 TTTCTTTTGT

                 *                                                           
      17712 TCTTATTTATATTTTGTTTGTTTGATAAAAATTAAAAACTTATATATTGTTATTTTAAACAACTT
          1 TCTTAATTATATTTTGTTTGTTTGATAAAAATTAAAAAC-T-TATATTGTTATTTTAAACAACTT

                            
      17777 TTAAGGCTTGCTGAAG
         64 TTAAGGCTTGCTGAAG

                                         *   **                              
      17793 TCTTAATTATATTTTGTTTGTTTGATAAAGATTGGAAACTTATATTGTTATTTTAAACAACTTTT
          1 TCTTAATTATATTTTGTTTGTTTGATAAAAATTAAAAACTTATATTGTTATTTTAAACAACTTTT

                   
      17858 AAGGCTT
         66 AAGGCTT

      17865 ATTGAACTGA


Statistics
Matches: 68,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  79   32  0.47
  80    1  0.01
  81   35  0.51

ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49


Consensus pattern (79 bp):   
TCTTAATTATATTTTGTTTGTTTGATAAAAATTAAAAACTTATATTGTTATTTTAAACAACTTTT
AAGGCTTGCTGAAG
Done.