Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008641.1 Corchorus capsularis cultivar CVL-1 contig08662, 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: 22025
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34


Found at i:685 original size:24 final size:24

Alignment explanation


    Indices: 654--699  Score: 92
    Period size: 24  Copynumber: 1.9  Consensus size: 24

        644 GTGGTTTATG

                                    
        654 TTTTCTTCACTTTGGATTTCTTTT
          1 TTTTCTTCACTTTGGATTTCTTTT

                                  
        678 TTTTCTTCACTTTGGATTTCTT
          1 TTTTCTTCACTTTGGATTTCTT

        700 GGGTTTTGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.09, C:0.17, G:0.09, T:0.65


Consensus pattern (24 bp):   
TTTTCTTCACTTTGGATTTCTTTT

Found at i:6504 original size:16 final size:16

Alignment explanation


    Indices: 6465--6506  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6455 TCCACAATAA

                    *       
       6465 ATAAACAAGCAAGTTC
          1 ATAAACAAACAAGTTC

             * *            
       6481 AGATACAAACAAGTTC
          1 ATAAACAAACAAGTTC

                      
       6497 ATAAACAAAC
          1 ATAAACAAAC

       6507 TACTGCATAA


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.55, C:0.19, G:0.10, T:0.17


Consensus pattern (16 bp):   
ATAAACAAACAAGTTC

Found at i:20168 original size:93 final size:93

Alignment explanation


    Indices: 20004--20181  Score: 311
    Period size: 93  Copynumber: 1.9  Consensus size: 93

      19994 GTAGGGCTTG

                                                              *             *
      20004 ACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGACGGAACCAAGGCTTAG
          1 ACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGACAGAACCAAGGCTTAA

                                        
      20069 ATTGACTCATATGGAAACGATTAAATTA
         66 ATTGACTCATATGGAAACGATTAAATTA

                *                                            *               
      20097 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCAAGGCTTAA
          1 ACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGACAGAACCAAGGCTTAA

                    *           
      20162 ATTGACTCGTATGGAAACGA
         66 ATTGACTCATATGGAAACGA

      20182 GTTTGACTTG


Statistics
Matches: 80,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  93   80  1.00

ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26


Consensus pattern (93 bp):   
ACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGACAGAACCAAGGCTTAA
ATTGACTCATATGGAAACGATTAAATTA

Found at i:20170 original size:69 final size:69

Alignment explanation


    Indices: 20089--20410  Score: 581
    Period size: 69  Copynumber: 4.7  Consensus size: 69

      20079 ATGGAAACGA

                   *                                                         
      20089 TTAAATTAACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA
          1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA

                
      20154 AGGC
         66 AGGC

                                         *                            *      
      20158 TTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCA
          1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA

                
      20223 AGGC
         66 AGGC

                                             *                               
      20227 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCTATGTGGCTTGGATAGAACCA
          1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA

                
      20292 AGGC
         66 AGGC

                                         *      *                     *      
      20296 TTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGAAAAAGCCTATGTGGCTTGGATGGAACCA
          1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA

                
      20361 AGGC
         66 AGGC

                                                          
      20365 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
          1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA

      20411 ATTCTTGAAA


Statistics
Matches: 241,  Mismatches: 12, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  69  241  1.00

ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28


Consensus pattern (69 bp):   
TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA
AGGC

Found at i:21563 original size:13 final size:13

Alignment explanation


    Indices: 21545--21586  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

      21535 TAGAGCCTCT

                         
      21545 TTTTTTCTTTTTC
          1 TTTTTTCTTTTTC

                       *  
      21558 TTTTTT-TCTTCTC
          1 TTTTTTCT-TTTTC

               *         
      21571 TTTATTCTTTTTC
          1 TTTTTTCTTTTTC

               
      21584 TTT
          1 TTT

      21587 CATTTTTTAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  12    1  0.04
  13   22  0.92
  14    1  0.04

ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81


Consensus pattern (13 bp):   
TTTTTTCTTTTTC
Done.