Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014661.1 Corchorus capsularis cultivar CVL-1 contig14682, 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: 39330
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:6555 original size:21 final size:21

Alignment explanation


    Indices: 6508--6552  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       6498 CAACCAATTC

                          *   *  
       6508 ATTAATTAATTAGTTATATTA
          1 ATTAATTAATTAGTAATAATA

                                  
       6529 ATTAATTAATTAGATAATAATA
          1 ATTAATTAATTAG-TAATAATA

              
       6551 AT
          1 AT

       6553 AATAATCCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   13  0.62
  22    8  0.38

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (21 bp):   
ATTAATTAATTAGTAATAATA

Found at i:22821 original size:89 final size:89

Alignment explanation


    Indices: 22723--22899  Score: 345
    Period size: 89  Copynumber: 2.0  Consensus size: 89

      22713 CCTTAAGTTT

                                                                             
      22723 ATACGGATTGTCACTTTGCACCCATCTTTTTTATTTTGACCAAAACGCACCCTAAAGTTTTATTT
          1 ATACGGATTGTCACTTTGCACCCATCTTTTTTATTTTGACCAAAACGCACCCTAAAGTTTTATTT

                                    
      22788 TTGTGCCACTTTGCACCCTCCGTC
         66 TTGTGCCACTTTGCACCCTCCGTC

                                                    *                        
      22812 ATACGGATTGTCACTTTGCACCCATCTTTTTTATTTTGACTAAAACGCACCCTAAAGTTTTATTT
          1 ATACGGATTGTCACTTTGCACCCATCTTTTTTATTTTGACCAAAACGCACCCTAAAGTTTTATTT

                                   
      22877 TTGTGCCACTTTGCACCCTCCGT
         66 TTGTGCCACTTTGCACCCTCCGT

      22900 TATGATAGGA


Statistics
Matches: 87,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  89   87  1.00

ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39


Consensus pattern (89 bp):   
ATACGGATTGTCACTTTGCACCCATCTTTTTTATTTTGACCAAAACGCACCCTAAAGTTTTATTT
TTGTGCCACTTTGCACCCTCCGTC

Found at i:27344 original size:122 final size:122

Alignment explanation


    Indices: 27127--27371  Score: 463
    Period size: 122  Copynumber: 2.0  Consensus size: 122

      27117 GTGGTCTGAA

                                   *                                         
      27127 GAGATTGTTTGATAGCAATATCTGCAAATTTCACATATTTAGTTGGAACTTTAATGTGGAGCTTT
          1 GAGATTGTTTGATAGCAATATCTACAAATTTCACATATTTAGTTGGAACTTTAATGTGGAGCTTT

                                                       *             
      27192 TTGACCAATAGATGTACCAGCAATGTTTATCATAGATTTTACTGTGTAAACTTTTTT
         66 TTGACCAATAGATGTACCAGCAATGTTTATCATAGATTTTACTCTGTAAACTTTTTT

                                             *                               
      27249 GAGATTGTTTGATAGCAATATCTACAAATTTCATATATTTAGTTGGAACTTTAATGTGGAGCTTT
          1 GAGATTGTTTGATAGCAATATCTACAAATTTCACATATTTAGTTGGAACTTTAATGTGGAGCTTT

                                                                     
      27314 TTGACCAATAGATGTACCAGCAATGTTTATCATAGATTTTACTCTGTAAACTTTTTT
         66 TTGACCAATAGATGTACCAGCAATGTTTATCATAGATTTTACTCTGTAAACTTTTTT

             
      27371 G
          1 G

      27372 CTAGCAATTA


Statistics
Matches: 120,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 122  120  1.00

ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41


Consensus pattern (122 bp):   
GAGATTGTTTGATAGCAATATCTACAAATTTCACATATTTAGTTGGAACTTTAATGTGGAGCTTT
TTGACCAATAGATGTACCAGCAATGTTTATCATAGATTTTACTCTGTAAACTTTTTT

Found at i:29316 original size:25 final size:24

Alignment explanation


    Indices: 29288--29354  Score: 80
    Period size: 26  Copynumber: 2.7  Consensus size: 24

      29278 TCTCTAACAT

                             *       
      29288 AAAAAGTCTTCCTTTTGGTGCCAAA
          1 AAAAAGTCTTCCTTTTGAT-CCAAA

                              *       
      29313 AAAAAGTCTTCCTTTAATTATCCAAA
          1 AAAAAGTCTTCCTTT--TGATCCAAA

               *            
      29339 AAAGAGTCTTCCTTTT
          1 AAAAAGTCTTCCTTTT

      29355 TTACTTTCTC


Statistics
Matches: 37,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  24    1  0.03
  25   15  0.41
  26   19  0.51
  27    2  0.05

ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36


Consensus pattern (24 bp):   
AAAAAGTCTTCCTTTTGATCCAAA

Found at i:31253 original size:2 final size:2

Alignment explanation


    Indices: 31246--31277  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      31236 TAGTAATCTA

                                                           
      31246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      31278 GTCTGGACGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.