Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010708.1 Corchorus capsularis cultivar CVL-1 contig10729, 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: 31629
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Found at i:47 original size:33 final size:33

Alignment explanation


    Indices: 1--119  Score: 175
    Period size: 33  Copynumber: 3.6  Consensus size: 33

                   *            *   *        
          1 TGGGGAGACTCCACCGTGGCGGAGTCGCCCTAG
          1 TGGGGAGGCTCCACCGTGGCAGAGCCGCCCTAG

                    *                  *     
         34 TGGGGAGGTTCCACCGTGGCAGAGCCGTCCTAG
          1 TGGGGAGGCTCCACCGTGGCAGAGCCGCCCTAG

                        *                    
         67 TGGGGAGGCTCCGCCGTGGCAGAGCCGCCCTAG
          1 TGGGGAGGCTCCACCGTGGCAGAGCCGCCCTAG

                        *       
        100 TGGGGAGGCTCCGCCGTGGC
          1 TGGGGAGGCTCCACCGTGGC

        120 TAAGGGCAAA


Statistics
Matches: 78,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   78  1.00

ACGTcount: A:0.13, C:0.30, G:0.42, T:0.15


Consensus pattern (33 bp):   
TGGGGAGGCTCCACCGTGGCAGAGCCGCCCTAG

Found at i:3732 original size:55 final size:55

Alignment explanation


    Indices: 3648--3765  Score: 193
    Period size: 55  Copynumber: 2.1  Consensus size: 55

       3638 GGGAGAGGCA

                                          *                        
       3648 TAGTTTTGAATCTAAGGCTTAAACCCATTTTCTTTTCTATTGTTTAAAATGCCAT
          1 TAGTTTTGAATCTAAGGCTTAAACCCATTTCCTTTTCTATTGTTTAAAATGCCAT

                          *                        *                
       3703 TAGTTTTGAATCTTCA-GCTTAAACCCATTTCCTTTTCTTTTGTTTAAAATGCCAT
          1 TAGTTTTGAATC-TAAGGCTTAAACCCATTTCCTTTTCTATTGTTTAAAATGCCAT

                    
       3758 TAGTTTTG
          1 TAGTTTTG

       3766 TCTTGTGTTA


Statistics
Matches: 59,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  55   57  0.97
  56    2  0.03

ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47


Consensus pattern (55 bp):   
TAGTTTTGAATCTAAGGCTTAAACCCATTTCCTTTTCTATTGTTTAAAATGCCAT

Found at i:9383 original size:17 final size:18

Alignment explanation


    Indices: 9357--9391  Score: 63
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       9347 GGATTTTGAA

                              
       9357 AATGTATTTGTTTTGTAT
          1 AATGTATTTGTTTTGTAT

                              
       9375 AATGT-TTTGTTTTGTAT
          1 AATGTATTTGTTTTGTAT

       9392 GGAACATTGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   12  0.71
  18    5  0.29

ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63


Consensus pattern (18 bp):   
AATGTATTTGTTTTGTAT

Found at i:21061 original size:12 final size:12

Alignment explanation


    Indices: 21044--21068  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      21034 GATTGCAGTA

                        
      21044 TTCTTCTCCTTC
          1 TTCTTCTCCTTC

                        
      21056 TTCTTCTCCTTC
          1 TTCTTCTCCTTC

             
      21068 T
          1 T

      21069 CATTACCAGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60


Consensus pattern (12 bp):   
TTCTTCTCCTTC

Found at i:24466 original size:9 final size:9

Alignment explanation


    Indices: 24439--24469  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

      24429 TAAACTCCTT

                     
      24439 CCATTCAAC
          1 CCATTCAAC

            *        
      24448 ACATTCAAC
          1 CCATTCAAC

                     
      24457 CCATTCAAC
          1 CCATTCAAC

                
      24466 CCAT
          1 CCAT

      24470 CATGTATTGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23


Consensus pattern (9 bp):   
CCATTCAAC
Done.