Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014242.1 Corchorus capsularis cultivar CVL-1 contig14263, 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: 10324
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31


Found at i:7448 original size:31 final size:30

Alignment explanation


    Indices: 7401--7560  Score: 129
    Period size: 31  Copynumber: 5.4  Consensus size: 30

       7391 ACGGTGTCCG

                    *                      
       7401 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
          1 ACGT-GCATGCCACGTGTACCAAAAAGTGAC

             *                             
       7432 ATGTGACATGCCACGTGTACCAAAAAGT---
          1 ACGTG-CATGCCACGTGTACCAAAAAGTGAC

                         *                
       7460 -C--G--TGCCACATGTACCAAAAAGTGAC
          1 ACGTGCATGCCACGTGTACCAAAAAGTGAC

              *     *                      
       7485 ACATGTCACGCCACGTGTACCAAAAAGTGAC
          1 ACGTG-CATGCCACGTGTACCAAAAAGTGAC

                          *   **      *  * 
       7516 ACGTGGCATGCCACATGTTTCAAAAAATGGC
          1 ACGT-GCATGCCACGTGTACCAAAAAGTGAC

                          
       7547 ACGTGGCATGCCAC
          1 ACGT-GCATGCCAC

       7561 ATGCACAAAA


Statistics
Matches: 105,  Mismatches: 13, Indels: 22
        0.75            0.09        0.16

Matches are distributed among these distances:
  22   19  0.18
  25    1  0.01
  26    1  0.01
  28    1  0.01
  30    1  0.01
  31   81  0.77
  32    1  0.01

ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17


Consensus pattern (30 bp):   
ACGTGCATGCCACGTGTACCAAAAAGTGAC

Found at i:7472 original size:22 final size:22

Alignment explanation


    Indices: 7440--7481  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       7430 ACATGTGACA

                  *               
       7440 TGCCACGTGTACCAAAAAGTCG
          1 TGCCACATGTACCAAAAAGTCG

                                
       7462 TGCCACATGTACCAAAAAGT
          1 TGCCACATGTACCAAAAAGT

       7482 GACACATGTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19


Consensus pattern (22 bp):   
TGCCACATGTACCAAAAAGTCG

Found at i:7498 original size:53 final size:53

Alignment explanation


    Indices: 7410--7512  Score: 161
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       7400 GACGTGGCAC

                 *                 **     *                      
       7410 GCCACGTGTACCAAAAAGTGACATGTGACATGCCACGTGTACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGACACGCCACGTGTACCAAAAAGTCGT

                                       *                      
       7463 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
          1 GCCACATGTACCAAAAAGTGACACATGACACGCCACGTGTACCAAAAAGT

       7513 GACACGTGGC


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  53   45  1.00

ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGACACGCCACGTGTACCAAAAAGTCGT

Found at i:10303 original size:2 final size:2

Alignment explanation


    Indices: 10296--10324  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      10286 TATAACCCAC

                                                       
      10296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.