Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016391.1 Corchorus capsularis cultivar CVL-1 contig16412, 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: 13855
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32


Found at i:425 original size:28 final size:27

Alignment explanation


    Indices: 352--431  Score: 97
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        342 CCTAAATGCA

                       *            *  
        352 AAAAAATGACCTAAATGCCCCTGGATG
          1 AAAAAATGACCAAAATGCCCCTGGGTG

            **            *            
        379 TGAAAATGACCAAATTGCCCCTGGGTG
          1 AAAAAATGACCAAAATGCCCCTGGGTG

                                 *    
        406 CAAAAAATGACCAAAATGCCCTTGGG
          1 -AAAAAATGACCAAAATGCCCCTGGG

        432 CGACCCTAAT


Statistics
Matches: 43,  Mismatches: 9, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  27   22  0.51
  28   21  0.49

ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19


Consensus pattern (27 bp):   
AAAAAATGACCAAAATGCCCCTGGGTG

Found at i:9894 original size:80 final size:77

Alignment explanation


    Indices: 9791--9987  Score: 216
    Period size: 77  Copynumber: 2.5  Consensus size: 77

       9781 CCGAGTACAC

                              *          *   *                           *   
       9791 AATTAAACACATAGTCTGGAAATAGCATCCACTTCTGAATAATACCATAAACTCCGAATACCAGT
          1 AATTAAACACATAGTCTGAAAATA-C--CAACTACTGAATAATACCATAAACTCCGAATACAAGT

                    *      
       9856 ACTGAATACTAACAT
         63 ACTGAATAATAACAT

             *                                 *  *          *               
       9871 AGTTAAACACACTA-TCTGAAAATACCAACTACTGCATGATACCATAAATTCCGAATACAAGTAC
          1 AATTAAACACA-TAGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTAC

                    * *  
       9935 TGAATAATGATAT
         65 TGAATAATAACAT

                        *                           
       9948 AATTAAACACATTGTCTGAGAATACTACCAACTACTGAAT
          1 AATTAAACACATAGTCTGA-AA-A-TACCAACTACTGAAT

       9988 GGAACCGAAT


Statistics
Matches: 98,  Mismatches: 14, Indels: 10
        0.80            0.11        0.08

Matches are distributed among these distances:
  76    1  0.01
  77   58  0.59
  78    2  0.02
  79    2  0.02
  80   33  0.34
  81    2  0.02

ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26


Consensus pattern (77 bp):   
AATTAAACACATAGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTACT
GAATAATAACAT

Found at i:12490 original size:50 final size:50

Alignment explanation


    Indices: 12430--12549  Score: 129
    Period size: 48  Copynumber: 2.4  Consensus size: 50

      12420 GAAGTCCAGA

                *                  *                      *    
      12430 CTTTAATTCAAAGGTGACATTTATTTCACAAATTACTT-TAAAAATTCAAT
          1 CTTTTATTCAAAGGTGACATTT-CTTCACAAATTACTTGTAAAAATCCAAT

                            *           *     *               
      12480 CTTTTATTCAAAGGTGTCA--TCTTCACTAATTATTTGTAAAAATCCAAT
          1 CTTTTATTCAAAGGTGACATTTCTTCACAAATTACTTGTAAAAATCCAAT

                    *    *  *     
      12528 CTTTTATTTAAAGATGGCATTT
          1 CTTTTATTCAAAGGTGACATTT

      12550 TAAAAACCCC


Statistics
Matches: 58,  Mismatches: 9, Indels: 6
        0.79            0.12        0.08

Matches are distributed among these distances:
  47   12  0.21
  48   28  0.48
  50   18  0.31

ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42


Consensus pattern (50 bp):   
CTTTTATTCAAAGGTGACATTTCTTCACAAATTACTTGTAAAAATCCAAT
Done.