Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013101.1 Corchorus capsularis cultivar CVL-1 contig13122, 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: 3440
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31


Found at i:2923 original size:21 final size:21

Alignment explanation


    Indices: 2897--2938  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2887 AGCACAAGTG

                    *            
       2897 ACCGGCCATGCGACTTGGAGA
          1 ACCGGCCACGCGACTTGGAGA

                                 
       2918 ACCGGCCACGCGACTTGGAGA
          1 ACCGGCCACGCGACTTGGAGA

       2939 TGCCCGCGCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.24, C:0.31, G:0.33, T:0.12


Consensus pattern (21 bp):   
ACCGGCCACGCGACTTGGAGA

Found at i:2964 original size:33 final size:32

Alignment explanation


    Indices: 2918--3025  Score: 135
    Period size: 33  Copynumber: 3.3  Consensus size: 32

       2908 GACTTGGAGA

                          *                  
       2918 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
          1 ACCGGCCACGCGACATGGAGATGCCCG-GCAAC

                    *                      * 
       2951 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACATGGAGATGCCCGG-CAAC

                              **         *  
       2984 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
          1 ACCGGCCACGCGACATGGAGATGCCCGGCAAC

                      
       3016 ACCCGGCCAC
          1 A-CCGGCCAC

       3026 TTGACTCGCC


Statistics
Matches: 65,  Mismatches: 8, Indels: 4
        0.84            0.10        0.05

Matches are distributed among these distances:
  32    4  0.06
  33   61  0.94

ACGTcount: A:0.20, C:0.43, G:0.29, T:0.08


Consensus pattern (32 bp):   
ACCGGCCACGCGACATGGAGATGCCCGGCAAC

Found at i:3039 original size:33 final size:32

Alignment explanation


    Indices: 2918--3058  Score: 122
    Period size: 33  Copynumber: 4.3  Consensus size: 32

       2908 GACTTGGAGA

                          *  ***          *  
       2918 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
          1 ACCGGCCACGCGACATGCCCATGCCCG-GCCAC

                    *        ***             
       2951 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACATGCCCATGCCCGGCCA-C

                             *              
       2984 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
          1 ACCGGCCACGCGACATGCCCATGCCCGGCCAC

                      **                      
       3016 ACCCGGCCACTTGAC-TCGCCCATGCCCGGCCAC
          1 A-CCGGCCACGCGACAT-GCCCATGCCCGGCCAC

                      
       3049 AACCGGCCAC
          1 -ACCGGCCAC

       3059 ATGATCCTTT


Statistics
Matches: 95,  Mismatches: 9, Indels: 8
        0.85            0.08        0.07

Matches are distributed among these distances:
  32    6  0.06
  33   88  0.93
  34    1  0.01

ACGTcount: A:0.20, C:0.44, G:0.27, T:0.09


Consensus pattern (32 bp):   
ACCGGCCACGCGACATGCCCATGCCCGGCCAC

Found at i:3326 original size:17 final size:19

Alignment explanation


    Indices: 3294--3329  Score: 58
    Period size: 17  Copynumber: 2.0  Consensus size: 19

       3284 CATTGGGCCT

                               
       3294 TTATTCTATCTTAGTTTAG
          1 TTATTCTATCTTAGTTTAG

                               
       3313 TTATT-TAT-TTAGTTTAG
          1 TTATTCTATCTTAGTTTAG

       3330 AAGACATTGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    9  0.53
  18    3  0.18
  19    5  0.29

ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61


Consensus pattern (19 bp):   
TTATTCTATCTTAGTTTAG
Done.