Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009211.1 Corchorus capsularis cultivar CVL-1 contig09232, 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: 19279
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29


Found at i:2927 original size:27 final size:26

Alignment explanation


    Indices: 2888--2970  Score: 105
    Period size: 27  Copynumber: 3.1  Consensus size: 26

       2878 TTTATACCAA

                                       
       2888 CCACCACCTCCTCCTCCCCATCCCCAT
          1 CCACCACCTCCTCCTCCCCA-CCCCAT

                    *                   
       2915 CCACCACCGCCTCCTCCACCACCACCA-
          1 CCACCACCTCCTCCTCC-CCACC-CCAT

                       *               
       2942 CCACCACCTCCCCCTCCCCCACCCCAT
          1 CCACCACCTCCTCCT-CCCCACCCCAT

              
       2969 CC
          1 CC

       2971 CCATCCAAAA


Statistics
Matches: 49,  Mismatches: 3, Indels: 8
        0.82            0.05        0.13

Matches are distributed among these distances:
  26    3  0.06
  27   38  0.78
  28    8  0.16

ACGTcount: A:0.17, C:0.70, G:0.01, T:0.12


Consensus pattern (26 bp):   
CCACCACCTCCTCCTCCCCACCCCAT

Found at i:3011 original size:24 final size:24

Alignment explanation


    Indices: 2984--3033  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2974 TCCAAAACTG

                                    
       2984 CCACCGCCGCCACCACCACCTCCT
          1 CCACCGCCGCCACCACCACCTCCT

                 *     *     *      
       3008 CCACCTCCGCCGCCACCGCCTCCT
          1 CCACCGCCGCCACCACCACCTCCT

              
       3032 CC
          1 CC

       3034 TCCTCCTCCA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.12, C:0.68, G:0.10, T:0.10


Consensus pattern (24 bp):   
CCACCGCCGCCACCACCACCTCCT

Found at i:3032 original size:27 final size:27

Alignment explanation


    Indices: 2987--3056  Score: 95
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       2977 AAAACTGCCA

                       *               
       2987 CCGCCGCCACCACCACCTCCTCCACCT
          1 CCGCCGCCACCGCCACCTCCTCCACCT

                          *        *   
       3014 CCGCCGCCACCGCCTCCTCCTCCTCCT
          1 CCGCCGCCACCGCCACCTCCTCCACCT

              *     *       
       3041 CCACCGCCGCCGCCAC
          1 CCGCCGCCACCGCCAC

       3057 GGCCACCACC


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   37  1.00

ACGTcount: A:0.10, C:0.67, G:0.11, T:0.11


Consensus pattern (27 bp):   
CCGCCGCCACCGCCACCTCCTCCACCT

Found at i:12348 original size:16 final size:16

Alignment explanation


    Indices: 12327--12367  Score: 55
    Period size: 19  Copynumber: 2.4  Consensus size: 16

      12317 ACACTCTGAT

                            
      12327 CACAACTATTCTAAAC
          1 CACAACTATTCTAAAC

                               
      12343 CACAACATCTATTCTAAAC
          1 CAC-A-A-CTATTCTAAAC

                  
      12362 CACAAC
          1 CACAAC

      12368 ATCAACGAGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  16    4  0.18
  17    2  0.09
  18    2  0.09
  19   14  0.64

ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22


Consensus pattern (16 bp):   
CACAACTATTCTAAAC

Found at i:12356 original size:19 final size:19

Alignment explanation


    Indices: 12332--12370  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      12322 CTGATCACAA

                               
      12332 CTATTCTAAACCACAACAT
          1 CTATTCTAAACCACAACAT

                               
      12351 CTATTCTAAACCACAACAT
          1 CTATTCTAAACCACAACAT

             
      12370 C
          1 C

      12371 AACGAGTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26


Consensus pattern (19 bp):   
CTATTCTAAACCACAACAT
Done.