Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002483.1 Corchorus capsularis cultivar CVL-1 contig02490, 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, 616

Length: 1028
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19


Found at i:589 original size:13 final size:13

Alignment explanation


    Indices: 571--617  Score: 62
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        561 CATCCATCAG

                         
        571 CAAGTGCCGATGC
          1 CAAGTGCCGATGC

                         
        584 CAAGTGCC-AT-C
          1 CAAGTGCCGATGC

                           
        595 AGCAAGTGCCGATGC
          1 --CAAGTGCCGATGC

                    
        610 CAAGTGCC
          1 CAAGTGCC

        618 ATCGGAGAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
  11    1  0.03
  12    2  0.07
  13   24  0.80
  14    2  0.07
  15    1  0.03

ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15


Consensus pattern (13 bp):   
CAAGTGCCGATGC

Found at i:632 original size:26 final size:26

Alignment explanation


    Indices: 564--620  Score: 114
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        554 CAAGTGCCAT

                                      
        564 CCATCAGCAAGTGCCGATGCCAAGTG
          1 CCATCAGCAAGTGCCGATGCCAAGTG

                                      
        590 CCATCAGCAAGTGCCGATGCCAAGTG
          1 CCATCAGCAAGTGCCGATGCCAAGTG

                 
        616 CCATC
          1 CCATC

        621 GGAGAATGCC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   31  1.00

ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16


Consensus pattern (26 bp):   
CCATCAGCAAGTGCCGATGCCAAGTG

Found at i:637 original size:26 final size:26

Alignment explanation


    Indices: 575--698  Score: 81
    Period size: 32  Copynumber: 4.3  Consensus size: 26

        565 CATCAGCAAG

                  *                    
        575 TGCCGATGCCAAGTGCCATC--AGCAA
          1 TGCCGACGCCAAGTGCCATCGGAG-AA

                   *                   
        600 GTGCCGATGCCAAGTGCCATCGGAGAA
          1 -TGCCGACGCCAAGTGCCATCGGAGAA

                             *              
        627 TGCCGACGCCAAGGCCAAGATCCATCGGAGAA
          1 TGCCGACGCCAA-G---TG--CCATCGGAGAA

                                            
        659 TGCCGACGCCAAGGTCAAGTGCCATCGGAGAA
          1 TGCCGACG-C-----CAAGTGCCATCGGAGAA

                    
        691 TGCCGACG
          1 TGCCGACG

        699 AAGGGTGTCC


Statistics
Matches: 81,  Mismatches: 3, Indels: 22
        0.76            0.03        0.21

Matches are distributed among these distances:
  26   31  0.38
  27    3  0.04
  28    2  0.02
  30    1  0.01
  32   38  0.47
  33    1  0.01
  34    1  0.01
  37    1  0.01
  38    3  0.04

ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13


Consensus pattern (26 bp):   
TGCCGACGCCAAGTGCCATCGGAGAA

Found at i:644 original size:32 final size:32

Alignment explanation


    Indices: 608--698  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        598 AAGTGCCGAT

                                            
        608 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
          1 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG

                                             
        640 GCCAAGAT-CCATCGGAGAATGCCGACGCCAAG
          1 GCCAAG-TGCCATCGGAGAATGCCGACGCCAAG

             *                         
        672 GTCAAGTGCCATCGGAGAATGCCGACG
          1 GCCAAGTGCCATCGGAGAATGCCGACG

        699 AAGGGTGTCC


Statistics
Matches: 56,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  31    1  0.02
  32   54  0.96
  33    1  0.02

ACGTcount: A:0.29, C:0.30, G:0.31, T:0.11


Consensus pattern (32 bp):   
GCCAAGTGCCATCGGAGAATGCCGACGCCAAG

Found at i:756 original size:12 final size:12

Alignment explanation


    Indices: 735--764  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        725 CAAAAAAAAT

                        
        735 CCCATGGAAACC
          1 CCCATGGAAACC

                 *      
        747 CCCATTGAAACC
          1 CCCATGGAAACC

                  
        759 CCCATG
          1 CCCATG

        765 ACACTTAAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.30, C:0.43, G:0.13, T:0.13


Consensus pattern (12 bp):   
CCCATGGAAACC
Done.