Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003869.1 Corchorus capsularis cultivar CVL-1 contig03877, 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, 665

Length: 1109
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31


Found at i:416 original size:21 final size:21

Alignment explanation


    Indices: 392--498  Score: 124
    Period size: 21  Copynumber: 4.7  Consensus size: 21

        382 TGGAGATCGC

                                 
        392 ACATGACCGGCCATCCATTAG
          1 ACATGACCGGCCATCCATTAG

                                 
        413 ACATGACCGGCCATCCATTAG
          1 ACATGACCGGCCATCCATTAG

                           *             
        434 ACATGACCGGCCATGGCATGGTAACATCG
          1 ACATGACCGGCCAT-CCAT--T---A--G

                                  
        463 CACATGACCGGCCATCCATTAG
          1 -ACATGACCGGCCATCCATTAG

                          
        485 ACATGACCGGCCAT
          1 ACATGACCGGCCAT

        499 GGCATGGTTC


Statistics
Matches: 75,  Mismatches: 2, Indels: 18
        0.79            0.02        0.19

Matches are distributed among these distances:
  21   49  0.65
  22    4  0.05
  24    2  0.03
  27    2  0.03
  29    4  0.05
  30   14  0.19

ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18


Consensus pattern (21 bp):   
ACATGACCGGCCATCCATTAG

Found at i:470 original size:30 final size:28

Alignment explanation


    Indices: 434--524  Score: 88
    Period size: 30  Copynumber: 3.4  Consensus size: 28

        424 CATCCATTAG

                                          
        434 ACATGACCGGCCATGGCATGGTAACATCGC
          1 ACATGACCGGCCATGGCATGGT--CATCGC

                           *            
        464 ACATGACCGGCCAT-CCAT--T-A--G-
          1 ACATGACCGGCCATGGCATGGTCATCGC

                                          
        485 ACATGACCGGCCATGGCATGGTTCCATCGC
          1 ACATGACCGGCCATGGCATGG-T-CATCGC

                      
        515 ACATGACCGG
          1 ACATGACCGG

        525 ACACTTGGCC


Statistics
Matches: 50,  Mismatches: 2, Indels: 18
        0.71            0.03        0.26

Matches are distributed among these distances:
  21   14  0.28
  22    4  0.08
  24    1  0.02
  25    1  0.02
  27    2  0.04
  29    4  0.08
  30   24  0.48

ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18


Consensus pattern (28 bp):   
ACATGACCGGCCATGGCATGGTCATCGC

Found at i:489 original size:51 final size:51

Alignment explanation


    Indices: 413--524  Score: 206
    Period size: 51  Copynumber: 2.2  Consensus size: 51

        403 CATCCATTAG

                                                               
        413 ACATGACCGGCCATCCATTAGACATGACCGGCCATGGCATGGTAACATCGC
          1 ACATGACCGGCCATCCATTAGACATGACCGGCCATGGCATGGTAACATCGC

                                                       **      
        464 ACATGACCGGCCATCCATTAGACATGACCGGCCATGGCATGGTTCCATCGC
          1 ACATGACCGGCCATCCATTAGACATGACCGGCCATGGCATGGTAACATCGC

                      
        515 ACATGACCGG
          1 ACATGACCGG

        525 ACACTTGGCC


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  51   59  1.00

ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18


Consensus pattern (51 bp):   
ACATGACCGGCCATCCATTAGACATGACCGGCCATGGCATGGTAACATCGC
Done.