Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010903.1 Corchorus capsularis cultivar CVL-1 contig10924, 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: 10444
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:321 original size:33 final size:32

Alignment explanation


    Indices: 279--345  Score: 107
    Period size: 33  Copynumber: 2.1  Consensus size: 32

        269 ATGTACCAAA

                                             
        279 AAGATTACCAATTTTCTATCTAATTTTTTTATG
          1 AAGATTACCAATTTTCTATCT-ATTTTTTTATG

                                 *       *  
        312 AAGATTACCAATTTTCTATCTTTTTTTTTTTG
          1 AAGATTACCAATTTTCTATCTATTTTTTTATG

              
        344 AA
          1 AA

        346 AAAACTATAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   11  0.34
  33   21  0.66

ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54


Consensus pattern (32 bp):   
AAGATTACCAATTTTCTATCTATTTTTTTATG

Found at i:689 original size:32 final size:31

Alignment explanation


    Indices: 653--716  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 31

        643 TTCATTAATG

                       *                    
        653 GTGAAGATCACTAATTTTCTATCTAATTTTTT
          1 GTGAAGATCACCAATTTTCTATCT-ATTTTTT

                    **              *      
        685 GTGAAGATTGCCAATTTTCTATCTTTTTTTT
          1 GTGAAGATCACCAATTTTCTATCTATTTTTT

             
        716 G
          1 G

        717 AAAAAAAATC


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  31    7  0.25
  32   21  0.75

ACGTcount: A:0.23, C:0.12, G:0.12, T:0.52


Consensus pattern (31 bp):   
GTGAAGATCACCAATTTTCTATCTATTTTTT

Found at i:4044 original size:16 final size:16

Alignment explanation


    Indices: 4023--4057  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4013 AGAGTTACAA

                            
       4023 GAAGCTTTATGAAAAT
          1 GAAGCTTTATGAAAAT

                            
       4039 GAAGCTTTATGAAAAT
          1 GAAGCTTTATGAAAAT

               
       4055 GAA
          1 GAA

       4058 AGAGAAGCAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29


Consensus pattern (16 bp):   
GAAGCTTTATGAAAAT

Found at i:5596 original size:22 final size:23

Alignment explanation


    Indices: 5553--5596  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       5543 ATGATTATAA

                 *    *            
       5553 CCACAGCAGTTAAAGGATAAAGT
          1 CCACAACAGTCAAAGGATAAAGT

                                  
       5576 CCACAACAGTCAAA-GATAAAG
          1 CCACAACAGTCAAAGGATAAAG

       5597 ATAAATCTAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  22    7  0.37
  23   12  0.63

ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14


Consensus pattern (23 bp):   
CCACAACAGTCAAAGGATAAAGT
Done.