Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013669.1 Corchorus capsularis cultivar CVL-1 contig13690, 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: 14086
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:5326 original size:17 final size:17

Alignment explanation


    Indices: 5292--5327  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       5282 TTATATTGGA

                         *   
       5292 TCTAAATTAATCTGAAG
          1 TCTAAATTAATCTAAAG

                       *     
       5309 TCTAAATTAATTTAAAG
          1 TCTAAATTAATCTAAAG

              
       5326 TC
          1 TC

       5328 AAGTATGAGA


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

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39


Consensus pattern (17 bp):   
TCTAAATTAATCTAAAG

Found at i:5460 original size:32 final size:34

Alignment explanation


    Indices: 5424--5504  Score: 112
    Period size: 38  Copynumber: 2.3  Consensus size: 34

       5414 CTAACCATCT

                                              
       5424 AAACAAGCTTTTTGGTTC-AATGCC-AAAAAAAA
          1 AAACAAGCTTTTTGGTTCTAATGCCAAAAAAAAA

                                                  
       5456 AAACAAGCTTTTTGGTTCTTTTTAATGCCAAAAAAAAA
          1 AAACAAGCTTTTTGGTTC----TAATGCCAAAAAAAAA

                       
       5494 AAACAAGCTTT
          1 AAACAAGCTTT

       5505 CTGAGTTTCA


Statistics
Matches: 43,  Mismatches: 0, Indels: 6
        0.88            0.00        0.12

Matches are distributed among these distances:
  32   18  0.42
  37    6  0.14
  38   19  0.44

ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30


Consensus pattern (34 bp):   
AAACAAGCTTTTTGGTTCTAATGCCAAAAAAAAA

Found at i:11390 original size:2 final size:2

Alignment explanation


    Indices: 11385--11412  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      11375 CAATAAATAA

                                                     
      11385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      11413 TCAAATTGGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:12158 original size:11 final size:11

Alignment explanation


    Indices: 12115--12152  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      12105 TTCCTATATA

                *      
      12115 AAATAAATTAT
          1 AAATTAATTAT

                        
      12126 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      12137 AAATTAATTAT
          1 AAATTAATTAT

                 
      12148 AAATT
          1 AAATT

      12153 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:13578 original size:31 final size:31

Alignment explanation


    Indices: 13543--13607  Score: 130
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      13533 GATGAAATTC

                                           
      13543 AATCTATTGTAATTTATGTTATGAACTATGT
          1 AATCTATTGTAATTTATGTTATGAACTATGT

                                           
      13574 AATCTATTGTAATTTATGTTATGAACTATGT
          1 AATCTATTGTAATTTATGTTATGAACTATGT

               
      13605 AAT
          1 AAT

      13608 TTCATTTTCA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48


Consensus pattern (31 bp):   
AATCTATTGTAATTTATGTTATGAACTATGT
Done.