Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012512.1 Corchorus capsularis cultivar CVL-1 contig12533, 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: 4614
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:671 original size:20 final size:20

Alignment explanation


    Indices: 646--685  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        636 CGGCTCAACC

                      *         
        646 CCTAGATCTATTTTTTTACA
          1 CCTAGATCTAATTTTTTACA

                                
        666 CCTAGATCTAATTTTTTACA
          1 CCTAGATCTAATTTTTTACA

        686 TCCATTCCTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47


Consensus pattern (20 bp):   
CCTAGATCTAATTTTTTACA

Found at i:3075 original size:25 final size:25

Alignment explanation


    Indices: 3014--3075  Score: 58
    Period size: 25  Copynumber: 2.5  Consensus size: 25

       3004 ATTTGTTAAA

                                      
       3014 AAATTATT-ATTAAAGTTAATTAATT
          1 AAATT-TTGATTAAAGTTAATTAATT

              *            *           
       3039 --TTTTTGGAATTAATGTTAATTAATT
          1 AAATTTT-G-ATTAAAGTTAATTAATT

                        
       3064 AAATTTTGATTA
          1 AAATTTTGATTA

       3076 TTAAAAAATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 10
        0.69            0.07        0.24

Matches are distributed among these distances:
  22    2  0.07
  23    2  0.07
  25   20  0.69
  26    1  0.03
  27    4  0.14

ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52


Consensus pattern (25 bp):   
AAATTTTGATTAAAGTTAATTAATT

Found at i:3372 original size:14 final size:14

Alignment explanation


    Indices: 3353--3393  Score: 73
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       3343 TACCCCCCGC

                       *  
       3353 GATCCACGTTCTGG
          1 GATCCACGTTCCGG

                          
       3367 GATCCACGTTCCGG
          1 GATCCACGTTCCGG

                         
       3381 GATCCACGTTCCG
          1 GATCCACGTTCCG

       3394 AATTTGGGTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  14   26  1.00

ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24


Consensus pattern (14 bp):   
GATCCACGTTCCGG

Found at i:4461 original size:158 final size:158

Alignment explanation


    Indices: 4173--4489  Score: 616
    Period size: 158  Copynumber: 2.0  Consensus size: 158

       4163 TAATACCTAT

                                                                             
       4173 ATCATTACACCTATAAAGGTATCAACATTAAACCTAATGTCTATTTTCCCATTATTTTCCCCACA
          1 ATCATTACACCTATAAAGGTATCAACATTAAACCTAATGTCTATTTTCCCATTATTTTCCCCACA

                                                                             
       4238 ATTAACCGGATTGTAAAGGGTAGCATTCCTAGTTGACTTCATCACAACAAACGGCCTACATCCCT
         66 ATTAACCGGATTGTAAAGGGTAGCATTCCTAGTTGACTTCATCACAACAAACGGCCTACATCCCT

                                        
       4303 TTCCGCCCAAATCCGACCATCTCAAGGG
        131 TTCCGCCCAAATCCGACCATCTCAAGGG

                                    *                                        
       4331 ATCATTACACCTATAAAGGTATCATCATTAAACCTAATGTCTATTTTCCCATTATTTTCCCCACA
          1 ATCATTACACCTATAAAGGTATCAACATTAAACCTAATGTCTATTTTCCCATTATTTTCCCCACA

                                                                  *          
       4396 ATTAACCGGATTGTAAAGGGTAGCATTCCTAGTTGACTTCATCACAACAAACGGTCTACATCCCT
         66 ATTAACCGGATTGTAAAGGGTAGCATTCCTAGTTGACTTCATCACAACAAACGGCCTACATCCCT

                                        
       4461 TTCCGCCCAAATCCGACCATCTCAAGGG
        131 TTCCGCCCAAATCCGACCATCTCAAGGG

             
       4489 A
          1 A

       4490 CCAAATTATC


Statistics
Matches: 157,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 158  157  1.00

ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29


Consensus pattern (158 bp):   
ATCATTACACCTATAAAGGTATCAACATTAAACCTAATGTCTATTTTCCCATTATTTTCCCCACA
ATTAACCGGATTGTAAAGGGTAGCATTCCTAGTTGACTTCATCACAACAAACGGCCTACATCCCT
TTCCGCCCAAATCCGACCATCTCAAGGG
Done.