Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009357.1 Corchorus capsularis cultivar CVL-1 contig09378, 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: 13813
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--33  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

                                                             
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         34 ATATATATAT


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

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:38 original size:2 final size:2

Alignment explanation


    Indices: 33--61  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

         23 TCTCTCTCTC

                                                       
         33 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         62 GTACGAAATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:6853 original size:9 final size:9

Alignment explanation


    Indices: 6839--6869  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

       6829 TGTAGAGCAG

                     
       6839 GAAGGCCAA
          1 GAAGGCCAA

                     
       6848 GAAGGCCAA
          1 GAAGGCCAA

              *      
       6857 GAGGGCCAA
          1 GAAGGCCAA

                
       6866 GAAG
          1 GAAG

       6870 TTCAAGAAGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.42, C:0.19, G:0.39, T:0.00


Consensus pattern (9 bp):   
GAAGGCCAA

Found at i:12420 original size:22 final size:23

Alignment explanation


    Indices: 12378--12430  Score: 81
    Period size: 22  Copynumber: 2.3  Consensus size: 23

      12368 AAGTAAGTAC

                                    
      12378 ATTAATTAGAAAAAAACTCAATTG
          1 ATTAATTAG-AAAAAACTCAATTG

                        *          
      12402 ATTAATTAG-AACAACTCAATTG
          1 ATTAATTAGAAAAAACTCAATTG

                   
      12424 ATTAATT
          1 ATTAATT

      12431 CATAATTAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  22   19  0.68
  24    9  0.32

ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34


Consensus pattern (23 bp):   
ATTAATTAGAAAAAACTCAATTG

Found at i:13604 original size:15 final size:15

Alignment explanation


    Indices: 13584--13613  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      13574 ATCAGGTCGC

                      *    
      13584 CACGATACACGATAT
          1 CACGATACACAATAT

                           
      13599 CACGATACACAATAT
          1 CACGATACACAATAT

      13614 TTCAACCGAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20


Consensus pattern (15 bp):   
CACGATACACAATAT
Done.