Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007157.1 Corchorus capsularis cultivar CVL-1 contig07178, 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: 21132
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:797 original size:3 final size:3

Alignment explanation


    Indices: 789--832  Score: 88
    Period size: 3  Copynumber: 14.7  Consensus size: 3

        779 CAGCGCCACC

                                                                      
        789 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT

        833 CCTTTTCCGT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (3 bp):   
CTT

Found at i:1761 original size:16 final size:16

Alignment explanation


    Indices: 1740--1771  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1730 ATCCATGTCC

                            
       1740 TGTTAACATTTAAGGT
          1 TGTTAACATTTAAGGT

                            
       1756 TGTTAACATTTAAGGT
          1 TGTTAACATTTAAGGT

       1772 GATTCAAAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44


Consensus pattern (16 bp):   
TGTTAACATTTAAGGT

Found at i:10234 original size:19 final size:20

Alignment explanation


    Indices: 10188--10247  Score: 86
    Period size: 19  Copynumber: 3.0  Consensus size: 20

      10178 TCGCTGCTCA

                            *   
      10188 AATAATCTCATCTGTATAGT
          1 AATAATCTCATCTGTACAGT

                     *           
      10208 ACATAATCTAATCTGTACAGT
          1 A-ATAATCTCATCTGTACAGT

                                
      10229 -ATAATCTCATCTGTACAGT
          1 AATAATCTCATCTGTACAGT

      10248 TGCTAAACAG


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  19   18  0.50
  20    1  0.03
  21   17  0.47

ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37


Consensus pattern (20 bp):   
AATAATCTCATCTGTACAGT

Found at i:10845 original size:3 final size:3

Alignment explanation


    Indices: 10837--10904  Score: 136
    Period size: 3  Copynumber: 22.7  Consensus size: 3

      10827 GGTAGAGGTA

                                                                           
      10837 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

                                      
      10885 TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TT

      10905 TTGGCATTAG


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   65  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:15785 original size:51 final size:51

Alignment explanation


    Indices: 15698--15799  Score: 150
    Period size: 51  Copynumber: 2.0  Consensus size: 51

      15688 ACACTATCTC

                                        *                      
      15698 CATCTGTTTCATTCCGCAAAATCATGGGTTGAAAATCACCATTCAAAGCAG
          1 CATCTGTTTCATTCCGCAAAATCATGGGCTGAAAATCACCATTCAAAGCAG

                 *                   *     *     *     *       
      15749 CATCTTTTTCATTCCGCAAAATCATTGGCTGGAAATCTCCATTTAAAGCAG
          1 CATCTGTTTCATTCCGCAAAATCATGGGCTGAAAATCACCATTCAAAGCAG

      15800 TTGCTAACAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  51   45  1.00

ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30


Consensus pattern (51 bp):   
CATCTGTTTCATTCCGCAAAATCATGGGCTGAAAATCACCATTCAAAGCAG

Found at i:20465 original size:66 final size:66

Alignment explanation


    Indices: 20385--20516  Score: 255
    Period size: 66  Copynumber: 2.0  Consensus size: 66

      20375 ATCCCAATAC

                                                                             
      20385 GTTAGCTTGGGTGAGTGAATTAAAAGTATTTAAAATATTATTAATTAAGTAGTATTCCAATATAT
          1 GTTAGCTTGGGTGAGTGAATTAAAAGTATTTAAAATATTATTAATTAAGTAGTATTCCAATATAT

             
      20450 T
         66 T

                                                               *             
      20451 GTTAGCTTGGGTGAGTGAATTAAAAGTATTTAAAATATTATTAATTAAGTATTATTCCAATATAT
          1 GTTAGCTTGGGTGAGTGAATTAAAAGTATTTAAAATATTATTAATTAAGTAGTATTCCAATATAT

             
      20516 T
         66 T

      20517 ATTTTAAGGA


Statistics
Matches: 65,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  66   65  1.00

ACGTcount: A:0.38, C:0.05, G:0.16, T:0.42


Consensus pattern (66 bp):   
GTTAGCTTGGGTGAGTGAATTAAAAGTATTTAAAATATTATTAATTAAGTAGTATTCCAATATAT
T
Done.