Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014438.1 Corchorus capsularis cultivar CVL-1 contig14459, 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: 25350
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:3080 original size:25 final size:25

Alignment explanation


    Indices: 3052--3101  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       3042 TGCTGCAACA

                                     
       3052 TGATCTGGGTTTTGTGCATGATCTG
          1 TGATCTGGGTTTTGTGCATGATCTG

                                     
       3077 TGATCTGGGTTTTGTGCATGATCTG
          1 TGATCTGGGTTTTGTGCATGATCTG

       3102 GGCTTTCACT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.12, C:0.12, G:0.32, T:0.44


Consensus pattern (25 bp):   
TGATCTGGGTTTTGTGCATGATCTG

Found at i:3524 original size:17 final size:17

Alignment explanation


    Indices: 3502--3536  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3492 CACGTATAAC

                             
       3502 TGCTTAGCATGTCAATT
          1 TGCTTAGCATGTCAATT

                             
       3519 TGCTTAGCATGTCAATT
          1 TGCTTAGCATGTCAATT

             
       3536 T
          1 T

       3537 ACAAAACTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43


Consensus pattern (17 bp):   
TGCTTAGCATGTCAATT

Found at i:5582 original size:70 final size:70

Alignment explanation


    Indices: 5508--5712  Score: 356
    Period size: 70  Copynumber: 2.9  Consensus size: 70

       5498 TACACAAATA

                         *                                   *   *           
       5508 AATTGTCAAATCTTTAATTTCATCTATAACTACCAACATACTAAATACATAAACAAATAAATTAC
          1 AATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAAATAAATAAATTAC

                 
       5573 AAAGG
         66 AAAGG

                 *                          *  *                             
       5578 AATTGCCAAATCTCTAATTTCATCTATAACTATCATCATACTAAATACACAAATAAATAAATTAC
          1 AATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAAATAAATAAATTAC

                 
       5643 AAAGG
         66 AAAGG

                                                                             
       5648 AATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAAATAAATAAATTAC
          1 AATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAAATAAATAAATTAC

       5713 CACGGAAAAT


Statistics
Matches: 126,  Mismatches: 9, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  70  126  1.00

ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30


Consensus pattern (70 bp):   
AATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAAATAAATAAATTAC
AAAGG

Found at i:25279 original size:33 final size:33

Alignment explanation


    Indices: 25237--25301  Score: 96
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      25227 CTTTTACACT

                                              
      25237 GAGCCTCCCCACTAGGACGG-TTCAGCCACGGCG
          1 GAGCCTCCCCACTAGGACGGCTTC-GCCACGGCG

                         *  *               
      25270 GAGCCTCCCCACTGGGGCGGCTTCGCCACGGC
          1 GAGCCTCCCCACTAGGACGGCTTCGCCACGGC

      25302 AGGCCGCCCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  33   26  0.90
  34    3  0.10

ACGTcount: A:0.14, C:0.42, G:0.32, T:0.12


Consensus pattern (33 bp):   
GAGCCTCCCCACTAGGACGGCTTCGCCACGGCG

Found at i:25321 original size:32 final size:32

Alignment explanation


    Indices: 25282--25350  Score: 120
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      25272 GCCTCCCCAC

                                            
      25282 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
          1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

                       *       *            
      25314 TGGGGCGGCTTTGCCACGGTAGGCCGCCCTCA
          1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

                 
      25346 TGGGG
          1 TGGGG


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.09, C:0.35, G:0.41, T:0.16


Consensus pattern (32 bp):   
TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
Done.