Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013920.1 Corchorus capsularis cultivar CVL-1 contig13941, 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: 43233
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:13483 original size:10 final size:10

Alignment explanation


    Indices: 13468--13492  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      13458 TAACTCCAAT

                      
      13468 TATGGACTTA
          1 TATGGACTTA

                      
      13478 TATGGACTTA
          1 TATGGACTTA

                 
      13488 TATGG
          1 TATGG

      13493 GCTGAATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40


Consensus pattern (10 bp):   
TATGGACTTA

Found at i:14082 original size:17 final size:17

Alignment explanation


    Indices: 14037--14084  Score: 53
    Period size: 17  Copynumber: 2.8  Consensus size: 17

      14027 AAGTAACTAA

                              
      14037 GAAAAATAAAAAGTAAAC
          1 GAAAAATAAAAAG-AAAC

            *      *         
      14055 TAAAAA-CAAAAGAAAC
          1 GAAAAATAAAAAGAAAC

                   *      
      14071 GAAAAATTAAAAGA
          1 GAAAAATAAAAAGA

      14085 TAATAGTAAG


Statistics
Matches: 25,  Mismatches: 4, Indels: 3
        0.78            0.12        0.09

Matches are distributed among these distances:
  16    9  0.36
  17   11  0.44
  18    5  0.20

ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10


Consensus pattern (17 bp):   
GAAAAATAAAAAGAAAC

Found at i:20244 original size:27 final size:27

Alignment explanation


    Indices: 20206--20276  Score: 115
    Period size: 27  Copynumber: 2.6  Consensus size: 27

      20196 GGGTCATTTA

                                       
      20206 AGGGGCATTTTGGTCATTTTCGACTCC
          1 AGGGGCATTTTGGTCATTTTCGACTCC

                                *  *  *
      20233 AGGGGCATTTTGGTCATTTTTGAGTCT
          1 AGGGGCATTTTGGTCATTTTCGACTCC

                             
      20260 AGGGGCATTTTGGTCAT
          1 AGGGGCATTTTGGTCAT

      20277 GTTGGGTCTA


Statistics
Matches: 41,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   41  1.00

ACGTcount: A:0.15, C:0.15, G:0.30, T:0.39


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTTCGACTCC

Found at i:23486 original size:13 final size:14

Alignment explanation


    Indices: 23468--23496  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      23458 TAAATTGGAC

                          
      23468 TTTGCATTCAT-CA
          1 TTTGCATTCATGCA

                          
      23481 TTTGCATTCATGCA
          1 TTTGCATTCATGCA

              
      23495 TT
          1 TT

      23497 AAGTCGAATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48


Consensus pattern (14 bp):   
TTTGCATTCATGCA

Found at i:25168 original size:28 final size:28

Alignment explanation


    Indices: 25137--25202  Score: 123
    Period size: 28  Copynumber: 2.4  Consensus size: 28

      25127 ACGACAAACA

                                        
      25137 GTACGGACGCGCTAAAGACATCAACGTT
          1 GTACGGACGCGCTAAAGACATCAACGTT

                               *        
      25165 GTACGGACGCGCTAAAGACGTCAACGTT
          1 GTACGGACGCGCTAAAGACATCAACGTT

                      
      25193 GTACGGACGC
          1 GTACGGACGC

      25203 ACTGAAGCTG


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   37  1.00

ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17


Consensus pattern (28 bp):   
GTACGGACGCGCTAAAGACATCAACGTT

Done.