Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013866.1 Corchorus olitorius cultivar O-4 contig13899, 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: 30272
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:13989 original size:2 final size:2

Alignment explanation


    Indices: 13982--14008  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      13972 AACCACAGGG

                                                    
      13982 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 T

      14009 TTTACCCTAA


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

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:17876 original size:30 final size:29

Alignment explanation


    Indices: 17819--17895  Score: 120
    Period size: 30  Copynumber: 2.6  Consensus size: 29

      17809 TTTTTTTTTT

                        *                
      17819 AAATATAGAGTTGGCAATTTCGCCAAAAA
          1 AAATATAGAGTTAGCAATTTCGCCAAAAA

                                           
      17848 AAATATAGAGTTAGCAATTAGT-GCCAAAAA
          1 AAATATAGAGTTAGCAATT--TCGCCAAAAA

                              
      17878 AAATATAGAGTTAGCAAT
          1 AAATATAGAGTTAGCAAT

      17896 ATGTTAACAA


Statistics
Matches: 45,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  29   18  0.40
  30   26  0.58
  31    1  0.02

ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25


Consensus pattern (29 bp):   
AAATATAGAGTTAGCAATTTCGCCAAAAA

Found at i:18188 original size:13 final size:13

Alignment explanation


    Indices: 18170--18197  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      18160 CGGGACCTGA

                         
      18170 AAGACGATCTCCT
          1 AAGACGATCTCCT

                         
      18183 AAGACGATCTCCT
          1 AAGACGATCTCCT

              
      18196 AA
          1 AA

      18198 ATTCACTTCG


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21


Consensus pattern (13 bp):   
AAGACGATCTCCT

Found at i:18854 original size:227 final size:227

Alignment explanation


    Indices: 18454--18898  Score: 827
    Period size: 227  Copynumber: 2.0  Consensus size: 227

      18444 TTGACAAATA

                *           *                                                
      18454 ATTCTAGAGATGGAAGTAGTAAGGTATAGGGGCAACAAAGGAGATCATCATCACACTGCTGCTCC
          1 ATTCGAGAGATGGAAGCAGTAAGGTATAGGGGCAACAAAGGAGATCATCATCACACTGCTGCTCC

                   *                                                         
      18519 AAGCTGGGTACCGCCGATTATAGCTGATTTCAAGATAAATACGAACGCCTCTTTTAATGTGGAGA
         66 AAGCTGGATACCGCCGATTATAGCTGATTTCAAGATAAATACGAACGCCTCTTTTAATGTGGAGA

                                                                             
      18584 AGGGTGAAGCAGGCTTAGGGGTGGTGATAAGAGATAGACAAGGGATAGTAGTGGTGTCTGCTACC
        131 AGGGTGAAGCAGGCTTAGGGGTGGTGATAAGAGATAGACAAGGGATAGTAGTGGTGTCTGCTACC

                                            
      18649 GCTAGAATCAATAATGTTTCTAGGCAAGAGGG
        196 GCTAGAATCAATAATGTTTCTAGGCAAGAGGG

                                     *                           *           
      18681 ATTCGAGAGATGGAAGCAGTAAGGTGTAGGGGCAACAAAGGAGATCATCATCATACTGCTGCTCC
          1 ATTCGAGAGATGGAAGCAGTAAGGTATAGGGGCAACAAAGGAGATCATCATCACACTGCTGCTCC

                                                       * *                   
      18746 AAGCTGGATACCGCCGATTATAGCTGATTTCAAGATAAATACGGAGGCCTCTTTTAATGTGGAGA
         66 AAGCTGGATACCGCCGATTATAGCTGATTTCAAGATAAATACGAACGCCTCTTTTAATGTGGAGA

                                                                             
      18811 AGGGTGAAGCAGGCTTAGGGGTGGTGATAAGAGATAGACAAGGGATAGTAGTGGTGTCTGCTACC
        131 AGGGTGAAGCAGGCTTAGGGGTGGTGATAAGAGATAGACAAGGGATAGTAGTGGTGTCTGCTACC

                                   
      18876 GCTAGAATCAATAATGTTTCTAG
        196 GCTAGAATCAATAATGTTTCTAG

      18899 CCCTTTATTT


Statistics
Matches: 211,  Mismatches: 7, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 227  211  1.00

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


Consensus pattern (227 bp):   
ATTCGAGAGATGGAAGCAGTAAGGTATAGGGGCAACAAAGGAGATCATCATCACACTGCTGCTCC
AAGCTGGATACCGCCGATTATAGCTGATTTCAAGATAAATACGAACGCCTCTTTTAATGTGGAGA
AGGGTGAAGCAGGCTTAGGGGTGGTGATAAGAGATAGACAAGGGATAGTAGTGGTGTCTGCTACC
GCTAGAATCAATAATGTTTCTAGGCAAGAGGG
Done.