Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011939.1 Corchorus olitorius cultivar O-4 contig11972, 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: 15695
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30


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

Alignment explanation


    Indices: 1--54  Score: 108
    Period size: 2  Copynumber: 27.0  Consensus size: 2

                                                                          
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

                             
         43 CT CT CT CT CT CT
          1 CT CT CT CT CT CT

         55 TTTTCTTTTT


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   52  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:10645 original size:284 final size:284

Alignment explanation


    Indices: 10135--10690  Score: 1051
    Period size: 284  Copynumber: 2.0  Consensus size: 284

      10125 TGAGACCAAT

                                             *                               
      10135 ACAATTTATCAAGCTTTTCTAAATGATTAATTTGTTTGATAATAATTTGTTCATTCTCAACTCTA
          1 ACAATTTATCAAGCTTTTCTAAATGATTAATTTCTTTGATAATAATTTGTTCATTCTCAACTCTA

                                     *                       *               
      10200 TTAAAGTCTAAAGCAATATGGTTAATAGATGATTGTATATTATTGAGCTTATTCTTTAGATTATT
         66 TTAAAGTCTAAAGCAATATGGTTAAAAGATGATTGTATATTATTGAGCTCATTCTTTAGATTATT

                                                                             
      10265 AATAGAGGATTTAACATTACCAAACACGTTCTTCTACCAATCTTTAGAAAGAAAAGCTAATTTTA
        131 AATAGAGGATTTAACATTACCAAACACGTTCTTCTACCAATCTTTAGAAAGAAAAGCTAATTTTA

                                                                             
      10330 AAGATTTAGAAACGAAATCAAAACCAAAAGAACCAATCCTAGGTTGAGACCAAATATGTTTAACA
        196 AAGATTTAGAAACGAAATCAAAACCAAAAGAACCAATCCTAGGTTGAGACCAAATATGTTTAACA

                                    
      10395 ATCTGTTTGTAAACAATCTGTTTA
        261 ATCTGTTTGTAAACAATCTGTTTA

                                                                             
      10419 ACAATTTATCAAGCTTTTCTAAATGATTAATTTCTTTGATAATAATTTGTTCATTCTCAACTCTA
          1 ACAATTTATCAAGCTTTTCTAAATGATTAATTTCTTTGATAATAATTTGTTCATTCTCAACTCTA

                                                                             
      10484 TTAAAGTCTAAAGCAATATGGTTAAAAGATGATTGTATATTATTGAGCTCATTCTTTAGATTATT
         66 TTAAAGTCTAAAGCAATATGGTTAAAAGATGATTGTATATTATTGAGCTCATTCTTTAGATTATT

                                               *                             
      10549 AATAGAGGATTTAACATTACCAAACACGTTCTTCTGCCAATCTTTAGAAAGAAAAGCTAATTTTA
        131 AATAGAGGATTTAACATTACCAAACACGTTCTTCTACCAATCTTTAGAAAGAAAAGCTAATTTTA

              *                                                              
      10614 AATATTT-GAAAACGAAATCAAAACCAAAAGAACCAATCCTAGGTTGAGACCAAATATGTTTAAC
        196 AAGATTTAG-AAACGAAATCAAAACCAAAAGAACCAATCCTAGGTTGAGACCAAATATGTTTAAC

                         
      10678 AATCTGTTTGTAA
        260 AATCTGTTTGTAA

      10691 TCATCTTTCC


Statistics
Matches: 266,  Mismatches: 5, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
 283    1  0.00
 284  265  1.00

ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36


Consensus pattern (284 bp):   
ACAATTTATCAAGCTTTTCTAAATGATTAATTTCTTTGATAATAATTTGTTCATTCTCAACTCTA
TTAAAGTCTAAAGCAATATGGTTAAAAGATGATTGTATATTATTGAGCTCATTCTTTAGATTATT
AATAGAGGATTTAACATTACCAAACACGTTCTTCTACCAATCTTTAGAAAGAAAAGCTAATTTTA
AAGATTTAGAAACGAAATCAAAACCAAAAGAACCAATCCTAGGTTGAGACCAAATATGTTTAACA
ATCTGTTTGTAAACAATCTGTTTA

Found at i:12487 original size:15 final size:14

Alignment explanation


    Indices: 12467--12503  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 14

      12457 AGGTTGAAAG

                           
      12467 AAAACAATTAAACAT
          1 AAAACAATTAAAC-T

                          
      12482 AAAACAATTAAACT
          1 AAAACAATTAAACT

                    
      12496 AGAAACAA
          1 A-AAACAA

      12504 GACAAGTAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14    2  0.10
  15   19  0.90

ACGTcount: A:0.68, C:0.14, G:0.03, T:0.16


Consensus pattern (14 bp):   
AAAACAATTAAACT
Done.