Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018102.1 Corchorus olitorius cultivar O-4 contig18135, 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: 18479
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31


Found at i:11459 original size:190 final size:190

Alignment explanation


    Indices: 11136--11516  Score: 735
    Period size: 190  Copynumber: 2.0  Consensus size: 190

      11126 AGGAGGTGTG

                                                              *              
      11136 AATTCACCTGAGGGTTTACTTAACTCAAATGATACCCACAAACATTAAAAGCAAGATAGCAAAGA
          1 AATTCACCTGAGGGTTTACTTAACTCAAATGATACCCACAAACATTAAAAACAAGATAGCAAAGA

                                                                             
      11201 GAGAATTTTTCTTTTAAAAACATATCATAGCATAGAACAAACCTAGTCAAAAATCAATTTTGTTC
         66 GAGAATTTTTCTTTTAAAAACATATCATAGCATAGAACAAACCTAGTCAAAAATCAATTTTGTTC

                                                           *            
      11266 AATTTCCATAATCAAGCAACTAGCTAGAAATAGCCTTTCAAAGAAATTAATTCTCAATCA
        131 AATTTCCATAATCAAGCAACTAGCTAGAAATAGCCTTTCAAAGAAATCAATTCTCAATCA

                                             *                               
      11326 AATTCACCTGAGGGTTTACTTAACTCAAATGATTCCCACAAACATTAAAAACAAGATAGCAAAGA
          1 AATTCACCTGAGGGTTTACTTAACTCAAATGATACCCACAAACATTAAAAACAAGATAGCAAAGA

                                                                             
      11391 GAGAATTTTTCTTTTAAAAACATATCATAGCATAGAACAAACCTAGTCAAAAATCAATTTTGTTC
         66 GAGAATTTTTCTTTTAAAAACATATCATAGCATAGAACAAACCTAGTCAAAAATCAATTTTGTTC

                                                                        
      11456 AATTTCCATAATCAAGCAACTAGCTAGAAATAGCCTTTCAAAGAAATCAATTCTCAATCA
        131 AATTTCCATAATCAAGCAACTAGCTAGAAATAGCCTTTCAAAGAAATCAATTCTCAATCA

             
      11516 A
          1 A

      11517 TTCTATGCAA


Statistics
Matches: 188,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 190  188  1.00

ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28


Consensus pattern (190 bp):   
AATTCACCTGAGGGTTTACTTAACTCAAATGATACCCACAAACATTAAAAACAAGATAGCAAAGA
GAGAATTTTTCTTTTAAAAACATATCATAGCATAGAACAAACCTAGTCAAAAATCAATTTTGTTC
AATTTCCATAATCAAGCAACTAGCTAGAAATAGCCTTTCAAAGAAATCAATTCTCAATCA

Found at i:12674 original size:30 final size:29

Alignment explanation


    Indices: 12635--12704  Score: 79
    Period size: 30  Copynumber: 2.3  Consensus size: 29

      12625 TTAGACAAAC

                *                      *   
      12635 ATTCTATCAATCAATCAACAA-ATCATTGCA
          1 ATTCAATCAATCAAT-AACAAGAT-ATGGCA

                            *            
      12665 ATTCAATCAATCAATAGCAAGATATGGCA
          1 ATTCAATCAATCAATAACAAGATATGGCA

                       
      12694 ATTCAAATCAA
          1 ATTC-AATCAA

      12705 CAACTGAAAG


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  29   13  0.37
  30   22  0.63

ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27


Consensus pattern (29 bp):   
ATTCAATCAATCAATAACAAGATATGGCA

Found at i:12715 original size:29 final size:29

Alignment explanation


    Indices: 12662--12717  Score: 71
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      12652 ACAAATCATT

                                *        
      12662 GCAATTCAATCAATCAATAGCAAGATATG
          1 GCAATTCAATCAATCAATAGAAAGATATG

                                         
      12691 GCAATTCAAATCAA-CAACT-GAAAGATA
          1 GCAATTC-AATCAATCAA-TAGAAAGATA

      12718 GAATAAGCAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  29   17  0.71
  30    7  0.29

ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21


Consensus pattern (29 bp):   
GCAATTCAATCAATCAATAGAAAGATATG
Done.