Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000564.1 Corchorus olitorius cultivar O-4 contig00564, 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, 693

Length: 1156
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:218 original size:67 final size:68

Alignment explanation


    Indices: 91--222  Score: 232
    Period size: 67  Copynumber: 2.0  Consensus size: 68

         81 TAAGAGACTA

                                                                             
         91 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT
          1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT

               
        156 TAT
         66 TAT

                                                                *            
        159 TTAATCAAGTTACATCGATA-ATCTATATAAAATAGGGTTTTAATTTG-AACTCATTTTCCTATT
          1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGG-TTTAATTTGTAACCCATTTTCCTATT

             
        222 T
         65 T

        223 AAATTTAGGT


Statistics
Matches: 62,  Mismatches: 1, Indels: 3
        0.94            0.02        0.05

Matches are distributed among these distances:
  67   33  0.53
  68   29  0.47

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43


Consensus pattern (68 bp):   
TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT
TAT

Found at i:229 original size:68 final size:68

Alignment explanation


    Indices: 91--229  Score: 228
    Period size: 68  Copynumber: 2.0  Consensus size: 68

         81 TAAGAGACTA

                                                                             
         91 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT
          1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT

            *  
        156 TAT
         66 AAT

                                                                *            
        159 TTAATCAAGTTACATCGATA-ATCTATATAAAATAGGGTTTTAATTTG-AACTCATTTTCCTATT
          1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGG-TTTAATTTGTAACCCATTTTCCTATT

                 
        222 TAAAT
         65 T-AAT

               
        227 TTA
          1 TTA

        230 GGTTATTCAC


Statistics
Matches: 67,  Mismatches: 2, Indels: 4
        0.92            0.03        0.05

Matches are distributed among these distances:
  67   33  0.49
  68   34  0.51

ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43


Consensus pattern (68 bp):   
TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGTAACCCATTTTCCTATTT
AAT
Done.