Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017318.1 Corchorus olitorius cultivar O-4 contig17351, 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: 20938
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:5301 original size:14 final size:14

Alignment explanation


    Indices: 5282--5310  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5272 GAAAACAAAT

                          
       5282 AAAGTTAGTTCATA
          1 AAAGTTAGTTCATA

                          
       5296 AAAGTTAGTTCATA
          1 AAAGTTAGTTCATA

             
       5310 A
          1 A

       5311 TAATACATCA


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34


Consensus pattern (14 bp):   
AAAGTTAGTTCATA

Found at i:12830 original size:22 final size:21

Alignment explanation


    Indices: 12810--12851  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 21

      12800 TCTTCTTTGA

                                 
      12810 GTTTTT-GAAAAAAAAAATTT
          1 GTTTTTCGAAAAAAAAAATTT

                                  
      12830 GTTTTTGCGAAAAAAAAAATTT
          1 GTTTTT-CGAAAAAAAAAATTT

      12852 CTTGTTTTTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20    6  0.30
  22   14  0.70

ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38


Consensus pattern (21 bp):   
GTTTTTCGAAAAAAAAAATTT

Found at i:20796 original size:3 final size:3

Alignment explanation


    Indices: 20788--20873  Score: 109
    Period size: 3  Copynumber: 28.0  Consensus size: 3

      20778 GTAAAGCAAG

                        *   *                                            
      20788 AAT AAT AAT GAT GAT AAT ATAT ATAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT

                            *               *           *      
      20835 AAT AAT AAT AAT GAT AAT AAT AAT GAT AAT AAT GAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

      20874 GGAAGAAAAG


Statistics
Matches: 74,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
   3   67  0.91
   4    7  0.09

ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35


Consensus pattern (3 bp):   
AAT

Done.