Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015227.1 Corchorus olitorius cultivar O-4 contig15260, 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: 36334
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:13354 original size:72 final size:72

Alignment explanation


    Indices: 13267--13405  Score: 251
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      13257 AAAGACAAGC

                                                                      *      
      13267 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
          1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATCGGATAT

                   
      13332 CCTGCTG
         66 CCTGCTG

                     *                                 *                     
      13339 CAAGGTGTGGACATTGTCAAAAGATGGGGCACACGAAAGATCAGTGCTATGAGATCATCGGATAT
          1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATCGGATAT

              
      13404 CC
         66 CC

      13406 CGCAGGTTGG


Statistics
Matches: 64,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  72   64  1.00

ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22


Consensus pattern (72 bp):   
CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATCGGATAT
CCTGCTG

Found at i:23637 original size:3 final size:3

Alignment explanation


    Indices: 23629--23655  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      23619 TAATTAGCTC

                                               
      23629 ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT

      23656 GGTTGCGAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:28191 original size:20 final size:20

Alignment explanation


    Indices: 28166--28205  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      28156 TTAGGTTCAA

                                
      28166 CTCTCACGGAATATGAGTTT
          1 CTCTCACGGAATATGAGTTT

                        *       
      28186 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATATGAGTTT

      28206 GTTTGTAATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATATGAGTTT
Done.