Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018956.1 Corchorus olitorius cultivar O-4 contig18989, 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: 16759
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:4919 original size:6 final size:6

Alignment explanation


    Indices: 4908--4938  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       4898 GAGTCCAAGA

                                                
       4908 ATAATT ATAATT ATAATT ATAATT ATAATT A
          1 ATAATT ATAATT ATAATT ATAATT ATAATT A

       4939 GTAAAAAATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (6 bp):   
ATAATT

Found at i:8203 original size:31 final size:31

Alignment explanation


    Indices: 8171--8323  Score: 157
    Period size: 31  Copynumber: 5.0  Consensus size: 31

       8161 GTGTCTGACA

                                    *     *
       8171 TGGCATGCCACGTGTACCAAAAAGCGACACA
          1 TGGCATGCCACGTGTACCAAAAAGTGACACG

                  *    *    *              
       8202 TGGCATACCACATGTATCAAAAAGTGACACG
          1 TGGCATGCCACGTGTACCAAAAAGTGACACG

              *  **   *                     
       8233 TGTCACACCATGTGTACCAAAAAAGTGACACG
          1 TGGCATGCCACGTGTACC-AAAAAGTGACACG

              *  *    *                    
       8265 TGTCACGCCATGTGTACCAAAAAGTGACACG
          1 TGGCATGCCACGTGTACCAAAAAGTGACACG

                     *    *               
       8296 TGGCATGCCTCGTGCA-CAAAAAG-GACAC
          1 TGGCATGCCACGTGTACCAAAAAGTGACAC

       8324 TGACACGTGT


Statistics
Matches: 105,  Mismatches: 16, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  29    5  0.05
  30    7  0.07
  31   63  0.60
  32   30  0.29

ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17


Consensus pattern (31 bp):   
TGGCATGCCACGTGTACCAAAAAGTGACACG

Found at i:15397 original size:36 final size:36

Alignment explanation


    Indices: 15350--15419  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      15340 TTCAATAACC

                         *      *               
      15350 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
      15386 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

      15420 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.