Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018718.1 Corchorus olitorius cultivar O-4 contig18751, 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: 7467
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34


Found at i:320 original size:36 final size:36

Alignment explanation


    Indices: 268--374  Score: 124
    Period size: 36  Copynumber: 3.0  Consensus size: 36

        258 CCAATTATGT

                       *           *            
        268 ATTAGGCGACTTAGGCCAGCGGCCTTATAACCAAAC
          1 ATTAGGCGACTAAGGCCAGCGGCATTATAACCAAAC

               *                *  *     *    **
        304 ATTGGGCGACTAAGGCCAGCAGCGTTATAGCCAAGT
          1 ATTAGGCGACTAAGGCCAGCGGCATTATAACCAAAC

                      *                *       
        340 ATTAGGCGACCAAGGCCAGCGGCATTACAACCAAA
          1 ATTAGGCGACTAAGGCCAGCGGCATTATAACCAAA

        375 GATAAGCAAT


Statistics
Matches: 57,  Mismatches: 14, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  36   57  1.00

ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17


Consensus pattern (36 bp):   
ATTAGGCGACTAAGGCCAGCGGCATTATAACCAAAC

Found at i:2465 original size:16 final size:16

Alignment explanation


    Indices: 2444--2486  Score: 61
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       2434 TGTGGCTTTG

                             
       2444 TAAGTGAGTATCT-CAC
          1 TAAGTGAGTAT-TACAC

                            
       2460 TAAGTGAGTATTACAC
          1 TAAGTGAGTATTACAC

            *          
       2476 CAAGTGAGTAT
          1 TAAGTGAGTAT

       2487 GGTACCAAGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  15    1  0.04
  16   24  0.96

ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30


Consensus pattern (16 bp):   
TAAGTGAGTATTACAC

Found at i:4895 original size:21 final size:21

Alignment explanation


    Indices: 4869--4925  Score: 105
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       4859 CTAAGGAAGA

                                 
       4869 AGTTTCAAGCTCATCAGAGTT
          1 AGTTTCAAGCTCATCAGAGTT

                                 
       4890 AGTTTCAAGCTCATCAGAGTT
          1 AGTTTCAAGCTCATCAGAGTT

            *              
       4911 GGTTTCAAGCTCATC
          1 AGTTTCAAGCTCATC

       4926 GAAGTTGCCT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   35  1.00

ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33


Consensus pattern (21 bp):   
AGTTTCAAGCTCATCAGAGTT

Done.