Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000224.1 Corchorus olitorius cultivar O-4 contig00224, 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, 694

Length: 1158
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33


Found at i:191 original size:33 final size:31

Alignment explanation


    Indices: 118--222  Score: 120
    Period size: 33  Copynumber: 3.2  Consensus size: 31

        108 GCTATGATCA

                                       ** * 
        118 ACCAAAACAGATTTGTTTACATCACAATTAGC
          1 ACCAAAACAGATTTGTTT-CATCACAAACAAC

                                             
        150 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
        183 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   
        216 ACTCAAA
          1 AC-CAAA

        223 TTAGGTTTAG


Statistics
Matches: 64,  Mismatches: 4, Indels: 9
        0.83            0.05        0.12

Matches are distributed among these distances:
  32    7  0.11
  33   48  0.75
  34    9  0.14

ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Found at i:232 original size:33 final size:33

Alignment explanation


    Indices: 154--265  Score: 111
    Period size: 33  Copynumber: 3.4  Consensus size: 33

        144 ATTAGCATCC

                           *                  
        154 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTATCATCACAAACAACACCT

                          *                  
        187 AAAACAGATTTAGTGTCATCACAAACAACA-CT
          1 AAAACAGATTTAGTATCATCACAAACAACACCT

                **  *        *   *         *  
        219 CAAATTAGGTTTAGTATTATCGCAAACAACATCT
          1 -AAAACAGATTTAGTATCATCACAAACAACACCT

                  *      
        253 AAAACAAATTTAG
          1 AAAACAGATTTAG

        266 AATTACTCTT


Statistics
Matches: 65,  Mismatches: 11, Indels: 6
        0.79            0.13        0.07

Matches are distributed among these distances:
  32    6  0.09
  33   57  0.88
  34    2  0.03

ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCACAAACAACACCT
Done.