Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021104.1 Corchorus olitorius cultivar O-4 contig21137, 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: 8425
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:221 original size:39 final size:40

Alignment explanation


    Indices: 167--247  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        157 ATACCTAAGA

                                             *      
        167 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        206 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        246 AT
          1 AT

        248 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:4197 original size:3 final size:3

Alignment explanation


    Indices: 4189--4220  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       4179 GCCATAATAC

                                                      
       4189 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       4221 ATACTAAACT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:5134 original size:91 final size:91

Alignment explanation


    Indices: 4960--5143  Score: 271
    Period size: 91  Copynumber: 2.0  Consensus size: 91

       4950 GATGCTACAA

                           * *      *                   *                    
       4960 GTACTACTACACCCCTATTACTTAGGCTACTACCAATATCCAACGACTAGTGTGTCATTTTTAAA
          1 GTACTACTACACCCCCACTACTTAAGCTACTACCAATATCCAACAACTAGTGTGTCATTTTTAAA

                     *                
       5025 TTGGTAATATACCCCTAGAAGTGGGG
         66 TTGGTAATACACCCCTAGAAGTGGGG

                                                                             
       5051 GTACTACTACACCCCCCACTACTTAAG-TACTACCAATATCCAACAACTAGTGTGTCATTTTTAA
          1 GTACTACTACA-CCCCCACTACTTAAGCTACTACCAATATCCAACAACTAGTGTGTCATTTTTAA

                   *    ***            
       5115 ATTGGTAGTACATTTCTAGAAGTGGGG
         65 ATTGGTAATACACCCCTAGAAGTGGGG

              
       5142 GT
          1 GT

       5144 TTTAGTAGTA


Statistics
Matches: 83,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  91   71  0.86
  92   12  0.14

ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Consensus pattern (91 bp):   
GTACTACTACACCCCCACTACTTAAGCTACTACCAATATCCAACAACTAGTGTGTCATTTTTAAA
TTGGTAATACACCCCTAGAAGTGGGG

Found at i:7926 original size:2 final size:2

Alignment explanation


    Indices: 7919--7951  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       7909 CCAATCAATC

                                                            
       7919 AT AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT

       7952 GATAACAATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.