Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000636.1 Corchorus olitorius cultivar O-4 contig00636, 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: 2883
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36


Found at i:80 original size:22 final size:22

Alignment explanation


    Indices: 55--96  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

         45 AAAGCTTCAA

                 *         *      
         55 TGATTGTTCTAAAAAGTATAAG
          1 TGATTATTCTAAAAACTATAAG

                    *           
         77 TGATTATTTTAAAAACTATA
          1 TGATTATTCTAAAAACTATA

         97 TTATTATCTT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40


Consensus pattern (22 bp):   
TGATTATTCTAAAAACTATAAG

Found at i:673 original size:31 final size:31

Alignment explanation


    Indices: 635--733  Score: 114
    Period size: 31  Copynumber: 3.3  Consensus size: 31

        625 AAGTACCTAA

                     *                     
        635 TTAGTCCCTGTACTATTGAAAAAGGATCAAT
          1 TTAGTCCCTCTACTATTGAAAAAGGATCAAT

                      * *        ***       
        666 TTAGTCCCTCCATTA-TGAAATCTG-TCAAT
          1 TTAGTCCCTCTACTATTGAAAAAGGATCAAT

                                            
        695 TTAGTCCCTCTACTATTG-AAAAGAGATCAAT
          1 TTAGTCCCTCTACTATTGAAAAAG-GATCAAT

                    
        726 TTAGTCCC
          1 TTAGTCCC

        734 ACCGTGAAAC


Statistics
Matches: 54,  Mismatches: 11, Indels: 6
        0.76            0.15        0.08

Matches are distributed among these distances:
  29   20  0.37
  30    9  0.17
  31   25  0.46

ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34


Consensus pattern (31 bp):   
TTAGTCCCTCTACTATTGAAAAAGGATCAAT

Found at i:2255 original size:31 final size:30

Alignment explanation


    Indices: 2220--2320  Score: 107
    Period size: 31  Copynumber: 3.3  Consensus size: 30

       2210 TTGTTTCACG

                                           
       2220 GAGGGACTAAATTGATCTCTTTTCAATAGTA
          1 GAGGGACTAAATTGATC-CTTTTCAATAGTA

                      *       **        * *
       2251 GAGGGACTAAGTTGA-CAGATTTC-ATAATG
          1 GAGGGACTAAATTGATC-CTTTTCAATAGTA

                                           
       2280 GAGGGACTAAATTGATCCTTTTTCAATAGTA
          1 GAGGGACTAAATTGATCC-TTTTCAATAGTA

            *         
       2311 CAGGGACTAA
          1 GAGGGACTAA

       2321 TTAGGTACTT


Statistics
Matches: 55,  Mismatches: 12, Indels: 6
        0.75            0.16        0.08

Matches are distributed among these distances:
  29   18  0.33
  30   10  0.18
  31   27  0.49

ACGTcount: A:0.34, C:0.13, G:0.23, T:0.31


Consensus pattern (30 bp):   
GAGGGACTAAATTGATCCTTTTCAATAGTA
Done.