Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015191.1 Corchorus olitorius cultivar O-4 contig15224, 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: 41711
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:18566 original size:27 final size:28

Alignment explanation


    Indices: 18514--18569  Score: 105
    Period size: 27  Copynumber: 2.0  Consensus size: 28

      18504 ATTTGGCCCA

                                        
      18514 AATTATTTTATAGAATAATCTAATTAGT
          1 AATTATTTTATAGAATAATCTAATTAGT

                                        
      18542 AATTATTTTATAG-ATAATCTAATTAGT
          1 AATTATTTTATAGAATAATCTAATTAGT

             
      18569 A
          1 A

      18570 CCATTTTATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  27   15  0.54
  28   13  0.46

ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46


Consensus pattern (28 bp):   
AATTATTTTATAGAATAATCTAATTAGT

Found at i:28245 original size:9 final size:9

Alignment explanation


    Indices: 28199--28242  Score: 52
    Period size: 9  Copynumber: 4.9  Consensus size: 9

      28189 TCAATCATTG

                     
      28199 CTCTGTTTC
          1 CTCTGTTTC

                     
      28208 CTCTGTTTC
          1 CTCTGTTTC

             *   *   
      28217 CCCTGATTC
          1 CTCTGTTTC

             *      *
      28226 CCCTGTTTT
          1 CTCTGTTTC

                    
      28235 CTCTGTTT
          1 CTCTGTTT

      28243 TCTTGGAGAA


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   9   30  1.00

ACGTcount: A:0.02, C:0.34, G:0.11, T:0.52


Consensus pattern (9 bp):   
CTCTGTTTC

Found at i:34389 original size:12 final size:12

Alignment explanation


    Indices: 34372--34397  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      34362 GAATTAGTGA

                        
      34372 TACTAGAGATTT
          1 TACTAGAGATTT

                        
      34384 TACTAGAGATTT
          1 TACTAGAGATTT

              
      34396 TA
          1 TA

      34398 ATACCACAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42


Consensus pattern (12 bp):   
TACTAGAGATTT

Found at i:41433 original size:109 final size:110

Alignment explanation


    Indices: 41242--41454  Score: 322
    Period size: 109  Copynumber: 1.9  Consensus size: 110

      41232 TACCCTCTAG

                                             *                               
      41242 ACTTTAATTGTGTCACTTTCCTCTTTAAATTTGGAAAATCAAGACAATACACCTCTTCACGTTAC
          1 ACTTTAATTGTGTCACTTTCCTCTTTAAATTTGAAAAATCAAGACAATACACCTCTTCACGTTAC

            *                              *             
      41307 TAATTCAGTTAAGTCCCA-CATATTTGCTAATGACATGAGTTTAA
         66 CAATTCAGTTAAGTCCCACCATATTTGCTAAAGACATGAGTTTAA

                                      *                        *     *       
      41351 ACTTTAATTGTGTCACTTTCCTCTTTGAATTTGAAAAATCAAGACAATACATCTCTTTACGTTAC
          1 ACTTTAATTGTGTCACTTTCCTCTTTAAATTTGAAAAATCAAGACAATACACCTCTTCACGTTAC

             **                         *           
      41416 CGTTTCCA-TTAAGTCCCACCATATTTGTTAAAGACATGA
         66 CAATT-CAGTTAAGTCCCACCATATTTGCTAAAGACATGA

      41455 ATGATGATGT


Statistics
Matches: 93,  Mismatches: 9, Indels: 3
        0.89            0.09        0.03

Matches are distributed among these distances:
 109   73  0.78
 110   20  0.22

ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37


Consensus pattern (110 bp):   
ACTTTAATTGTGTCACTTTCCTCTTTAAATTTGAAAAATCAAGACAATACACCTCTTCACGTTAC
CAATTCAGTTAAGTCCCACCATATTTGCTAAAGACATGAGTTTAA
Done.