Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023378.1 Corchorus olitorius cultivar O-4 contig23411, 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: 14535
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31


Found at i:8220 original size:22 final size:22

Alignment explanation


    Indices: 8178--8220  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8168 TTTTCCGCAA

                      *     *     
       8178 CAAGTCCTGGGCAGGAGTTGTC
          1 CAAGTCCTGGACAGGACTTGTC

                         *       
       8200 CAAGTCCTGGACATGACTTGT
          1 CAAGTCCTGGACAGGACTTGT

       8221 TCTGAATTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26


Consensus pattern (22 bp):   
CAAGTCCTGGACAGGACTTGTC

Found at i:8276 original size:21 final size:21

Alignment explanation


    Indices: 8250--8291  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8240 TTCAACAGAC

                                 
       8250 CAAGTCCTGGGCAGAAGTTGT
          1 CAAGTCCTGGGCAGAAGTTGT

                          *      
       8271 CAAGTCCTGGGCAGGAGTTGT
          1 CAAGTCCTGGGCAGAAGTTGT

       8292 TCTGAATTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24


Consensus pattern (21 bp):   
CAAGTCCTGGGCAGAAGTTGT

Found at i:8296 original size:71 final size:71

Alignment explanation


    Indices: 8178--8362  Score: 307
    Period size: 71  Copynumber: 2.6  Consensus size: 71

       8168 TTTTCCGCAA

                                            *  *                        *    
       8178 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACATGACTTGTTCTGAATTTTCTTCCGTTTTTC
          1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC

                   
       8243 AACAGAC
         65 AACAGAC

                          *                      *                           
       8250 CAAGTCCTGGGCAGAAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCA
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA

                  
       8315 ACAGAC
         66 ACAGAC

              *                                       
       8321 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT

       8363 CCTGTTTTTA


Statistics
Matches: 105,  Mismatches: 8, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  71   85  0.81
  72   20  0.19

ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30


Consensus pattern (71 bp):   
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC

Found at i:8350 original size:21 final size:21

Alignment explanation


    Indices: 8324--8363  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8314 AACAGACCAG

                         *       
       8324 GTCCTGGGCAGGAGTTGTCAA
          1 GTCCTGGGCAGGACTTGTCAA

                               
       8345 GTCCTGGGCAGGACTTGTC
          1 GTCCTGGGCAGGACTTGTC

       8364 CTGTTTTTAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25


Consensus pattern (21 bp):   
GTCCTGGGCAGGACTTGTCAA

Found at i:12611 original size:21 final size:21

Alignment explanation


    Indices: 12586--12626  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      12576 TTAGAAACCC

                                  
      12586 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
      12607 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

      12627 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:13764 original size:21 final size:21

Alignment explanation


    Indices: 13734--13773  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      13724 AACAGACCAG

                         *       
      13734 GTCCTGGGCAGGAGTTGTCAA
          1 GTCCTGGGCAGGACTTGTCAA

                 *             
      13755 GTCCTTGGCAGGACTTGTC
          1 GTCCTGGGCAGGACTTGTC

      13774 CTGTTTTTAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.15, C:0.23, G:0.35, T:0.28


Consensus pattern (21 bp):   
GTCCTGGGCAGGACTTGTCAA
Done.