Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022966.1 Corchorus olitorius cultivar O-4 contig22999, 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: 18851
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:16138 original size:49 final size:49

Alignment explanation


    Indices: 16060--16189  Score: 167
    Period size: 49  Copynumber: 2.7  Consensus size: 49

      16050 TCAAAGCAAT

                                                             
      16060 CTTTTACGTTTCCT-GCA-CTTTTTCTCAATTTTTACAACAAAATTGAA
          1 CTTTTACGTTTCCTCGCACCTTTTTCTCAATTTTTACAACAAAATTGAA

                  *                            *  *          
      16107 CTTTTAAGTTTCCTCGCACCTTTTTCTCAATTTTTGCATCAAAATTGAA
          1 CTTTTACGTTTCCTCGCACCTTTTTCTCAATTTTTACAACAAAATTGAA

                    *            *     *       
      16156 -TATTTACTTTTCCTCGCATCGTTTTTATCAATTT
          1 CT-TTTACGTTTCCTCGCA-CCTTTTTCTCAATTT

      16190 CTGGACAAAA


Statistics
Matches: 72,  Mismatches: 7, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  47   13  0.18
  48    4  0.06
  49   42  0.58
  50   13  0.18

ACGTcount: A:0.24, C:0.22, G:0.07, T:0.48


Consensus pattern (49 bp):   
CTTTTACGTTTCCTCGCACCTTTTTCTCAATTTTTACAACAAAATTGAA

Found at i:16539 original size:17 final size:17

Alignment explanation


    Indices: 16517--16551  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      16507 GCATGAAAAG

                             
      16517 ACAAGAAAATATAGAGA
          1 ACAAGAAAATATAGAGA

                  *     *    
      16534 ACAAGAGAATATTGAGA
          1 ACAAGAAAATATAGAGA

             
      16551 A
          1 A

      16552 TAAAAAAAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.60, C:0.06, G:0.20, T:0.14


Consensus pattern (17 bp):   
ACAAGAAAATATAGAGA

Found at i:18520 original size:2 final size:2

Alignment explanation


    Indices: 18515--18540  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      18505 TTATATTTGT

                                                  
      18515 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      18541 AATAAAAAGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:18693 original size:14 final size:15

Alignment explanation


    Indices: 18661--18694  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      18651 AAAACTCTAT

                           
      18661 TTTTATTTATAATTA
          1 TTTTATTTATAATTA

                    *      
      18676 TTTTATTTTTAA-TA
          1 TTTTATTTATAATTA

                 
      18690 TTTTA
          1 TTTTA

      18695 CTATTTTTTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14    7  0.39
  15   11  0.61

ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71


Consensus pattern (15 bp):   
TTTTATTTATAATTA
Done.