Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012261.1 Corchorus olitorius cultivar O-4 contig12294, 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: 7528
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28


Found at i:5858 original size:134 final size:134

Alignment explanation


    Indices: 5618--5876  Score: 455
    Period size: 134  Copynumber: 1.9  Consensus size: 134

       5608 CTGCTTCAGC

                       *                            *              *         
       5618 AGCCTTTTGCTGCCGCGACAGGGGAGCCTTCCGCAAGCAGCGCAAGGCTGCTCCGTGAGGCTACC
          1 AGCCTTTTGCTACCGCGACAGGGGAGCCTTCCGCAAGCAGAGCAAGGCTGCTCCGCGAGGCTACC

                     *        *                                              
       5683 TGCTGCAACTGCATAATAGCAGCAAGCAAGGCAGCCTGCTGCCGCCACAGCGCACCAGGCAGCAG
         66 TGCTGCAACCGCATAATAACAGCAAGCAAGGCAGCCTGCTGCCGCCACAGCGCACCAGGCAGCAG

                
       5748 CAGT
        131 CAGT

                                                                             
       5752 AGCCTTTTGCTACCGCGACAGGGGAGCCTTCCGCAAGCAGAGCAAGGCTGCTCCGCGAGGCTACC
          1 AGCCTTTTGCTACCGCGACAGGGGAGCCTTCCGCAAGCAGAGCAAGGCTGCTCCGCGAGGCTACC

                  *                        *                            
       5817 TGCTGCTACCGCATAATAACAGCAAGCAAGGTAGCCTGCTGCCGCCACAGCGCACCAGGC
         66 TGCTGCAACCGCATAATAACAGCAAGCAAGGCAGCCTGCTGCCGCCACAGCGCACCAGGC

       5877 CGCGCAAAGC


Statistics
Matches: 118,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 134  118  1.00

ACGTcount: A:0.23, C:0.34, G:0.29, T:0.14


Consensus pattern (134 bp):   
AGCCTTTTGCTACCGCGACAGGGGAGCCTTCCGCAAGCAGAGCAAGGCTGCTCCGCGAGGCTACC
TGCTGCAACCGCATAATAACAGCAAGCAAGGCAGCCTGCTGCCGCCACAGCGCACCAGGCAGCAG
CAGT

Found at i:6311 original size:22 final size:22

Alignment explanation


    Indices: 6239--6355  Score: 80
    Period size: 22  Copynumber: 5.3  Consensus size: 22

       6229 AAGAAGCAAG

                         *         
       6239 GTCGA-TAAGGAGAAGCAAAGTA
          1 GTCGACTAAGGAGCAG-AAAGTA

                 *                   
       6261 GTCGAATAAGAAAGAGCA-AAAGTA
          1 GTCGACTAAG---GAGCAGAAAGTA

                               *  
       6285 GTCGACTAAGGAGCAGAAAATA
          1 GTCGACTAAGGAGCAGAAAGTA

                         *      *  
       6307 GTCGACTAA-GAGAAGTAAATTA
          1 GTCGACTAAGGAGCAG-AAAGTA

              *          *  *    *
       6329 -TGGACTAAGGAGAAGCAAGTC
          1 GTCGACTAAGGAGCAGAAAGTA

                  
       6350 GTCGAC
          1 GTCGAC

       6356 AATAAGCCAA


Statistics
Matches: 77,  Mismatches: 10, Indels: 16
        0.75            0.10        0.16

Matches are distributed among these distances:
  21   20  0.26
  22   34  0.44
  23    4  0.05
  24   15  0.19
  26    4  0.05

ACGTcount: A:0.44, C:0.12, G:0.28, T:0.15


Consensus pattern (22 bp):   
GTCGACTAAGGAGCAGAAAGTA

Found at i:6786 original size:16 final size:15

Alignment explanation


    Indices: 6747--6789  Score: 77
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       6737 AACAGAGGTT

                           
       6747 AACAGAAAACAATTA
          1 AACAGAAAACAATTA

                           
       6762 AACAGAAAACAATTA
          1 AACAGAAAACAATTA

                         
       6777 AACTAGAAAACAA
          1 AAC-AGAAAACAA

       6790 AACAAAGTAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   18  0.67
  16    9  0.33

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
AACAGAAAACAATTA
Done.