Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009706.1 Corchorus olitorius cultivar O-4 contig09738, 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: 9260
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31


Found at i:3484 original size:33 final size:33

Alignment explanation


    Indices: 3445--3578  Score: 196
    Period size: 33  Copynumber: 4.1  Consensus size: 33

       3435 AACCAACTCG

                            *             *  
       3445 AAATGCAAAGCAAATCCTCCAATCCCCAATACA
          1 AAATGCAAAGCAAATCATCCAATCCCCAATCCA

             *              *                
       3478 ATATGCAAAGCAAATCGTCCAATCCCCAATCCA
          1 AAATGCAAAGCAAATCATCCAATCCCCAATCCA

                  *                          
       3511 AAATGCCAAGCAAATCATCCAATCCCCAATCCA
          1 AAATGCAAAGCAAATCATCCAATCCCCAATCCA

                  *             *     *      
       3544 AAATGCCAAGCAAATCATCCGATCCCAAATCCA
          1 AAATGCAAAGCAAATCATCCAATCCCCAATCCA

              
       3577 AA
          1 AA

       3579 TGAAAAAATA


Statistics
Matches: 93,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   93  1.00

ACGTcount: A:0.43, C:0.34, G:0.07, T:0.16


Consensus pattern (33 bp):   
AAATGCAAAGCAAATCATCCAATCCCCAATCCA

Found at i:3676 original size:124 final size:126

Alignment explanation


    Indices: 3512--3737  Score: 332
    Period size: 124  Copynumber: 1.8  Consensus size: 126

       3502 CCCAATCCAA

                            *                  *               *             
       3512 AATGCCAAGCAAATCATCCAATCCCCAATCCAAAATGCCAAGCAAATCATCCGATCCCAAATCCA
          1 AATGCCAAGCAAATCAGCCAATCCCCAATCCAAAACGCCAAGCAAATCATCAGATCCCAAATCCA

                       *          *                                      
       3577 AATG-AAAAAATAA-TAATTTGGTGTAGCAATAAGGAAGAGAGGAGAAAGAGAGAATCGAT
         66 AATGAAAAAAAAAATTAATTTGATGTAGCAATAAGGAAGAGAGGAGAAAGAGAGAATCGAT

                                                             *    *    *     
       3636 AATGCCAAGCAAATC-GCCAATTCCCCAATCCAAAACGCCAAGCAAATCGTCAGGTCCCCAATCC
          1 AATGCCAAGCAAATCAGCCAA-TCCCCAATCCAAAACGCCAAGCAAATCATCAGATCCCAAATCC

                                         **       
       3700 AAATGAAAAAAAAAATTAATTTGATGTAGGGATAAGGA
         65 AAATGAAAAAAAAAATTAATTTGATGTAGCAATAAGGA

       3738 TAAGGAAGAG


Statistics
Matches: 89,  Mismatches: 10, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
 123    4  0.04
 124   58  0.65
 125    8  0.09
 126   19  0.21

ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17


Consensus pattern (126 bp):   
AATGCCAAGCAAATCAGCCAATCCCCAATCCAAAACGCCAAGCAAATCATCAGATCCCAAATCCA
AATGAAAAAAAAAATTAATTTGATGTAGCAATAAGGAAGAGAGGAGAAAGAGAGAATCGAT

Found at i:3681 original size:33 final size:33

Alignment explanation


    Indices: 3639--3702  Score: 101
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       3629 AATCGATAAT

                             *               
       3639 GCCAAGCAAATCGCCAATTCCCCAATCCAAAAC
          1 GCCAAGCAAATCGCCAAGTCCCCAATCCAAAAC

                         *  *              
       3672 GCCAAGCAAATCGTCAGGTCCCCAATCCAAA
          1 GCCAAGCAAATCGCCAAGTCCCCAATCCAAA

       3703 TGAAAAAAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   28  1.00

ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12


Consensus pattern (33 bp):   
GCCAAGCAAATCGCCAAGTCCCCAATCCAAAAC

Found at i:9011 original size:30 final size:30

Alignment explanation


    Indices: 8975--9032  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       8965 ATGAAAGATA

                                           
       8975 AATTATTTTAAGAAG-CTAAAAAGAAAAATG
          1 AATTATTTTAAGAAGTC-AAAAAGAAAAATG

                        *               
       9005 AATTATTTTAAGGAGTCAAAAAGAAAAA
          1 AATTATTTTAAGAAGTCAAAAAGAAAAA

       9033 AGTTCAACGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  30   25  0.96
  31    1  0.04

ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26


Consensus pattern (30 bp):   
AATTATTTTAAGAAGTCAAAAAGAAAAATG
Done.