Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021282.1 Corchorus olitorius cultivar O-4 contig21315, 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: 4770
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:20 original size:2 final size:2

Alignment explanation


    Indices: 15--46  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

          5 CACACACACA

                                                           
         15 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

         47 TTACACAAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
CT

Found at i:698 original size:121 final size:122

Alignment explanation


    Indices: 527--749  Score: 304
    Period size: 121  Copynumber: 1.8  Consensus size: 122

        517 TGTGGGACTG

                *     *            *                                      *  
        527 CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTCCGCTGCTGGAAAGTGCTGCT-CACTTTAA
          1 CCTTACTGACATGTCACTCTGCCAAGGAGGAGGTTCCGCTGCTGGAAAGTGCTGCTGCACTTCAA

                    *                                                
        591 CCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCCGGTGCAA
         66 CCAAAGTCATATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCCGGTGCAA

                           *                    * *      *                   
        648 CCTTACTGACATGTCGCTCTGCCAAGGAGGAGGTTCTGTTGCTGGGAAGTGCTGCTGGGCACTTC
          1 CCTTACTGACATGTCACTCTGCCAAGGAGGAGGTTCCGCTGCTGGAAAGTGCTGCT--GCACTTC

              * *         *        *             
        713 AATCGAAGTCATATTCTTCATCAGCAAAGGAGGTCAG
         64 AACCAAAGTCATATCCTTCATCAACAAAGGAGGTCAG

        750 TAGCGTGGTT


Statistics
Matches: 86,  Mismatches: 13, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
 121   49  0.57
 124   37  0.43

ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25


Consensus pattern (122 bp):   
CCTTACTGACATGTCACTCTGCCAAGGAGGAGGTTCCGCTGCTGGAAAGTGCTGCTGCACTTCAA
CCAAAGTCATATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCCGGTGCAA

Found at i:837 original size:21 final size:20

Alignment explanation


    Indices: 788--841  Score: 81
    Period size: 20  Copynumber: 2.6  Consensus size: 20

        778 TAAGGTGTCA

                 *              
        788 TTCTGTCGAGAAGGAAGCAT
          1 TTCTGCCGAGAAGGAAGCAT

                *                
        808 TTCTACCGAGAAGGAAGCATT
          1 TTCTGCCGAGAAGGAAGCA-T

                         
        829 TTCTGCCGAGAAG
          1 TTCTGCCGAGAAG

        842 TGCTGCTGGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  20   17  0.57
  21   13  0.43

ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24


Consensus pattern (20 bp):   
TTCTGCCGAGAAGGAAGCAT

Found at i:2738 original size:31 final size:31

Alignment explanation


    Indices: 2703--2774  Score: 85
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2693 TAAATTATTG

                            *               
       2703 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
          1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA

                     *           *          
       2734 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
          1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA

                      
       2765 CAAATTAAAA
          1 CAAATTAAAA

       2775 GCTGATAGAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  30    7  0.21
  31   24  0.71
  32    3  0.09

ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25


Consensus pattern (31 bp):   
CAAATTAAAAAAATGAAAGCATTAAATTAAA

Found at i:4606 original size:58 final size:57

Alignment explanation


    Indices: 4512--4620  Score: 164
    Period size: 58  Copynumber: 1.9  Consensus size: 57

       4502 ATTAATCAAA

                                                         *           
       4512 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAACGTTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAACGTTTTAGGACCAAGACT

                *            *            *       *             
       4569 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACC
          1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAACGTTTTAGGACC

       4621 GAGGCATGAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  57   13  0.28
  58   33  0.72

ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Consensus pattern (57 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAACGTTTTAGGACCAAGACT
Done.