Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018742.1 Corchorus olitorius cultivar O-4 contig18775, 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: 28526
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31


Found at i:19088 original size:110 final size:110

Alignment explanation


    Indices: 18906--19128  Score: 428
    Period size: 110  Copynumber: 2.0  Consensus size: 110

      18896 AAATTCAAGC

                                     *                                       
      18906 CCAATAATACATAATACCATAACTGTGAAATGAAGTTTACCCCACCAACAATAATCACCCAATAA
          1 CCAATAATACATAATACCATAACTGGGAAATGAAGTTTACCCCACCAACAATAATCACCCAATAA

                                                         
      18971 AAGAAACTTGAACTATACTTTGCTGCAAGATCCCAAAATCACCAT
         66 AAGAAACTTGAACTATACTTTGCTGCAAGATCCCAAAATCACCAT

                                                                 *           
      19016 CCAATAATACATAATACCATAACTGGGAAATGAAGTTTACCCCACCAACAATACTCACCCAATAA
          1 CCAATAATACATAATACCATAACTGGGAAATGAAGTTTACCCCACCAACAATAATCACCCAATAA

                                                         
      19081 AAGAAACTTGAACTATACTTTGCTGCAAGATCCCAAAATCACCAT
         66 AAGAAACTTGAACTATACTTTGCTGCAAGATCCCAAAATCACCAT

               
      19126 CCA
          1 CCA

      19129 GAACCACCTT


Statistics
Matches: 111,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 110  111  1.00

ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22


Consensus pattern (110 bp):   
CCAATAATACATAATACCATAACTGGGAAATGAAGTTTACCCCACCAACAATAATCACCCAATAA
AAGAAACTTGAACTATACTTTGCTGCAAGATCCCAAAATCACCAT

Found at i:25939 original size:26 final size:26

Alignment explanation


    Indices: 25896--25950  Score: 85
    Period size: 25  Copynumber: 2.2  Consensus size: 26

      25886 AAAGCTTTTT

                       *              
      25896 TTTTAATACTTGATAAAAAAATTTAA
          1 TTTTAATACTTAATAAAAAAATTTAA

                                     *
      25922 TTTT-ATACTTAATAAAAAAATTTAT
          1 TTTTAATACTTAATAAAAAAATTTAA

                
      25947 TTTT
          1 TTTT

      25951 TTTATATATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  25   23  0.85
  26    4  0.15

ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49


Consensus pattern (26 bp):   
TTTTAATACTTAATAAAAAAATTTAA

Found at i:26997 original size:22 final size:22

Alignment explanation


    Indices: 26971--27013  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      26961 TTTATACCAA

                                   
      26971 TCTTCTTATTCAAAG-TTACTAT
          1 TCTTCTTATTC-AAGTTTACTAT

                                 
      26993 TCTTCTTATTCAAGTTTACTA
          1 TCTTCTTATTCAAGTTTACTA

      27014 AAAAAAACCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  21    3  0.15
  22   17  0.85

ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51


Consensus pattern (22 bp):   
TCTTCTTATTCAAGTTTACTAT

Found at i:27139 original size:20 final size:19

Alignment explanation


    Indices: 27111--27156  Score: 56
    Period size: 20  Copynumber: 2.4  Consensus size: 19

      27101 TTATATAAGA

                *               
      27111 TTATTAAAAAACTGTAGAGG
          1 TTATCAAAAAACTG-AGAGG

                       *     * 
      27131 TTATCAAAAAATTGAGATG
          1 TTATCAAAAAACTGAGAGG

                   
      27150 TTATCAA
          1 TTATCAA

      27157 CAAATTTAAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  19   11  0.48
  20   12  0.52

ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33


Consensus pattern (19 bp):   
TTATCAAAAAACTGAGAGG

Found at i:27152 original size:19 final size:20

Alignment explanation


    Indices: 27111--27162  Score: 61
    Period size: 19  Copynumber: 2.6  Consensus size: 20

      27101 TTATATAAGA

                *      *        
      27111 TTATTAAAAAACTGTAGAGG
          1 TTATCAAAAAATTGTAGAGG

                              * 
      27131 TTATCAAAAAATTG-AGATG
          1 TTATCAAAAAATTGTAGAGG

                   *     
      27150 TTATCAACAAATT
          1 TTATCAAAAAATT

      27163 TAATAATGAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  19   16  0.57
  20   12  0.43

ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33


Consensus pattern (20 bp):   
TTATCAAAAAATTGTAGAGG
Done.