Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012865.1 Corchorus olitorius cultivar O-4 contig12898, 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: 18672
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:1829 original size:19 final size:18

Alignment explanation


    Indices: 1802--1837  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1792 GTTGAAGAAA

                              
       1802 AAAATGAAAAAAGAAAAG
          1 AAAATGAAAAAAGAAAAG

                        *     
       1820 AAAATGGAAAAATGAAAA
          1 AAAAT-GAAAAAAGAAAA

       1838 AATGGAAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08


Consensus pattern (18 bp):   
AAAATGAAAAAAGAAAAG

Found at i:2783 original size:15 final size:16

Alignment explanation


    Indices: 2763--2811  Score: 55
    Period size: 19  Copynumber: 2.9  Consensus size: 16

       2753 AAGAAAATTA

                            
       2763 AAGAAAACAATTAA-C
          1 AAGAAAACAATTAATC

                  *            
       2778 AAGAAAGCAATGAATAATC
          1 AAGAAAACAAT---TAATC

                           
       2797 AAGAAAACAATTAAT
          1 AAGAAAACAATTAAT

       2812 AAAAACCTCC


Statistics
Matches: 28,  Mismatches: 2, Indels: 7
        0.76            0.05        0.19

Matches are distributed among these distances:
  15   10  0.36
  16    4  0.14
  18    3  0.11
  19   11  0.39

ACGTcount: A:0.63, C:0.10, G:0.10, T:0.16


Consensus pattern (16 bp):   
AAGAAAACAATTAATC

Found at i:2799 original size:19 final size:19

Alignment explanation


    Indices: 2777--2813  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       2767 AAACAATTAA

                   *           
       2777 CAAGAAAGCAATGAATAAT
          1 CAAGAAAACAATGAATAAT

                        *     
       2796 CAAGAAAACAATTAATAA
          1 CAAGAAAACAATGAATAA

       2814 AAACCTCCAA


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

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16


Consensus pattern (19 bp):   
CAAGAAAACAATGAATAAT

Found at i:8123 original size:20 final size:20

Alignment explanation


    Indices: 8077--8126  Score: 66
    Period size: 19  Copynumber: 2.5  Consensus size: 20

       8067 CTGGCAAAAT

                          * * * 
       8077 CTAACCCGACCGCGGGTATC
          1 CTAACCCGACCGCGCGAAAC

                                
       8097 C-AACCCGACCGCGCGAAAC
          1 CTAACCCGACCGCGCGAAAC

                       
       8116 CTAACCCGACC
          1 CTAACCCGACC

       8127 CAACCCGATT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  19   16  0.62
  20   10  0.38

ACGTcount: A:0.26, C:0.46, G:0.20, T:0.08


Consensus pattern (20 bp):   
CTAACCCGACCGCGCGAAAC

Found at i:8912 original size:22 final size:22

Alignment explanation


    Indices: 8874--8917  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8864 TATTTCAGTT

                                   
       8874 TTTTTTTAAAGATTAATCTGTTC
          1 TTTTTTT-AAGATTAATCTGTTC

                             *    
       8897 TTTTTTT-AGATGTAATTTGTT
          1 TTTTTTTAAGAT-TAATCTGTT

       8918 TCAATGTTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  21    4  0.21
  22    8  0.42
  23    7  0.37

ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61


Consensus pattern (22 bp):   
TTTTTTTAAGATTAATCTGTTC

Found at i:11508 original size:2 final size:2

Alignment explanation


    Indices: 11503--11539  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      11493 TGTGTGTGTC

                                     *                             
      11503 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11540 CCACAAATCC


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:11851 original size:22 final size:22

Alignment explanation


    Indices: 11806--11993  Score: 143
    Period size: 22  Copynumber: 8.4  Consensus size: 22

      11796 TTGGAAACAT

                           *     *
      11806 CTTTGCAGAG-ATT-CTTTCTT
          1 CTTTGCAGAGCATTATTTTCTA

                                  
      11826 CTTTGCAGAGCATTATTTTCTA
          1 CTTTGCAGAGCATTATTTTCTA

                                * 
      11848 CTTTGCAGAGCATTATTTTCCA
          1 CTTTGCAGAGCATTATTTTCTA

                                     
      11870 CTTTGCAGAGCATTATTTTCTTCAA
          1 CTTTGCAGAGCATTATTTTC-T--A

                *  ***   *       **   
      11895 CTTCAGCTTTGCACTATTGGAAAC-A
          1 CTT-TGCAGAGCATTATT---TTCTA

                            *     *
      11920 TCTTTGCAGAG-ATT-CTTTCTG
          1 -CTTTGCAGAGCATTATTTTCTA

                      *           
      11941 CTTTGCAGAGTATTATTTTCTA
          1 CTTTGCAGAGCATTATTTTCTA

                                * 
      11963 CTTTGCAGAGCATTATTTTCCA
          1 CTTTGCAGAGCATTATTTTCTA

                     
      11985 CTTTGCAGA
          1 CTTTGCAGA

      11994 ACACTTCTTG


Statistics
Matches: 131,  Mismatches: 24, Indels: 24
        0.73            0.13        0.13

Matches are distributed among these distances:
  20   21  0.16
  21    6  0.05
  22   80  0.61
  23    1  0.01
  24    2  0.02
  25    8  0.06
  26   12  0.09
  29    1  0.01

ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43


Consensus pattern (22 bp):   
CTTTGCAGAGCATTATTTTCTA

Done.