Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015529.1 Corchorus olitorius cultivar O-4 contig15562, 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: 3652
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:500 original size:19 final size:19

Alignment explanation


    Indices: 476--513  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        466 GAGAAATAAA

                               
        476 TTTTCCTGAATACTAATTT
          1 TTTTCCTGAATACTAATTT

                     *         
        495 TTTTCCTGATTACTAATTT
          1 TTTTCCTGAATACTAATTT

        514 GTAAGTATTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55


Consensus pattern (19 bp):   
TTTTCCTGAATACTAATTT

Found at i:2526 original size:28 final size:29

Alignment explanation


    Indices: 2495--2559  Score: 73
    Period size: 27  Copynumber: 2.3  Consensus size: 29

       2485 TCCACTTTAA

                        *                 
       2495 AAGGGTAAATTTCGTAATTTAACATC-TT-
          1 AAGGGTAAATTTAGTAATTTAAC-TCGTTC

                   *            *        
       2523 AAGGGT-GATTTAGTAATTTTACTCGTTC
          1 AAGGGTAAATTTAGTAATTTAACTCGTTC

                     
       2551 AAGGGTAAA
          1 AAGGGTAAA

       2560 ATTGTAACTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 5
        0.77            0.10        0.13

Matches are distributed among these distances:
  26    2  0.07
  27   15  0.50
  28   12  0.40
  29    1  0.03

ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37


Consensus pattern (29 bp):   
AAGGGTAAATTTAGTAATTTAACTCGTTC

Found at i:2728 original size:17 final size:16

Alignment explanation


    Indices: 2706--2745  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 16

       2696 CCACTTCTTC

                   *         
       2706 CTTTTTCCTTTCTTATT
          1 CTTTTTCATTTCTT-TT

                            
       2723 CTTTTTCATTTCTTTT
          1 CTTTTTCATTTCTTTT

            *      
       2739 TTTTTTC
          1 CTTTTTC

       2746 TTTGGGCCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  16    8  0.38
  17   13  0.62

ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75


Consensus pattern (16 bp):   
CTTTTTCATTTCTTTT

Found at i:2882 original size:12 final size:12

Alignment explanation


    Indices: 2855--2893  Score: 64
    Period size: 12  Copynumber: 3.4  Consensus size: 12

       2845 CCAAGCGGCT

                        
       2855 TTCTTTTT-TT-
          1 TTCTTTTTCTTC

                        
       2865 TTCTTTTTCTTC
          1 TTCTTTTTCTTC

                        
       2877 TTCTTTTTCTTC
          1 TTCTTTTTCTTC

                 
       2889 TTCTT
          1 TTCTT

       2894 ATTATTCCGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  10    8  0.30
  11    2  0.07
  12   17  0.63

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (12 bp):   
TTCTTTTTCTTC
Done.