Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011318.1 Corchorus olitorius cultivar O-4 contig11351, 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: 2930
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35


Found at i:649 original size:21 final size:21

Alignment explanation


    Indices: 614--675  Score: 81
    Period size: 21  Copynumber: 2.9  Consensus size: 21

        604 CACCCTAGAG

                    *             
        614 TTTCTTTCCTTTTTCTTCTTCT
          1 TTTCTTT-TTTTTTCTTCTTCT

                                 
        636 TTTCTTTTTTTTTCTTCTTCT
          1 TTTCTTTTTTTTTCTTCTTCT

                       *        
        657 TCTTCTTTTTTCTT-TTCTT
          1 T-TTCTTTTTTTTTCTTCTT

        676 TAATGCACTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  21   19  0.51
  22   18  0.49

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (21 bp):   
TTTCTTTTTTTTTCTTCTTCT

Found at i:658 original size:24 final size:24

Alignment explanation


    Indices: 624--675  Score: 83
    Period size: 21  Copynumber: 2.3  Consensus size: 24

        614 TTTCTTTCCT

                                    
        624 TTTTCTTCTTCTT-TTC-TTTTT-
          1 TTTTCTTCTTCTTCTTCTTTTTTC

                                    
        645 TTTTCTTCTTCTTCTTCTTTTTTC
          1 TTTTCTTCTTCTTCTTCTTTTTTC

                   
        669 TTTTCTT
          1 TTTTCTT

        676 TAATGCACTT


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

Matches are distributed among these distances:
  21   13  0.46
  22    3  0.11
  23    5  0.18
  24    7  0.25

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


Consensus pattern (24 bp):   
TTTTCTTCTTCTTCTTCTTTTTTC

Found at i:999 original size:6 final size:6

Alignment explanation


    Indices: 975--1028  Score: 56
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        965 TCTTATACCT

                                          *      *                    
        975 TTTTCAA TTTTCAA TTTTCA TTTTCA CTTTCA CTTTCA CTTTTCA -TTTCA
          1 TTTTC-A TTTTC-A TTTTCA TTTTCA TTTTCA TTTTCA -TTTTCA TTTTCA

                
       1025 TTTT
          1 TTTT

       1029 TTTTTTAGAC


Statistics
Matches: 43,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
   5    5  0.12
   6   21  0.49
   7   17  0.40

ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61


Consensus pattern (6 bp):   
TTTTCA

Found at i:999 original size:13 final size:13

Alignment explanation


    Indices: 975--1022  Score: 53
    Period size: 13  Copynumber: 3.7  Consensus size: 13

        965 TCTTATACCT

                          
        975 TTTTCAATTTTCAA
          1 TTTTC-ATTTTCAA

                         
        989 TTTTCATTTTC-A
          1 TTTTCATTTTCAA

            *     *     *
       1001 CTTTCACTTTCAC
          1 TTTTCATTTTCAA

                     
       1014 TTTTCATTT
          1 TTTTCATTT

       1023 CATTTTTTTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 3
        0.78            0.14        0.08

Matches are distributed among these distances:
  12   10  0.36
  13   13  0.46
  14    5  0.18

ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60


Consensus pattern (13 bp):   
TTTTCATTTTCAA

Found at i:1461 original size:15 final size:16

Alignment explanation


    Indices: 1441--1470  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       1431 AAGTGCTATT

                            
       1441 TTTCTTTT-TTTTTCG
          1 TTTCTTTTCTTTTTCG

                           
       1456 TTTCTTTTCTTTTTC
          1 TTTCTTTTCTTTTTC

       1471 TTTTTTCGAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80


Consensus pattern (16 bp):   
TTTCTTTTCTTTTTCG
Done.