Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022091.1 Corchorus olitorius cultivar O-4 contig22124, 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: 3397
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28


Found at i:396 original size:15 final size:15

Alignment explanation


    Indices: 366--407  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        356 TTACTTTGCT

                            
        366 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        382 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        397 TTGCTTTCTGT
          1 TTGTTTTCTGT

        408 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:786 original size:24 final size:24

Alignment explanation


    Indices: 756--807  Score: 79
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        746 TTGTTTTGTG

                                     
        756 TTTTGCGTCGA-AAAAAAAAATAGT
          1 TTTTGCGTC-ATAAAAAAAAATAGT

                                  * 
        780 TTTTGCGTCATAAAAAAAAATATT
          1 TTTTGCGTCATAAAAAAAAATAGT

                
        804 TTTT
          1 TTTT

        808 TGTGTCTGCG


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  23    1  0.04
  24   25  0.96

ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38


Consensus pattern (24 bp):   
TTTTGCGTCATAAAAAAAAATAGT

Found at i:3211 original size:21 final size:21

Alignment explanation


    Indices: 3156--3222  Score: 71
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       3146 CCAAGCCATT

                     *            
       3156 ACCGGCCATTCACCGTGCCACC
          1 ACCGGCCATGC-CCGTGCCACC

                 ** *            
       3178 ACCGGTTAAGCCCGTGCCACC
          1 ACCGGCCATGCCCGTGCCACC

                         *     * 
       3199 ACCGGCCATGCCCATGCCATC
          1 ACCGGCCATGCCCGTGCCACC

               
       3220 ACC
          1 ACC

       3223 ATTCCAAGCC


Statistics
Matches: 36,  Mismatches: 9, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  21   29  0.81
  22    7  0.19

ACGTcount: A:0.19, C:0.48, G:0.19, T:0.13


Consensus pattern (21 bp):   
ACCGGCCATGCCCGTGCCACC
Done.