Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012746.1 Corchorus olitorius cultivar O-4 contig12779, 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: 11321
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:1715 original size:18 final size:17

Alignment explanation


    Indices: 1688--1726  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1678 AATACTCCGG

                             
       1688 CAAATCATCACCACTGA
          1 CAAATCATCACCACTGA

                         *    
       1705 CAAAGTCATCACCTCTGA
          1 CAAA-TCATCACCACTGA

                
       1723 CAAA
          1 CAAA

       1727 ATCAGATTGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  17    4  0.20
  18   16  0.80

ACGTcount: A:0.41, C:0.33, G:0.08, T:0.18


Consensus pattern (17 bp):   
CAAATCATCACCACTGA

Found at i:3547 original size:56 final size:57

Alignment explanation


    Indices: 3451--3558  Score: 191
    Period size: 56  Copynumber: 1.9  Consensus size: 57

       3441 CGCCCAACTA

                                               *                     
       3451 GGGCGGCCTAGCCATGGCCATGCCGCCCTCCTAGGGTGGCACCGAAAATTTTAAGTT
          1 GGGCGGCCTAGCCATGGCCATGCCGCCCTCCTAGGCTGGCACCGAAAATTTTAAGTT

                               *                                
       3508 GGGCGGCCTAGCCATGG-CTTGCCGCCCTCCTAGGCTGGCACCGAAAATTTT
          1 GGGCGGCCTAGCCATGGCCATGCCGCCCTCCTAGGCTGGCACCGAAAATTTT

       3559 CTTAAAATTT


Statistics
Matches: 49,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  56   32  0.65
  57   17  0.35

ACGTcount: A:0.18, C:0.31, G:0.30, T:0.21


Consensus pattern (57 bp):   
GGGCGGCCTAGCCATGGCCATGCCGCCCTCCTAGGCTGGCACCGAAAATTTTAAGTT
Done.