Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018434.1 Corchorus olitorius cultivar O-4 contig18467, 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: 10564
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:5291 original size:15 final size:17

Alignment explanation


    Indices: 5273--5309  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       5263 TTGATAGGGA

                             
       5273 GGAAAG-AAATA-GAAG
          1 GGAAAGAAAATATGAAG

                             
       5288 GGAAAGAAAATATGAAG
          1 GGAAAGAAAATATGAAG

                 
       5305 GGAAA
          1 GGAAA

       5310 TGGAGTCATG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  15    6  0.30
  16    5  0.25
  17    9  0.45

ACGTcount: A:0.59, C:0.00, G:0.32, T:0.08


Consensus pattern (17 bp):   
GGAAAGAAAATATGAAG

Found at i:5677 original size:2 final size:2

Alignment explanation


    Indices: 5643--5715  Score: 75
    Period size: 2  Copynumber: 39.0  Consensus size: 2

       5633 AATACTAATT

                                                             *            
       5643 TA TA TA T- TA -A TA T- TA T- TA TA T- TA TA TA TC TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

               *                        *                *       
       5680 TA CA TA TA TA TA TA TA TA TG TA TA TA TA TA GA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       5716 ATCACTTTTC


Statistics
Matches: 58,  Mismatches: 8, Indels: 10
        0.76            0.11        0.13

Matches are distributed among these distances:
   1    5  0.09
   2   53  0.91

ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5992 original size:13 final size:13

Alignment explanation


    Indices: 5976--6001  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       5966 ATTTTTAATA

                         
       5976 AAAATTAAAATTT
          1 AAAATTAAAATTT

                         
       5989 AAAATTAAAATTT
          1 AAAATTAAAATTT

       6002 TTATATAATC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (13 bp):   
AAAATTAAAATTT

Found at i:6131 original size:29 final size:30

Alignment explanation


    Indices: 6084--6144  Score: 88
    Period size: 29  Copynumber: 2.1  Consensus size: 30

       6074 GTTCTAATTA

                   *                 *    
       6084 ATGTATACATATAAATTATTCAATTTTATT
          1 ATGTATAAATATAAATTATTCAATTATATT

                                *         
       6114 ATGTATAAATA-AAATTATTTAATTATATT
          1 ATGTATAAATATAAATTATTCAATTATATT

              
       6143 AT
          1 AT

       6145 ATTATTTATG


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   18  0.64
  30   10  0.36

ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49


Consensus pattern (30 bp):   
ATGTATAAATATAAATTATTCAATTATATT
Done.