Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018019.1 Corchorus olitorius cultivar O-4 contig18052, 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: 7624
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2643 original size:2 final size:2

Alignment explanation


    Indices: 2638--2675  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       2628 GTTGAGTGTG

                        *   *                                       
       2638 TA TA TA TA AA TC TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2676 CAAATTCATA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:4537 original size:1 final size:1

Alignment explanation


    Indices: 4531--4556  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       4521 GGTTTAGTTT

                                      
       4531 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

       4557 CAGTTACTCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:6531 original size:24 final size:24

Alignment explanation


    Indices: 6499--6544  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6489 ATGTAATATT

                      *             
       6499 AGAGGGGGCTTGATTAGACTCGTC
          1 AGAGGGGGCTCGATTAGACTCGTC

                             *    
       6523 AGAGGGGGCTCGATTAGGCTCG
          1 AGAGGGGGCTCGATTAGACTCG

       6545 ACGAGCCTAC


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

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22


Consensus pattern (24 bp):   
AGAGGGGGCTCGATTAGACTCGTC
Done.