Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020485.1 Corchorus olitorius cultivar O-4 contig20518, 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: 8325
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Found at i:3239 original size:12 final size:12

Alignment explanation


    Indices: 3222--3255  Score: 52
    Period size: 11  Copynumber: 2.9  Consensus size: 12

       3212 TTATGCACCC

                        
       3222 AAAACATTTATT
          1 AAAACATTTATT

                        
       3234 AAAACATTTA-T
          1 AAAACATTTATT

               *       
       3245 AAAGCATTTAT
          1 AAAACATTTAT

       3256 ATAATGCAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  11   10  0.50
  12   10  0.50

ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38


Consensus pattern (12 bp):   
AAAACATTTATT

Found at i:4576 original size:3 final size:3

Alignment explanation


    Indices: 4568--4593  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       4558 CTTGGCCCAT

                                              
       4568 TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT

       4594 TTCCTTGTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:7280 original size:39 final size:38

Alignment explanation


    Indices: 7237--7388  Score: 153
    Period size: 39  Copynumber: 3.9  Consensus size: 38

       7227 CAGGTCTGCG

                                                   
       7237 TTTAGAATTTCATTAGAATCAAACCTGCTCAGGTCCTTA
          1 TTTAGAATTTCATT-GAATCAAACCTGCTCAGGTCCTTA

                        *  *             *        *
       7276 TTTAGAATTCTCGTTTAATCAAACCTGCTTAGGTCCTTG
          1 TTTAGAATT-TCATTGAATCAAACCTGCTCAGGTCCTTA

                        *  *  **         *         
       7315 TTTAGAATTTCCGTTCAAGAAAACCTGCTTAGGTCCTTA
          1 TTTAGAATTT-CATTGAATCAAACCTGCTCAGGTCCTTA

              *               *                 
       7354 TTCAGAATTTTCATTCGAGT-AAACCTGCTCAGGTC
          1 TTTAGAA-TTTCATT-GAATCAAACCTGCTCAGGTC

       7389 TCCATTTCGT


Statistics
Matches: 95,  Mismatches: 14, Indels: 8
        0.81            0.12        0.07

Matches are distributed among these distances:
  38    1  0.01
  39   86  0.91
  40    8  0.08

ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37


Consensus pattern (38 bp):   
TTTAGAATTTCATTGAATCAAACCTGCTCAGGTCCTTA
Done.