Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024735.1 Corchorus olitorius cultivar O-4 contig24768, 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: 21854
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:5615 original size:15 final size:14

Alignment explanation


    Indices: 5592--5621  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       5582 ATAAAAATTA

                          
       5592 AATATTTTTATTTT
          1 AATATTTTTATTTT

                           
       5606 AATATATTTTATTTT
          1 AATAT-TTTTATTTT

             
       5621 A
          1 A

       5622 TTGAAATTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (14 bp):   
AATATTTTTATTTT

Found at i:6345 original size:16 final size:16

Alignment explanation


    Indices: 6324--6354  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       6314 GTTCCACTGA

                            
       6324 GATGAAAAACCAAGTT
          1 GATGAAAAACCAAGTT

                     *     
       6340 GATGAAAAATCAAGT
          1 GATGAAAAACCAAGT

       6355 GCCTAACACG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19


Consensus pattern (16 bp):   
GATGAAAAACCAAGTT

Found at i:6639 original size:15 final size:15

Alignment explanation


    Indices: 6607--6636  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6597 TAAATTTCAA

                           
       6607 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
       6622 TAAAATAAAA-ATAT
          1 TAAAATAAAATATAT

             
       6636 T
          1 T

       6637 TAATTTTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:16851 original size:7 final size:7

Alignment explanation


    Indices: 16839--16869  Score: 62
    Period size: 7  Copynumber: 4.4  Consensus size: 7

      16829 AAAGTAAATC

                   
      16839 ACCCATT
          1 ACCCATT

                   
      16846 ACCCATT
          1 ACCCATT

                   
      16853 ACCCATT
          1 ACCCATT

                   
      16860 ACCCATT
          1 ACCCATT

               
      16867 ACC
          1 ACC

      16870 TATAGGCCCA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.29, C:0.45, G:0.00, T:0.26


Consensus pattern (7 bp):   
ACCCATT

Done.