Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019691.1 Corchorus olitorius cultivar O-4 contig19724, 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: 14120
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:9476 original size:19 final size:19

Alignment explanation


    Indices: 9452--9496  Score: 72
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       9442 TGAAAGATAG

                               
       9452 TTATTATAATTAATAACAA
          1 TTATTATAATTAATAACAA

                            *  
       9471 TTATTATAATTAATAATAA
          1 TTATTATAATTAATAACAA

             *     
       9490 TAATTAT
          1 TTATTAT

       9497 TTTCTGGTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTATTATAATTAATAACAA

Found at i:12149 original size:24 final size:24

Alignment explanation


    Indices: 12104--12150  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      12094 TTGTAGCTTT

                 *           *      
      12104 TGGACGTTTTGTCCCATGAACTTG
          1 TGGACATTTTGTCCCATAAACTTG

                                    
      12128 TGGACATTTTG-CCCTATAAACTT
          1 TGGACATTTTGTCCC-ATAAACTT

      12151 CAATTTTGAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    3  0.15
  24   17  0.85

ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38


Consensus pattern (24 bp):   
TGGACATTTTGTCCCATAAACTTG

Found at i:14001 original size:3 final size:3

Alignment explanation


    Indices: 13993--14120  Score: 222
    Period size: 3  Copynumber: 42.3  Consensus size: 3

      13983 TAGAAATTTC

                                                                    *    
      13993 TTA TTA TTA -TA TGCTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA
          1 TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                                                           
      14039 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                                         
      14087 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T


Statistics
Matches: 120,  Mismatches: 2, Indels: 6
        0.94            0.02        0.05

Matches are distributed among these distances:
   2    2  0.02
   3  115  0.96
   5    3  0.03

ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66


Consensus pattern (3 bp):   
TTA

Done.