Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013250.1 Corchorus olitorius cultivar O-4 contig13283, 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: 43548
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:9227 original size:22 final size:22

Alignment explanation


    Indices: 9182--9234  Score: 63
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       9172 ATCTTTCTGA

                              **  
       9182 TTAATTGTTTTCTTTAATTTTC
          1 TTAATTGTTTTCTTTAATAGTC

              *                    
       9204 TTGATTGTTTTC-TTAGATAGTC
          1 TTAATTGTTTTCTTTA-ATAGTC

                     
       9226 TTAATTGTT
          1 TTAATTGTT

       9235 AGTTTGATTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21    3  0.12
  22   23  0.88

ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62


Consensus pattern (22 bp):   
TTAATTGTTTTCTTTAATAGTC

Found at i:12993 original size:16 final size:15

Alignment explanation


    Indices: 12955--13002  Score: 64
    Period size: 16  Copynumber: 3.2  Consensus size: 15

      12945 CTAACTATTT

                            
      12955 ATTTT-CTTTGCATTG
          1 ATTTTGCTTTG-ATTG

                           
      12970 -TTTTGCTTTGATTG
          1 ATTTTGCTTTGATTG

                            
      12984 ATTATTGCTTTGATTG
          1 ATT-TTGCTTTGATTG

               
      13000 ATT
          1 ATT

      13003 GCTTATTCCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  14    8  0.27
  15    7  0.23
  16   15  0.50

ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60


Consensus pattern (15 bp):   
ATTTTGCTTTGATTG

Found at i:27950 original size:9 final size:9

Alignment explanation


    Indices: 27928--27960  Score: 50
    Period size: 9  Copynumber: 3.8  Consensus size: 9

      27918 TGAAAACAAT

                     
      27928 AAAC-AACA
          1 AAACAAACA

                     
      27936 AAACAAACA
          1 AAACAAACA

             *       
      27945 ACACAAACA
          1 AAACAAACA

                   
      27954 AAACAAA
          1 AAACAAA

      27961 GCAACTGTTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
   8    4  0.18
   9   18  0.82

ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00


Consensus pattern (9 bp):   
AAACAAACA
Done.