Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020739.1 Corchorus olitorius cultivar O-4 contig20772, 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: 9697
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35


Found at i:120 original size:21 final size:20

Alignment explanation


    Indices: 80--159  Score: 66
    Period size: 19  Copynumber: 4.3  Consensus size: 20

         70 CCGTTTAGTA

                         *      
         80 ATATT-TATA-ATTAAATAT
          1 ATATTATATATATAAAATAT

                                
         98 ATATTATATATATAAAATA-
          1 ATATTATATATATAAAATAT

                  *       *     
        117 ATATTAGATATATATAAT-T
          1 ATATTATATATATAAAATAT

             *             *    
        136 ACA-TATATA-ATAATATAT
          1 ATATTATATATATAAAATAT

                   
        154 A-ATTAT
          1 ATATTAT

        160 TAAACGGTTT


Statistics
Matches: 50,  Mismatches: 7, Indels: 10
        0.75            0.10        0.15

Matches are distributed among these distances:
  17    6  0.12
  18   15  0.30
  19   22  0.44
  20    7  0.14

ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45


Consensus pattern (20 bp):   
ATATTATATATATAAAATAT

Found at i:143 original size:12 final size:11

Alignment explanation


    Indices: 85--158  Score: 59
    Period size: 10  Copynumber: 6.7  Consensus size: 11

         75 TAGTAATATT

                       
         85 TATAATTAA-A
          1 TATAATTAATA

                         
         95 TATATATTATATA
          1 TATA-ATTA-ATA

                  *     
        108 TATAAAATAATA
          1 TAT-AATTAATA

                        
        120 T-TAGA-T-ATA
          1 TATA-ATTAATA

                        
        129 TATAATTACATA
          1 TATAATTA-ATA

                       
        141 TATAA-TAATA
          1 TATAATTAATA

                    
        151 TATAATTA
          1 TATAATTA

        159 TTAAACGGTT


Statistics
Matches: 53,  Mismatches: 1, Indels: 19
        0.73            0.01        0.26

Matches are distributed among these distances:
   9    5  0.09
  10   17  0.32
  11   10  0.19
  12   13  0.25
  13    7  0.13
  14    1  0.02

ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43


Consensus pattern (11 bp):   
TATAATTAATA

Found at i:7762 original size:16 final size:16

Alignment explanation


    Indices: 7741--7775  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       7731 TAATAAATAA

                            
       7741 TATATGTTTAATAGTC
          1 TATATGTTTAATAGTC

                            
       7757 TATATGTTTAATAGTC
          1 TATATGTTTAATAGTC

               
       7773 TAT
          1 TAT

       7776 GAAAACAAAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51


Consensus pattern (16 bp):   
TATATGTTTAATAGTC
Done.