Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010407.1 Corchorus olitorius cultivar O-4 contig10439, 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: 3421
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33


Found at i:3254 original size:47 final size:46

Alignment explanation


    Indices: 3201--3421  Score: 264
    Period size: 47  Copynumber: 4.7  Consensus size: 46

       3191 TATTTGCAAT

                        *            * **      *            
       3201 TTAGTTTAATTATCTGGACTTAAACCAGCCTCTT-TTCCTTTTACTAC
          1 TTAGTTTAATTACCTGGA-TTAAACTAATCTCTTCCT-CTTTTACTAC

                                    *                      
       3248 TTAGTTTAATTACCTAGGATTAAATTAATCTCTTCCTCTTTTACTAC
          1 TTAGTTTAATTACCT-GGATTAAACTAATCTCTTCCTCTTTTACTAC

                             *    *                        
       3295 TTAGTTTAATTACCTAGAATTACACTAATCTCTTCCTCTTTTACTAC
          1 TTAGTTTAATTACCT-GGATTAAACTAATCTCTTCCTCTTTTACTAC

                             *              * *            
       3342 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTACTCTTTTACTAC
          1 TTAGTTTAATTACCT-GGATTAAACTAATCTCTTCCTCTTTTACTAC

            *                *               
       3389 CTAGTTTAATTACCTAGAATTAAACTAATCTCT
          1 TTAGTTTAATTACCT-GGATTAAACTAATCTCT


Statistics
Matches: 158,  Mismatches: 14, Indels: 4
        0.90            0.08        0.02

Matches are distributed among these distances:
  47  154  0.97
  48    4  0.03

ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44


Consensus pattern (46 bp):   
TTAGTTTAATTACCTGGATTAAACTAATCTCTTCCTCTTTTACTAC

Found at i:3304 original size:94 final size:94

Alignment explanation


    Indices: 3201--3413  Score: 293
    Period size: 94  Copynumber: 2.3  Consensus size: 94

       3191 TATTTGCAAT

                        *  *  *        *       *                             
       3201 TTAGTTTAATTATCTGGACTTAAACCAGCCTCTT-TTCCTTTTACTACTTAGTTTAATTACCTAG
          1 TTAGTTTAATTACCTAGAATTAAACCAACCTCTTCCT-CTTTTACTACTTAGTTTAATTACCTAG

            *      *       * *            
       3265 GATTAAATTAATCTCTTCCTCTTTTACTAC
         65 AATTAAACTAATCTCCTACTCTTTTACTAC

                                  *  *  *                                    
       3295 TTAGTTTAATTACCTAGAATTACACTAATCTCTTCCTCTTTTACTACTTAGTTTAATTACCTAGA
          1 TTAGTTTAATTACCTAGAATTAAACCAACCTCTTCCTCTTTTACTACTTAGTTTAATTACCTAGA

                                         
       3360 ATTAAACTAATCTCCTACTCTTTTACTAC
         66 ATTAAACTAATCTCCTACTCTTTTACTAC

            *                        
       3389 CTAGTTTAATTACCTAGAATTAAAC
          1 TTAGTTTAATTACCTAGAATTAAAC

       3414 TAATCTCT


Statistics
Matches: 104,  Mismatches: 14, Indels: 2
        0.87            0.12        0.02

Matches are distributed among these distances:
  94  103  0.99
  95    1  0.01

ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44


Consensus pattern (94 bp):   
TTAGTTTAATTACCTAGAATTAAACCAACCTCTTCCTCTTTTACTACTTAGTTTAATTACCTAGA
ATTAAACTAATCTCCTACTCTTTTACTAC

Found at i:3416 original size:94 final size:94

Alignment explanation


    Indices: 3238--3421  Score: 314
    Period size: 94  Copynumber: 2.0  Consensus size: 94

       3228 GCCTCTTTTC

                                       *      *       * *            *       
       3238 CTTTTACTACTTAGTTTAATTACCTAGGATTAAATTAATCTCTTCCTCTTTTACTACTTAGTTTA
          1 CTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCCTACTCTTTTACTACCTAGTTTA

                          *              
       3303 ATTACCTAGAATTACACTAATCTCTTCCT
         66 ATTACCTAGAATTAAACTAATCTCTTCCT

                                                                             
       3332 CTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCCTACTCTTTTACTACCTAGTTTA
          1 CTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCCTACTCTTTTACTACCTAGTTTA

                                     
       3397 ATTACCTAGAATTAAACTAATCTCT
         66 ATTACCTAGAATTAAACTAATCTCT


Statistics
Matches: 84,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  94   84  1.00

ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44


Consensus pattern (94 bp):   
CTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCCTACTCTTTTACTACCTAGTTTA
ATTACCTAGAATTAAACTAATCTCTTCCT
Done.