Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021481.1 Corchorus olitorius cultivar O-4 contig21514, 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: 15630
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32


Found at i:2242 original size:100 final size:102

Alignment explanation


    Indices: 2125--2314  Score: 303
    Period size: 102  Copynumber: 1.9  Consensus size: 102

       2115 ATTAAAGAGT

                                      *  *             *        *            
       2125 CGTCTTCCGCTTATCCTTTGAACTGTTTTTCAATTCAATC-T-CAAAAGGACTGTCTTCCCCTTA
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGACCGTCTTCCCCTTA

              *  *                               
       2188 TCTTTTGAACTGTCTTCCAATTCAATCTTAAAAAGAC
         66 TCCTTCGAACTGTCTTCCAATTCAATCTTAAAAAGAC

                                                                        *    
       2225 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGACCGTCTTCCGCTTA
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGACCGTCTTCCCCTTA

                                     
       2290 TCCTTCGAACTGTCTTCCAATTCAA
         66 TCCTTCGAACTGTCTTCCAATTCAA

       2315 CCTTCTGTAT


Statistics
Matches: 81,  Mismatches: 7, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
 100   38  0.47
 101    1  0.01
 102   42  0.52

ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37


Consensus pattern (102 bp):   
CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGACCGTCTTCCCCTTA
TCCTTCGAACTGTCTTCCAATTCAATCTTAAAAAGAC

Found at i:2300 original size:52 final size:51

Alignment explanation


    Indices: 2125--2314  Score: 294
    Period size: 50  Copynumber: 3.7  Consensus size: 51

       2115 ATTAAAGAGT

                                      *  *            *        
       2125 CGTCTTCCGCTTATCCTTTGAACTGTTTTTCAATTCAATC-TCAAAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC

            *       *      *                                   
       2175 TGTCTTCCCCTTATCTTTTGAACTGTCTTCCAATTCAATCTTAAAAA-GAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC

                                                                
       2225 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTT-AAAAAGGAC

                              *                   
       2277 CGTCTTCCGCTTATCCTTCGAACTGTCTTCCAATTCAA
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAA

       2315 CCTTCTGTAT


Statistics
Matches: 127,  Mismatches: 10, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
  50   77  0.61
  51   10  0.08
  52   40  0.31

ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37


Consensus pattern (51 bp):   
CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
Done.