Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016295.1 Corchorus capsularis cultivar CVL-1 contig16316, 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: 12944
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:6456 original size:88 final size:86

Alignment explanation


    Indices: 6271--6464  Score: 257
    Period size: 88  Copynumber: 2.2  Consensus size: 86

       6261 TATGGATTAG

                          *                             * *         **  *    
       6271 GCTACTGCTTTAGATTTTTCCTTAGCAAATATCAGTTCTGCTAATACAGCTTGTTTTCCTTAGCA
          1 GCTACTGCTTTAGAATTTTCCTTAGCAAATATCAGTTCTGCTAAAAAAGCTTGTTTAACTAAGCA

                             *   
       6336 ATCAGTCATTTTGATTCTTTT
         66 ATCAGTCATTTTGATTCCTTT

                                    *              *                         
       6357 G-TCACTGCTTTAGAATTTTCCTTGGCAAATATCAGTTTGTGCTAAAAAAGCTTGTTTAACTCAA
          1 GCT-ACTGCTTTAGAATTTTCCTTAGCAAATATCAG-TTCTGCTAAAAAAGCTTGTTTAACT-AA

                           *        
       6421 GCAATCAGTCATTTTTATTCCTTT
         63 GCAATCAGTCATTTTGATTCCTTT

                                 
       6445 GCTACTGCTTTAG-ATTTTCC
          1 GCTACTGCTTTAGAATTTTCC

       6465 ATTTTCCCTT


Statistics
Matches: 94,  Mismatches: 10, Indels: 7
        0.85            0.09        0.06

Matches are distributed among these distances:
  85    1  0.01
  86   31  0.33
  87   27  0.29
  88   34  0.36
  89    1  0.01

ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43


Consensus pattern (86 bp):   
GCTACTGCTTTAGAATTTTCCTTAGCAAATATCAGTTCTGCTAAAAAAGCTTGTTTAACTAAGCA
ATCAGTCATTTTGATTCCTTT

Found at i:10966 original size:89 final size:89

Alignment explanation


    Indices: 10800--10992  Score: 255
    Period size: 89  Copynumber: 2.2  Consensus size: 89

      10790 GATTAGCATT

                 *     *                                *                    
      10800 CAATCGGTCATCTTGATTCTTTTGCTACTGCTTTAGATTTTTCCTTGGCAAATATATCAGTTTCT
          1 CAATCAGTCATTTTGATTCTTTTGCTACTGCTTTAGATTTTTCCATGGCAAATATATCAGTTTCT

                 *           **  *  
      10865 GCTAATACAGCTTGTTTTCCTTAG
         66 GCTAAGACAGCTTGTTTAACTCAG

                                    *                                      * 
      10889 CAATCAGTCATTTTGATTCTTTTGTTACTGCTTTAGATTTTTCCATGGC-AA-ATATCAGTTTGT
          1 CAATCAGTCATTTTGATTCTTTTGCTACTGCTTTAGATTTTTCCATGGCAAATATATCAGTTTCT

                     *                
      10952 GCTAAAAGAGAGCTTGTTTAACTCAG
         66 GCT--AAGACAGCTTGTTTAACTCAG

                  *        
      10978 CAATCAATCATTTTG
          1 CAATCAGTCATTTTG

      10993 GATTTTTGAT


Statistics
Matches: 91,  Mismatches: 11, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  87   14  0.15
  88    2  0.02
  89   75  0.82

ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43


Consensus pattern (89 bp):   
CAATCAGTCATTTTGATTCTTTTGCTACTGCTTTAGATTTTTCCATGGCAAATATATCAGTTTCT
GCTAAGACAGCTTGTTTAACTCAG
Done.