Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022678.1 Corchorus olitorius cultivar O-4 contig22711, 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: 7458
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:6630 original size:178 final size:178

Alignment explanation


    Indices: 6363--6686  Score: 483
    Period size: 178  Copynumber: 1.8  Consensus size: 178

       6353 AAGGTGATTT

                                                                             
       6363 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTA
          1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTA

                                               *                 *       **  
       6428 ATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCAGTTAACGGGAATAGACGGTC
         66 ATGTTTCAAGTATCAAAAATGCTTCC-AAAGAATTAGTTGTTTCAGTTAACGGAAATAGACAATC

                        *                                    
       6492 CACTTAATATTATATAACTTTTACTTCAGTTGTCTAATTGAGATAATTC
        130 CACTTAATATTACATAACTTTTACTTCAGTTGTCTAATTGAGATAATTC

                    *  *    *                            *                   
       6541 AAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
          1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTA

            *                                            *             *     
       6606 TTG-TTCAAGGTAT-AAAATATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATATACAAT
         66 ATGTTTCAA-GTATCAAAA-ATGCTTCCAAAGAATTAGTTGTTTCAGTTAACGGAAATAGACAAT

             *                
       6669 CTACTTAATATTACATAA
        129 CCACTTAATATTACATAA

       6687 TTTGTGCTTA


Statistics
Matches: 130,  Mismatches: 13, Indels: 6
        0.87            0.09        0.04

Matches are distributed among these distances:
 177   12  0.09
 178  118  0.91

ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35


Consensus pattern (178 bp):   
AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTA
ATGTTTCAAGTATCAAAAATGCTTCCAAAGAATTAGTTGTTTCAGTTAACGGAAATAGACAATCC
ACTTAATATTACATAACTTTTACTTCAGTTGTCTAATTGAGATAATTC

Found at i:7426 original size:1 final size:1

Alignment explanation


    Indices: 7420--7455  Score: 54
    Period size: 1  Copynumber: 36.0  Consensus size: 1

       7410 TCTTTTCTTT

                                  **            
       7420 AAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       7456 TCT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   33  1.00

ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06


Consensus pattern (1 bp):   
A

Done.