Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000027.1 Corchorus olitorius cultivar O-4 contig00027, 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, 877

Length: 1463
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38


Found at i:600 original size:15 final size:15

Alignment explanation


    Indices: 580--608  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        570 TGTTATAATA

                           
        580 ATATCTCAATTTCTC
          1 ATATCTCAATTTCTC

                          
        595 ATATCTCAATTTCT
          1 ATATCTCAATTTCT

        609 TTCCTTTGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48


Consensus pattern (15 bp):   
ATATCTCAATTTCTC

Found at i:717 original size:142 final size:140

Alignment explanation


    Indices: 450--704  Score: 410
    Period size: 142  Copynumber: 1.8  Consensus size: 140

        440 TGTCCATTGA

                  *                                                          
        450 TCTCATCTTCAATTTCTCTCCTTTGTATTATAAGTATATAATTTTCTTAAAAAATTATTTTAAAA
          1 TCTCATATTCAATTTCTCTCCTTTGTATTATAAGTATATAATTTTCTTAAAAAATTATTTTAAAA

                                *                                            
        515 TATATGTGGATGGAAACATATATATCTGAAATTGATTTATAGGTTATGGTTATTATGTTATAATA
         66 TATATGTGGAT-GAAACATACATATCTGAAATTGATTTATAGGTTATGGTTATTATGTTATAATA

                       
        580 ATATCTCAATT
        130 ATATCTCAATT

                              *             *                        *       
        591 TCTCATATCTCAATTTCTTTCCTTTGTATTATCAGTATATAATTTTCTT-AAAAATTGTTTTAAA
          1 TCTCATAT-TCAATTTCTCTCCTTTGTATTATAAGTATATAATTTTCTTAAAAAATTATTTTAAA

            *                                                    
        655 CTATATGTGGAT-AAA-A-ACATATCTGAAATTGATTTATAGGTTATGGTTAT
         65 ATATATGTGGATGAAACATACATATCTGAAATTGATTTATAGGTTATGGTTAT

        705 GTTATTATGT


Statistics
Matches: 107,  Mismatches: 6, Indels: 6
        0.90            0.05        0.05

Matches are distributed among these distances:
 137   33  0.31
 138    1  0.01
 139    3  0.03
 141   32  0.30
 142   38  0.36

ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46


Consensus pattern (140 bp):   
TCTCATATTCAATTTCTCTCCTTTGTATTATAAGTATATAATTTTCTTAAAAAATTATTTTAAAA
TATATGTGGATGAAACATACATATCTGAAATTGATTTATAGGTTATGGTTATTATGTTATAATAA
TATCTCAATT

Found at i:722 original size:14 final size:13

Alignment explanation


    Indices: 695--731  Score: 56
    Period size: 14  Copynumber: 2.7  Consensus size: 13

        685 GATTTATAGG

                          
        695 TTATGGTTATGTTA
          1 TTAT-GTTATGTTA

                          
        709 TTATGTTATGGTTA
          1 TTATGTTAT-GTTA

                     
        723 TTATGTTAT
          1 TTATGTTAT

        732 AAGTTTCCCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    5  0.23
  14   17  0.77

ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59


Consensus pattern (13 bp):   
TTATGTTATGTTA
Done.