Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015896.1 Corchorus olitorius cultivar O-4 contig15929, 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: 22861
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1229 original size:21 final size:19

Alignment explanation


    Indices: 1193--1231  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 19

       1183 GTTATTCACC

                       *       
       1193 AATTAAGCAATCGATAAAG
          1 AATTAAGCAATAGATAAAG

                                
       1212 AATTAAGAACAATAGATAAA
          1 AATTAAG--CAATAGATAAA

       1232 CCAAGCATAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    7  0.41
  21   10  0.59

ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21


Consensus pattern (19 bp):   
AATTAAGCAATAGATAAAG

Found at i:2357 original size:17 final size:18

Alignment explanation


    Indices: 2335--2368  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2325 ACTAAGTCTT

                              
       2335 AGAATTA-CTGCATTATC
          1 AGAATTATCTGCATTATC

                    *        
       2352 AGAATTATTTGCATTAT
          1 AGAATTATCTGCATTAT

       2369 TGCATCATAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    7  0.47
  18    8  0.53

ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41


Consensus pattern (18 bp):   
AGAATTATCTGCATTATC

Found at i:16692 original size:34 final size:33

Alignment explanation


    Indices: 16609--16692  Score: 87
    Period size: 34  Copynumber: 2.5  Consensus size: 33

      16599 GAAGACGGAC

                             *        * *    
      16609 CGCGCCAGCACGGGGCATAACCAGGCTAGCCCG
          1 CGCGCCAGCACGGGGCACAACCAGGCCAACCCG

              *     *  *       *              
      16642 CGTGCCAGTAGGGGGGCACCACCAGGCCAACCCG
          1 CGCGCCAGCA-CGGGGCACAACCAGGCCAACCCG

                             
      16676 CGCGCCAAGCACGGGGC
          1 CGCGCC-AGCACGGGGC

      16693 TGCAGCCTGC


Statistics
Matches: 39,  Mismatches: 10, Indels: 3
        0.75            0.19        0.06

Matches are distributed among these distances:
  33    8  0.21
  34   28  0.72
  35    3  0.08

ACGTcount: A:0.20, C:0.39, G:0.36, T:0.05


Consensus pattern (33 bp):   
CGCGCCAGCACGGGGCACAACCAGGCCAACCCG

Found at i:17034 original size:21 final size:21

Alignment explanation


    Indices: 17010--17050  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      17000 GTTTAAGAAA

                       **        
      17010 AGAAGTCGACTTGAGCAAGTG
          1 AGAAGTCGACTAAAGCAAGTG

                                
      17031 AGAAGTCGACTAAAGCAAGT
          1 AGAAGTCGACTAAAGCAAGT

      17051 TGATAAGAAG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17


Consensus pattern (21 bp):   
AGAAGTCGACTAAAGCAAGTG
Done.