Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013406.1 Corchorus olitorius cultivar O-4 contig13439, 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: 12572
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:2061 original size:21 final size:18

Alignment explanation


    Indices: 2021--2054  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2011 TTAATTTTAA

                *             
       2021 TTATTTTTTTATGTGTGT
          1 TTATGTTTTTATGTGTGT

                             
       2039 TTATGTTTTTAT-TGTG
          1 TTATGTTTTTATGTGTG

       2055 GTGGTTTGAT


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

Matches are distributed among these distances:
  17    4  0.27
  18   11  0.73

ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71


Consensus pattern (18 bp):   
TTATGTTTTTATGTGTGT

Found at i:2978 original size:37 final size:37

Alignment explanation


    Indices: 2930--3004  Score: 132
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       2920 CCCCGCTTTG

                                    *            
       2930 CATCATTTAAGTTTTTGCCTTCCTGAATGTTACTAAT
          1 CATCATTTAAGTTTTTGCCTTCCTAAATGTTACTAAT

                             *                   
       2967 CATCATTTAAGTTTTTGTCTTCCTAAATGTTACTAAT
          1 CATCATTTAAGTTTTTGCCTTCCTAAATGTTACTAAT

             
       3004 C
          1 C

       3005 TTTTACTTGA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  37   36  1.00

ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47


Consensus pattern (37 bp):   
CATCATTTAAGTTTTTGCCTTCCTAAATGTTACTAAT

Found at i:5200 original size:26 final size:27

Alignment explanation


    Indices: 5162--5234  Score: 85
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       5152 AGGGTCATCT

                                *       
       5162 AGGGACATTTTGGTCATTTTTACACT-A
          1 AGGG-CATTTTGGTCATTTTCACACTCA

                              *  * *   
       5189 AGGGCATTTTGGTCATTTGCAGATTCA
          1 AGGGCATTTTGGTCATTTTCACACTCA

            *                  
       5216 GGGGCATTTTGGTCATTTT
          1 AGGGCATTTTGGTCATTTT

       5235 AGGTCCACTT


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  26   17  0.44
  27   22  0.56

ACGTcount: A:0.21, C:0.14, G:0.25, T:0.41


Consensus pattern (27 bp):   
AGGGCATTTTGGTCATTTTCACACTCA

Found at i:6079 original size:19 final size:18

Alignment explanation


    Indices: 6055--6090  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6045 TGAAGATTTA

                               
       6055 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       6074 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       6091 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:11348 original size:30 final size:29

Alignment explanation


    Indices: 11305--11361  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 29

      11295 TTAGGATTAG

                                         
      11305 TTATTTATGCTTTAATTTGCAA-TTTCCT
          1 TTATTTATGCTTTAATTTGCAAGTTTCCT

                                *        
      11333 TTATCTTATGTCTTTAATTTTCAAGTTTC
          1 TTAT-TTATG-CTTTAATTTGCAAGTTTC

      11362 ATTAATAAAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  28    4  0.16
  29    5  0.20
  30   12  0.48
  31    4  0.16

ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58


Consensus pattern (29 bp):   
TTATTTATGCTTTAATTTGCAAGTTTCCT
Done.