Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019629.1 Corchorus olitorius cultivar O-4 contig19662, 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: 27308
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:5555 original size:16 final size:16

Alignment explanation


    Indices: 5534--5566  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       5524 TATCAAATAA

                            
       5534 TTACCCTATTGTTAAT
          1 TTACCCTATTGTTAAT

                            
       5550 TTACCCTATTGTTAAT
          1 TTACCCTATTGTTAAT

             
       5566 T
          1 T

       5567 GGATTTTGTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52


Consensus pattern (16 bp):   
TTACCCTATTGTTAAT

Found at i:21053 original size:18 final size:19

Alignment explanation


    Indices: 21026--21079  Score: 60
    Period size: 17  Copynumber: 3.0  Consensus size: 19

      21016 AAATTGACAG

                          *    
      21026 CAAAAA-AAAAAACGAAAA
          1 CAAAAACAAAAAACAAAAA

              *                
      21044 C-GAAAC-AAAAACAAAAA
          1 CAAAAACAAAAAACAAAAA

                         *     
      21061 CAAAAACAAAAAATAAAAA
          1 CAAAAACAAAAAACAAAAA

      21080 AATGAAAACG


Statistics
Matches: 29,  Mismatches: 4, Indels: 5
        0.76            0.11        0.13

Matches are distributed among these distances:
  17   14  0.48
  18    5  0.17
  19   10  0.34

ACGTcount: A:0.81, C:0.13, G:0.04, T:0.02


Consensus pattern (19 bp):   
CAAAAACAAAAAACAAAAA

Found at i:21079 original size:6 final size:6

Alignment explanation


    Indices: 21026--21072  Score: 60
    Period size: 6  Copynumber: 8.0  Consensus size: 6

      21016 AAATTGACAG

                   *       *       *                               
      21026 CAAAAA AAAAAA CGAAAA C-GAAA CAAAAA CAAAAA CAAAAA CAAAAA
          1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA

      21073 ATAAAAAAAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
   5    4  0.11
   6   31  0.89

ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00


Consensus pattern (6 bp):   
CAAAAA

Found at i:21196 original size:35 final size:35

Alignment explanation


    Indices: 21150--21232  Score: 130
    Period size: 35  Copynumber: 2.4  Consensus size: 35

      21140 ACTTTTATCA

                  *                            
      21150 AATTTTGAATTCATCAATAAATATTCATAAAGTAG
          1 AATTTTTAATTCATCAATAAATATTCATAAAGTAG

                                      *      * 
      21185 AATTTTTAATTCATCAATAAATATTCCTAAAGTTG
          1 AATTTTTAATTCATCAATAAATATTCATAAAGTAG

               *         
      21220 AATATTTAATTCA
          1 AATTTTTAATTCA

      21233 AAATAACTAG


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  35   44  1.00

ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41


Consensus pattern (35 bp):   
AATTTTTAATTCATCAATAAATATTCATAAAGTAG

Found at i:21937 original size:98 final size:93

Alignment explanation


    Indices: 21750--21940  Score: 301
    Period size: 98  Copynumber: 2.0  Consensus size: 93

      21740 TGGTCCTTGC

                                              *                              
      21750 TAGAGTTAATATATCGAGTATGAAAGGTCAAAACTCTCCCACGTTTGTGAAATTAAATTTCAGTT
          1 TAGAGTTAATATATCGAGTATGAAAGGTCAAAACCCTCCCACGTTTGTGAAATTAAATTTCAGTT

              *                         
      21815 AATACCTTACTACATCGACCAATAACTT
         66 AACACCTTACTACATCGACCAATAACTT

                   *                                                         
      21843 TAGAGTTGATATATCGAGTATGAAAGGTCAAAACCCTCCCCAGATGCGTTTGTGAAATTAAATTT
          1 TAGAGTTAATATATCGAGTATGAAAGGTCAAAACCCT-CCC--A--CGTTTGTGAAATTAAATTT

              *                              
      21908 CATTTAACACCTTACTACATCGACCAATAACTT
         61 CAGTTAACACCTTACTACATCGACCAATAACTT

      21941 GTTGATGGCT


Statistics
Matches: 89,  Mismatches: 4, Indels: 5
        0.91            0.04        0.05

Matches are distributed among these distances:
  93   35  0.39
  94    3  0.03
  96    1  0.01
  98   50  0.56

ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31


Consensus pattern (93 bp):   
TAGAGTTAATATATCGAGTATGAAAGGTCAAAACCCTCCCACGTTTGTGAAATTAAATTTCAGTT
AACACCTTACTACATCGACCAATAACTT
Done.