Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023519.1 Corchorus olitorius cultivar O-4 contig23552, 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: 21214
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:4113 original size:12 final size:12

Alignment explanation


    Indices: 4074--4114  Score: 64
    Period size: 12  Copynumber: 3.4  Consensus size: 12

       4064 TTATGACGAT

                        
       4074 GAGGAGGATGAG
          1 GAGGAGGATGAG

              *         
       4086 GACGAGGATGAG
          1 GAGGAGGATGAG

                       *
       4098 GAGGAGGATGAT
          1 GAGGAGGATGAG

                 
       4110 GAGGA
          1 GAGGA

       4115 AGACGACTCT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.34, C:0.02, G:0.54, T:0.10


Consensus pattern (12 bp):   
GAGGAGGATGAG

Found at i:4197 original size:15 final size:15

Alignment explanation


    Indices: 4179--4211  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       4169 GGACGACAAT

                *          
       4179 GATGCTGGTGATGAA
          1 GATGATGGTGATGAA

                           
       4194 GATGATGGTGATGAA
          1 GATGATGGTGATGAA

               
       4209 GAT
          1 GAT

       4212 TTTGATAGTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.30, C:0.03, G:0.39, T:0.27


Consensus pattern (15 bp):   
GATGATGGTGATGAA

Found at i:8943 original size:21 final size:21

Alignment explanation


    Indices: 8918--8957  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8908 GATGATGACA

                      *          
       8918 ATGAGGAGGATGAGGACGAGG
          1 ATGAGGAGGAGGAGGACGAGG

                               
       8939 ATGAGGAGGAGGAGGACGA
          1 ATGAGGAGGAGGAGGACGA

       8958 TTAGGAAGAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.35, C:0.05, G:0.53, T:0.07


Consensus pattern (21 bp):   
ATGAGGAGGAGGAGGACGAGG

Found at i:9091 original size:15 final size:15

Alignment explanation


    Indices: 9073--9103  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9063 TAGTGATTGC

                      *    
       9073 AATGATATTGGTGAT
          1 AATGATATTGATGAT

                           
       9088 AATGATATTGATGAT
          1 AATGATATTGATGAT

             
       9103 A
          1 A

       9104 GCAATGACAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39


Consensus pattern (15 bp):   
AATGATATTGATGAT

Found at i:17181 original size:30 final size:30

Alignment explanation


    Indices: 17145--17205  Score: 88
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      17135 TTTTCTTTTC

                                           
      17145 TTTTTTTCTTCAATAA-AGATTTTAGGAACT
          1 TTTTTTTCTTCAA-AACAGATTTTAGGAACT

                   *  *                   
      17175 TTTTTTTTTTGAAAACAGATTTTAGGAACT
          1 TTTTTTTCTTCAAAACAGATTTTAGGAACT

             
      17205 T
          1 T

      17206 AAATTGCAAG


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29    2  0.07
  30   26  0.93

ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51


Consensus pattern (30 bp):   
TTTTTTTCTTCAAAACAGATTTTAGGAACT

Found at i:20022 original size:2 final size:2

Alignment explanation


    Indices: 20015--20041  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      20005 ATACTACATG

                                                    
      20015 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      20042 TATGTAGATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.