Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007186.1 Corchorus olitorius cultivar O-4 contig07211, 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: 4101
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35


Found at i:116 original size:22 final size:22

Alignment explanation


    Indices: 26--211  Score: 94
    Period size: 22  Copynumber: 8.5  Consensus size: 22

         16 TCATAGTGTT

                      *       **   
         26 GGTTATCAAATTTTCATTGGGAA
          1 GGTTATCAAAATTTCA-TAAGAA

                                 * 
         49 -GTTATCAAAATTTCAT-AGTGA
          1 GGTTATCAAAATTTCATAAG-AA

             *            * *  * * 
         70 GATCT-TCAAAATTCCTTAGGGA
          1 GGT-TATCAAAATTTCATAAGAA

                 *                
         92 GGTTAACAAAATTTCATAAGAA
          1 GGTTATCAAAATTTCATAAGAA

                 **            *  
        114 GGTTAAAAAAATTT-ATAAAAA
          1 GGTTATCAAAATTTCATAAGAA

                *  *     *        *
        135 GGTTCTCGAAATTCCAT-AGTAT
          1 GGTTATCAAAATTTCATAAG-AA

            *     *            *  
        157 CGTTATTAAAATTTCATAAAAA
          1 GGTTATCAAAATTTCATAAGAA

                          *     * 
        179 GGTTATCAAAATTTTATAAGGA
          1 GGTTATCAAAATTTCATAAGAA

               *       
        201 GGTCATCAAAA
          1 GGTTATCAAAA

        212 ATAGTGTAAT


Statistics
Matches: 120,  Mismatches: 35, Indels: 17
        0.70            0.20        0.10

Matches are distributed among these distances:
  20    1  0.01
  21   19  0.16
  22   97  0.81
  23    3  0.03

ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33


Consensus pattern (22 bp):   
GGTTATCAAAATTTCATAAGAA

Found at i:324 original size:2 final size:2

Alignment explanation


    Indices: 317--371  Score: 73
    Period size: 2  Copynumber: 29.5  Consensus size: 2

        307 CTAAAACTAG

                                                                          
        317 TA TA TA TA TA TA TA -A TA TA TA TA T- TA TA TA TA -A TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                        *            
        356 TA TA TA -A AA TA TA TA T
          1 TA TA TA TA TA TA TA TA T

        372 GTTTTGTTTG


Statistics
Matches: 48,  Mismatches: 1, Indels: 8
        0.84            0.02        0.14

Matches are distributed among these distances:
   1    4  0.08
   2   44  0.92

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:336 original size:13 final size:12

Alignment explanation


    Indices: 317--371  Score: 73
    Period size: 11  Copynumber: 4.9  Consensus size: 12

        307 CTAAAACTAG

                        
        317 TATATATATATA
          1 TATATATATATA

                        
        329 TA-ATATATATA
          1 TATATATATATA

                        
        340 T-TATATATA-A
          1 TATATATATATA

                        
        350 TATATATATATA
          1 TATATATATATA

              *        
        362 -AAATATATAT
          1 TATATATATAT

        372 GTTTTGTTTG


Statistics
Matches: 39,  Mismatches: 1, Indels: 7
        0.83            0.02        0.15

Matches are distributed among these distances:
  10    2  0.05
  11   34  0.87
  12    3  0.08

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (12 bp):   
TATATATATATA

Found at i:3603 original size:2 final size:2

Alignment explanation


    Indices: 3596--3621  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       3586 TAGCTTGGAA

                                                  
       3596 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       3622 GCATATAATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.