Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020949.1 Corchorus olitorius cultivar O-4 contig20982, 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: 6178
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1074 original size:13 final size:13

Alignment explanation


    Indices: 1043--1202  Score: 99
    Period size: 13  Copynumber: 12.8  Consensus size: 13

       1033 GTGAAACAAG

                       * 
       1043 TCTTCATCAAAAT
          1 TCTTCATCAAAGT

             *           
       1056 TATTCATCAAAGT
          1 TCTTCATCAAAGT

                  *      
       1069 TCTTCAAC-AAG-
          1 TCTTCATCAAAGT

               *          
       1080 TCTCCA-CGAAAGT
          1 TCTTCATC-AAAGT

             *           
       1093 TATTCATCAAAGT
          1 TCTTCATCAAAGT

                  *      
       1106 TCTTCAAC-AAG-
          1 TCTTCATCAAAGT

               *  *      
       1117 TCTCCACCAAAGT
          1 TCTTCATCAAAGT

             *           
       1130 TATTCATCAAAGT
          1 TCTTCATCAAAGT

                  *      
       1143 TCTTCAAC-AAG-
          1 TCTTCATCAAAGT

              *            
       1154 TCCTCATCAAATTGT
          1 TCTTCATCAAA--GT

                  *      
       1169 TCTTCAAC-AAGT
          1 TCTTCATCAAAGT

                          
       1181 T-TTCACTC--AGT
          1 TCTTCA-TCAAAGT

                       
       1192 TCTTCATCAAA
          1 TCTTCATCAAA

       1203 TTTTCCACCA


Statistics
Matches: 112,  Mismatches: 21, Indels: 28
        0.70            0.13        0.17

Matches are distributed among these distances:
  10    1  0.01
  11   27  0.24
  12   25  0.22
  13   49  0.44
  14    4  0.04
  15    6  0.05

ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34


Consensus pattern (13 bp):   
TCTTCATCAAAGT

Found at i:1078 original size:37 final size:37

Alignment explanation


    Indices: 1037--1164  Score: 197
    Period size: 37  Copynumber: 3.5  Consensus size: 37

       1027 CCAAGAGTGA

                     *       *                   
       1037 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

                                                  
       1074 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC

                        *                        
       1111 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

                              
       1148 AACAAGTC-CTCATCAAA
          1 AACAAGTCTC-CATCAAA

       1165 TTGTTCTTCA


Statistics
Matches: 85,  Mismatches: 3, Indels: 6
        0.90            0.03        0.06

Matches are distributed among these distances:
  36    2  0.02
  37   82  0.96
  38    1  0.01

ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30


Consensus pattern (37 bp):   
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

Done.