Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012857.1 Corchorus capsularis cultivar CVL-1 contig12878, 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: 34814
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:1201 original size:33 final size:33

Alignment explanation


    Indices: 1159--1279  Score: 181
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       1149 TTTTTATACT

                                        *    
       1159 GAGCCTCCCCACTAGGACGGCTTCGCCACGGCG
          1 GAGCCTCCCCACTAGGACGGCTTCGCCATGGCG

                              *   *  *       
       1192 GAGCCTCCCCACTAGGACAGCTCCGGCATGGCG
          1 GAGCCTCCCCACTAGGACGGCTTCGCCATGGCG

                                              
       1225 GAGCCTCCCCACTAGGACGGC-TCAGCCATGGCG
          1 GAGCCTCCCCACTAGGACGGCTTC-GCCATGGCG

                 *                
       1258 GAGCCGCCCCACTAGGACGGCT
          1 GAGCCTCCCCACTAGGACGGCT

       1280 AGACAATTTT


Statistics
Matches: 78,  Mismatches: 8, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  32    1  0.01
  33   77  0.99

ACGTcount: A:0.17, C:0.40, G:0.31, T:0.12


Consensus pattern (33 bp):   
GAGCCTCCCCACTAGGACGGCTTCGCCATGGCG

Found at i:1313 original size:21 final size:21

Alignment explanation


    Indices: 1284--1326  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1274 ACGGCTAGAC

                *       *    *   
       1284 AATTTTTTTTTTTAAAATAAT
          1 AATTATTTTTTTAAAAAAAAT

                                 
       1305 AATTATTTTTTTAAAAAAAAT
          1 AATTATTTTTTTAAAAAAAAT

             
       1326 A
          1 A

       1327 GTCGAGGTCA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

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


Consensus pattern (21 bp):   
AATTATTTTTTTAAAAAAAAT

Found at i:8313 original size:2 final size:2

Alignment explanation


    Indices: 8302--8334  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       8292 CAATGGGTAC

                                                              
       8302 AT AT -T AT 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 AT AT AT AT

       8335 CTACCTAATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

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


Consensus pattern (2 bp):   
AT

Done.