Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007446.1 Corchorus capsularis cultivar CVL-1 contig07467, 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: 22229
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29


Found at i:12265 original size:183 final size:183

Alignment explanation


    Indices: 11966--12374  Score: 479
    Period size: 183  Copynumber: 2.2  Consensus size: 183

      11956 ACTAAACCCC

                              *        *   *                                *
      11966 CTGATTTTTGGCTTAATTGACTAATTTTGCCTAAATCACAAAAACCCTAATTCACCAAGCAAGCT
          1 CTGATTTTTGGCTTAATTAAC-AATTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCAAGCC

                         *                        *  *          *            
      12031 AATTTGCCGCCTATGTTGCAATTTTTGCAAAAAAGGACTCGGCTCATTAGGGGTAGCTTG-GTTC
         65 AATTTGCCGCCTAAGTTGCAATTTTTGCAAAAAAGGACACGCCTCATTAGGGATAGCTTGAGTTC

              *     *           *               *                   
      12095 ATTAAATTGGGCTT-ATATTTATGTGATATAACCTAGTTTT-AAGGGTTTAACCTA
        130 ATCAAATTAGG-TTCATATTCATGTGATATAACCTAATTTTCAAGGGTTT-ACCTA

                    *                                           * *     *    
      12149 CTGATTTTAGGCTTAATTAATCAATTTGGCCAAAATCACAAAAACCCTAATTTATCAAGCTAGCC
          1 CTGATTTTTGGCTTAATTAA-CAATTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCAAGCC

                                              *  *                  *      * 
      12214 AATTTGCCGCC-AAGTTGCAATTTTTGCAAAAATGGGTCACGACCT-ATTAGGGATTGCTTGATT
         65 AATTTGCCGCCTAAGTTGCAATTTTTGCAAAAA-AGGACACG-CCTCATTAGGGATAGCTTGAGT

                              *            *                        
      12277 TCATCAAATTAGGTTCATGTTCATGTGATATGACCTAATTTTCAAGGGTTTACCTA
        128 TCATCAAATTAGGTTCATATTCATGTGATATAACCTAATTTTCAAGGGTTTACCTA

                                       *          *    
      12333 CTGATTTTTGGC-TAATTTAACCAATTAGGCCGAAAATTACAA
          1 CTGATTTTTGGCTTAA-TTAA-CAATTTGGCC-AAAATCACAA

      12375 GAAAATTACC


Statistics
Matches: 192,  Mismatches: 26, Indels: 14
        0.83            0.11        0.06

Matches are distributed among these distances:
 182   20  0.10
 183   89  0.46
 184   66  0.34
 185   17  0.09

ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35


Consensus pattern (183 bp):   
CTGATTTTTGGCTTAATTAACAATTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCAAGCCA
ATTTGCCGCCTAAGTTGCAATTTTTGCAAAAAAGGACACGCCTCATTAGGGATAGCTTGAGTTCA
TCAAATTAGGTTCATATTCATGTGATATAACCTAATTTTCAAGGGTTTACCTA

Found at i:21926 original size:5 final size:5

Alignment explanation


    Indices: 21916--21940  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

      21906 GCAGATATAT

                                         
      21916 GTATG GTATG GTATG GTATG GTATG
          1 GTATG GTATG GTATG GTATG GTATG

      21941 TATAGTAACA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40


Consensus pattern (5 bp):   
GTATG

Done.