Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011450.1 Corchorus capsularis cultivar CVL-1 contig11471, 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: 15056
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27


Found at i:1204 original size:49 final size:48

Alignment explanation


    Indices: 1124--1554  Score: 245
    Period size: 49  Copynumber: 8.9  Consensus size: 48

       1114 AAATTTTCGG

                                                            
       1124 TTTTCACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
          1 TTTTCACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                *                **    *                 * * 
       1172 TTTTTACTTGCATTTTCCCAAGGTGCCTTTCCCGGACGGAAGGCACTGA
          1 TTTTCACTTGC-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                        *           **            **      * * 
       1221 TTATTGC-C-TGTTTTTCCCAAAACACCCTTCCCGGACAAAAGGCACTAA
          1 TT-TT-CACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                    *                     *          **  *   
       1269 TCTTT-ACCTG-TTTTCCCAAAATGCCCTTTCCGGACGGAAAACACTTA
          1 T-TTTCACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                               *                    *  * **   
       1316 TTTT-ACTTGCTATTTTCCAAAAATGCCCTTCCCGGACGGGAGACGCTTA
          1 TTTTCACTTGC--TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                ** * *                         *                
       1365 TTTTTTCCTACTTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCAGTTT-
          1 TTTTCACTTGCTTTTCCCAAAATG-CCCTTCCCGGACGGAAGG--CA-TTTA

             *    *                         ** *             *   
       1416 TCTTCATTTG--TTTCCCAAAATGCCCCTTCCTAGTCGGAAGGTCCCAGCTT-
          1 TTTTCACTTGCTTTTCCCAAAATG-CCCTTCCCGGACGGAAGG---CA-TTTA

             *    *               *                     * * 
       1466 TCTTCATTTG--TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAA
          1 TTTTCACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

                      *        *    *  *               
       1512 TTTTTCACTTACTTTTTCCTAAAACGCTCTTCCCGGACGGAAG
          1 -TTTTCACTTGC-TTTTCCCAAAATGCCCTTCCCGGACGGAAG

       1555 ACGTTAGTTC


Statistics
Matches: 304,  Mismatches: 59, Indels: 38
        0.76            0.15        0.09

Matches are distributed among these distances:
  45    2  0.01
  46    9  0.03
  47   38  0.12
  48   56  0.18
  49  132  0.43
  50   60  0.20
  51    5  0.02
  52    2  0.01

ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32


Consensus pattern (48 bp):   
TTTTCACTTGCTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA

Found at i:13460 original size:13 final size:13

Alignment explanation


    Indices: 13442--13467  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      13432 CTGAGATGTT

                         
      13442 CCTTTGTTATCTA
          1 CCTTTGTTATCTA

                         
      13455 CCTTTGTTATCTA
          1 CCTTTGTTATCTA

      13468 TCCACATCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54


Consensus pattern (13 bp):   
CCTTTGTTATCTA

Found at i:14790 original size:43 final size:43

Alignment explanation


    Indices: 14729--14813  Score: 161
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      14719 TGACCATTAT

                       *                               
      14729 ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCGC
          1 ATTTACTTTCAATTTCATTAAGCATATCCACATTTGTTTTCGC

                                                      
      14772 ATTTACTTTCAATTTCATTAAGCATATCCACATTTGTTTTCG
          1 ATTTACTTTCAATTTCATTAAGCATATCCACATTTGTTTTCG

      14814 TAGCATAGGG


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   41  1.00

ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48


Consensus pattern (43 bp):   
ATTTACTTTCAATTTCATTAAGCATATCCACATTTGTTTTCGC
Done.