Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005840.1 Corchorus capsularis cultivar CVL-1 contig05858, 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: 3473
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35


Found at i:895 original size:29 final size:29

Alignment explanation


    Indices: 837--910  Score: 96
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        827 GTAGATTAAG

                *        *               
        837 AATGTCCAAAAT-ACCCCCTAAATGCAAA
          1 AATGACCAAAATGCCCCCCTAAATGCAAA

                                 *   **  
        865 AATGACCAAAATGCCCCCCTAGATGTGAA
          1 AATGACCAAAATGCCCCCCTAAATGCAAA

                             
        894 AATGACCAAAATGCCCC
          1 AATGACCAAAATGCCCC

        911 TGGATGACCC


Statistics
Matches: 40,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  28   11  0.28
  29   29  0.73

ACGTcount: A:0.42, C:0.30, G:0.12, T:0.16


Consensus pattern (29 bp):   
AATGACCAAAATGCCCCCCTAAATGCAAA

Found at i:1294 original size:43 final size:44

Alignment explanation


    Indices: 1147--1297  Score: 196
    Period size: 44  Copynumber: 3.5  Consensus size: 44

       1137 AAGAGAGTAG

                *    *        *                         
       1147 TCTGTGGTCGACTTTGATGACTGTTGAAACTGAAAAAGACCTGT
          1 TCTGAGGTCAACTTTGATAACTGTTGAAACTGAAAAAGACCTGT

                                  **              *     
       1191 TCTGAGGTCAACTTTGATAACTACTGAAACTGAAAAAGTCCTGT
          1 TCTGAGGTCAACTTTGATAACTGTTGAAACTGAAAAAGACCTGT

                       *                     *          
       1235 TCTGAGGTCAATTTTGATAACTGTTG-AACTGAGAAAGACCTGT
          1 TCTGAGGTCAACTTTGATAACTGTTGAAACTGAAAAAGACCTGT

             *  *    *          
       1278 TTTGGGGTCGACTTTGATAA
          1 TCTGAGGTCAACTTTGATAA

       1298 TCTTATTGAA


Statistics
Matches: 92,  Mismatches: 15, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  43   31  0.34
  44   61  0.66

ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32


Consensus pattern (44 bp):   
TCTGAGGTCAACTTTGATAACTGTTGAAACTGAAAAAGACCTGT
Done.