Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010479.1 Corchorus capsularis cultivar CVL-1 contig10500, 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: 9360
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30


Found at i:313 original size:17 final size:19

Alignment explanation


    Indices: 291--333  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

        281 TTTTTACAGG

                               
        291 GAAGAGAA-AG-AGAGAGA
          1 GAAGAGAACAGAAGAGAGA

                          *    
        308 GAAGAGAACAGAAGTGAGA
          1 GAAGAGAACAGAAGAGAGA

                    
        327 GAA-AGAA
          1 GAAGAGAA

        334 TTAGGGTTTC


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  17    8  0.35
  18    6  0.26
  19    9  0.39

ACGTcount: A:0.58, C:0.02, G:0.37, T:0.02


Consensus pattern (19 bp):   
GAAGAGAACAGAAGAGAGA

Found at i:1955 original size:33 final size:33

Alignment explanation


    Indices: 1918--2025  Score: 110
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       1908 AAAGGATCAT

                                   *    *     
       1918 GTGGCCGGTTG-TGGCCGGGCATGACCATGTCGC
          1 GTGGCCGG-TGATGGCCGGGCATCACCAAGTCGC

                                   *         
       1951 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGATGGCCGGGCATCACCAAGTCGC

            *    *    *            **        
       1984 ATGGCTGGTGTTGGCCGGGCATCTTCAAGTCGC
          1 GTGGCCGGTGATGGCCGGGCATCACCAAGTCGC

            *   *    
       2017 ATGGTCGGT
          1 GTGGCCGGT

       2026 CACTTGTGCT


Statistics
Matches: 65,  Mismatches: 9, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  32    2  0.03
  33   63  0.97

ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23


Consensus pattern (33 bp):   
GTGGCCGGTGATGGCCGGGCATCACCAAGTCGC

Found at i:8489 original size:33 final size:34

Alignment explanation


    Indices: 8419--8559  Score: 128
    Period size: 33  Copynumber: 4.3  Consensus size: 34

       8409 AAAGGATCAT

                *                  **  *    **
       8419 GTGGTCGGTTG-TGGCCGGGCATGGCCGAGTCAT
          1 GTGGCCGGTTGATGGCCGGGCATCTCCAAGTCGC

                                   **   *     
       8452 GTGGCCGGTTG-TGGCCGGGCATGACCATGTCGC
          1 GTGGCCGGTTGATGGCCGGGCATCTCCAAGTCGC

                                      *       
       8485 GTGGCCGG-TGATGGCCGGGCATCTCTAAGTCGC
          1 GTGGCCGGTTGATGGCCGGGCATCTCCAAGTCGC

            *          *     *                
       8518 ATGGCCGG-TGTTGGCCAGGCATCTCCAAGTCGC
          1 GTGGCCGGTTGATGGCCGGGCATCTCCAAGTCGC

            *        
       8551 ATGGCCGGT
          1 GTGGCCGGT

       8560 CACTTGTGCT


Statistics
Matches: 92,  Mismatches: 14, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
  32    2  0.02
  33   90  0.98

ACGTcount: A:0.11, C:0.26, G:0.40, T:0.22


Consensus pattern (34 bp):   
GTGGCCGGTTGATGGCCGGGCATCTCCAAGTCGC
Done.