Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004872.1 Corchorus capsularis cultivar CVL-1 contig04890, 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: 9662
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33


Found at i:5606 original size:19 final size:16

Alignment explanation


    Indices: 5582--5624  Score: 52
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       5572 AGGTCAAAAT

                               
       5582 TAATAATTAAATTAATTAA
          1 TAATAATT-AATT--TTAA

                            
       5601 TAATAATT-ATTTTAA
          1 TAATAATTAATTTTAA

                     
       5616 TAATAATTA
          1 TAATAATTA

       5625 TCTTTAATTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  15   12  0.52
  17    3  0.13
  19    8  0.35

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


Consensus pattern (16 bp):   
TAATAATTAATTTTAA

Found at i:5617 original size:15 final size:16

Alignment explanation


    Indices: 5597--5632  Score: 65
    Period size: 15  Copynumber: 2.3  Consensus size: 16

       5587 ATTAAATTAA

                            
       5597 TTAATAATAATTAT-T
          1 TTAATAATAATTATCT

                            
       5612 TTAATAATAATTATCT
          1 TTAATAATAATTATCT

                 
       5628 TTAAT
          1 TTAAT

       5633 TACTCTCTAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   14  0.70
  16    6  0.30

ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53


Consensus pattern (16 bp):   
TTAATAATAATTATCT

Found at i:8283 original size:60 final size:60

Alignment explanation


    Indices: 8171--8285  Score: 149
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       8161 ATGAGAAATC

                                 *                    * *  *            
       8171 ACAAATACAGCCTACATAAAAGCGGCACAAAGGGCACATTGAGTTTATATGCAGTGGGAT
          1 ACAAATACAGCCTACATAAAACCGGCACAAAGGGCACATTGAATCTACATGCAGTGGGAT

                   *   *                      * **                 
       8231 ACAAATATAGCTTACATAAAACCGGCACAAAGGGTATGTTGAATCTACATGCAGT
          1 ACAAATACAGCCTACATAAAACCGGCACAAAGGGCACATTGAATCTACATGCAGT

       8286 AGGACTCGAA


Statistics
Matches: 46,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  60   46  1.00

ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22


Consensus pattern (60 bp):   
ACAAATACAGCCTACATAAAACCGGCACAAAGGGCACATTGAATCTACATGCAGTGGGAT
Done.