Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006120.1 Corchorus capsularis cultivar CVL-1 contig06138, 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: 17745
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:11930 original size:2 final size:2

Alignment explanation


    Indices: 11918--11952  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      11908 TGCAAAAGGG

                  *                                             
      11918 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11953 GAAAATCTCT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:13450 original size:22 final size:23

Alignment explanation


    Indices: 13425--13469  Score: 65
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      13415 TGGGTGGATT

                 *                 
      13425 ATATTTAT-ATTTAAAGTACTTG
          1 ATATTCATAATTTAAAGTACTTG

                                   
      13447 ATATTCATCAATTTAAAGTACTT
          1 ATATTCAT-AATTTAAAGTACTT

      13470 TAATTTAAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    7  0.35
  24   13  0.65

ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47


Consensus pattern (23 bp):   
ATATTCATAATTTAAAGTACTTG

Found at i:13476 original size:15 final size:15

Alignment explanation


    Indices: 13456--13484  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      13446 GATATTCATC

                           
      13456 AATTTAAAGTACTTT
          1 AATTTAAAGTACTTT

                          
      13471 AATTTAAAGTACTT
          1 AATTTAAAGTACTT

      13485 GCAAAGGGGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45


Consensus pattern (15 bp):   
AATTTAAAGTACTTT

Found at i:17479 original size:29 final size:28

Alignment explanation


    Indices: 17431--17485  Score: 74
    Period size: 29  Copynumber: 1.9  Consensus size: 28

      17421 AAGTGGAGCG

                         *              
      17431 AAAATAGCAAGTTGGTCCCTCAAGTGAA
          1 AAAATAGCAAGTTAGTCCCTCAAGTGAA

                       *         *     
      17459 AAAATATGCAATTTAGTCCCTGAAGTG
          1 AAAATA-GCAAGTTAGTCCCTCAAGTG

      17486 GAGTTAACTG


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

Matches are distributed among these distances:
  28    6  0.26
  29   17  0.74

ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25


Consensus pattern (28 bp):   
AAAATAGCAAGTTAGTCCCTCAAGTGAA
Done.