Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005828.1 Corchorus capsularis cultivar CVL-1 contig05846, 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: 3409
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34


Found at i:2079 original size:41 final size:41

Alignment explanation


    Indices: 1987--2079  Score: 134
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       1977 TCATCATAAT

                                                     
       1987 ATATCCTTCAAAAATAAATCCTTAAAAAAATACATTCTTAA
          1 ATATCCTTCAAAAATAAATCCTTAAAAAAATACATTCTTAA

                  *                 *    *   *        
       2028 ATA-CTTTTCAAAAATAAATCCTTTAAAAGATATATTCTTAA
          1 ATATC-CTTCAAAAATAAATCCTTAAAAAAATACATTCTTAA

                       
       2069 ATATCCTTCAA
          1 ATATCCTTCAA

       2080 CAACAGAGGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  40    1  0.02
  41   43  0.96
  42    1  0.02

ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35


Consensus pattern (41 bp):   
ATATCCTTCAAAAATAAATCCTTAAAAAAATACATTCTTAA

Found at i:3343 original size:2 final size:2

Alignment explanation


    Indices: 3336--3399  Score: 80
    Period size: 2  Copynumber: 32.5  Consensus size: 2

       3326 TTTCTACCAA

                                                          *               
       3336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC AT AT A- AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                                
       3376 AT ACT AT AT AT A- ACT AT AT AT AT A
          1 AT A-T AT AT AT AT A-T AT AT AT AT A

       3400 ACTACATATA


Statistics
Matches: 56,  Mismatches: 1, Indels: 10
        0.84            0.01        0.15

Matches are distributed among these distances:
   1    3  0.05
   2   50  0.89
   3    3  0.05

ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Done.