Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013915.1 Corchorus capsularis cultivar CVL-1 contig13936, 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: 11807
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:125 original size:28 final size:28

Alignment explanation


    Indices: 67--125  Score: 66
    Period size: 28  Copynumber: 2.1  Consensus size: 28

         57 TAAAATAATT

                               ***    * 
         67 ATAAAATATTGAATTTTTTTTTTAGATA
          1 ATAAAATATTGAATTTTTTAAATAGAAA

                                         
         95 ATAAAATATTGAATTTATTTAAAT-GAAA
          1 ATAAAATATTGAATTT-TTTAAATAGAAA

               
        123 ATA
          1 ATA

        126 GTGTTTTCAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  28   22  0.85
  29    4  0.15

ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46


Consensus pattern (28 bp):   
ATAAAATATTGAATTTTTTAAATAGAAA

Found at i:1063 original size:2 final size:2

Alignment explanation


    Indices: 1056--1087  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1046 GAGGCTCTCC

                                                           
       1056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1088 GTAGTATATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6307 original size:14 final size:15

Alignment explanation


    Indices: 6288--6318  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6278 TATCACGGCC

                           
       6288 AAACCT-AAACCCTA
          1 AAACCTAAAACCCTA

                           
       6302 AAACCTAAAACCCTA
          1 AAACCTAAAACCCTA

              
       6317 AA
          1 AA

       6319 CCTCATTATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.38
  15   10  0.62

ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13


Consensus pattern (15 bp):   
AAACCTAAAACCCTA

Done.