Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021413.1 Corchorus olitorius cultivar O-4 contig21446, 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: 19947
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:58 original size:25 final size:24

Alignment explanation


    Indices: 29--82  Score: 72
    Period size: 25  Copynumber: 2.2  Consensus size: 24

         19 ACCCGCTATT

                     **           *  
         29 TTTTTCTGCTTTTTTTTTCTTTTTC
          1 TTTTTCTGCGCTTTTTTT-TTTATC

                                    
         54 TTTTTCTGCGCTTTTTTTTTTATC
          1 TTTTTCTGCGCTTTTTTTTTTATC

                 
         78 TTTTT
          1 TTTTT

         83 AGATTTTCTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  24   10  0.38
  25   16  0.62

ACGTcount: A:0.02, C:0.15, G:0.06, T:0.78


Consensus pattern (24 bp):   
TTTTTCTGCGCTTTTTTTTTTATC

Found at i:5876 original size:1 final size:1

Alignment explanation


    Indices: 5870--5896  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       5860 ACAGTTTAGG

                                       
       5870 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

       5897 GGAAAGGGGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:19743 original size:20 final size:20

Alignment explanation


    Indices: 19718--19796  Score: 97
    Period size: 20  Copynumber: 4.0  Consensus size: 20

      19708 TCTCTGATCT

                      *         
      19718 CGTCTCTCTCGAATTTCTTC
          1 CGTCTCTCTCAAATTTCTTC

                                
      19738 CGTCTCTCTCAAATTTCTTC
          1 CGTCTCTCTCAAATTTCTTC

                       * *       
      19758 TC-TCTCTCTCGATTTTCTTC
          1 -CGTCTCTCTCAAATTTCTTC

            **                 
      19778 TATCTCTCTCAAATTTCTT
          1 CGTCTCTCTCAAATTTCTT

      19797 TTGATTGTTG


Statistics
Matches: 51,  Mismatches: 6, Indels: 4
        0.84            0.10        0.07

Matches are distributed among these distances:
  20   50  0.98
  21    1  0.02

ACGTcount: A:0.13, C:0.33, G:0.05, T:0.49


Consensus pattern (20 bp):   
CGTCTCTCTCAAATTTCTTC

Found at i:19775 original size:40 final size:41

Alignment explanation


    Indices: 19715--19796  Score: 130
    Period size: 40  Copynumber: 2.0  Consensus size: 41

      19705 CTCTCTCTGA

                                    *                
      19715 TCTCGTCTCTCTCGAATTTCTTCCGTCTCTCTCAAATTTCT
          1 TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT

                           *       *                 
      19756 TCTC-TCTCTCTCGATTTTCTTCTATCTCTCTCAAATTTCT
          1 TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT

             
      19796 T
          1 T

      19797 TTGATTGTTG


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  40   34  0.89
  41    4  0.11

ACGTcount: A:0.12, C:0.33, G:0.05, T:0.50


Consensus pattern (41 bp):   
TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT
Done.