Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013684.1 Corchorus capsularis cultivar CVL-1 contig13705, 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: 16949
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:3879 original size:11 final size:11

Alignment explanation


    Indices: 3865--3902  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       3855 ATTCATAACA

                       
       3865 AATTTATAATT
          1 AATTTATAATT

                       
       3876 AATTTATAATT
          1 AATTTATAATT

                        
       3887 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       3898 TATTT
          1 AATTT

       3903 TTTATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:4229 original size:29 final size:30

Alignment explanation


    Indices: 4186--4253  Score: 111
    Period size: 29  Copynumber: 2.3  Consensus size: 30

       4176 CGTTTAGATG

                                          
       4186 TTTTGCCCCCCGAACTTCAATTTT-GGACA
          1 TTTTGCCCCCCGAACTTCAATTTTGGGACA

                      *                  *
       4215 TTTTGCCCCCTGAACTTCAATTTTGGGACG
          1 TTTTGCCCCCCGAACTTCAATTTTGGGACA

                     
       4245 TTTTGCCCC
          1 TTTTGCCCC

       4254 ATCAACCTAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  29   23  0.64
  30   13  0.36

ACGTcount: A:0.16, C:0.31, G:0.16, T:0.37


Consensus pattern (30 bp):   
TTTTGCCCCCCGAACTTCAATTTTGGGACA

Found at i:6008 original size:16 final size:16

Alignment explanation


    Indices: 5983--6013  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       5973 TTTCATTGTG

                            
       5983 CTCTCATTTTCTTTCT
          1 CTCTCATTTTCTTTCT

                 *         
       5999 CTCTCTTTTTCTTTC
          1 CTCTCATTTTCTTTC

       6014 AATATCTTAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65


Consensus pattern (16 bp):   
CTCTCATTTTCTTTCT

Found at i:16539 original size:13 final size:13

Alignment explanation


    Indices: 16521--16545  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      16511 TTCAATGTTC

                         
      16521 TAAATATTATTTA
          1 TAAATATTATTTA

                        
      16534 TAAATATTATTT
          1 TAAATATTATTT

      16546 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA
Done.