Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007960.1 Corchorus capsularis cultivar CVL-1 contig07981, 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: 21537
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1226 original size:16 final size:16

Alignment explanation


    Indices: 1207--1245  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1197 CTTTCCTTTC

                         *  
       1207 CTTTTTCTTTTATTTT
          1 CTTTTTCTTTTATCTT

                  *    *    
       1223 CTTTTTATTTTCTCTT
          1 CTTTTTCTTTTATCTT

                   
       1239 CTTTTTC
          1 CTTTTTC

       1246 CCTTTACAAA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77


Consensus pattern (16 bp):   
CTTTTTCTTTTATCTT

Found at i:5378 original size:21 final size:20

Alignment explanation


    Indices: 5348--5386  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       5338 AATATCACGG

                                 
       5348 AAGACATGAAGAGACAATTCT
          1 AAGACATGAA-AGACAATTCT

                 *    *       
       5369 AAGACGTGAATGACAATT
          1 AAGACATGAAAGACAATT

       5387 AATAATGGCT


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    7  0.44
  21    9  0.56

ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21


Consensus pattern (20 bp):   
AAGACATGAAAGACAATTCT

Found at i:8154 original size:2 final size:2

Alignment explanation


    Indices: 8147--8193  Score: 62
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       8137 CAAATGTGAC

                                                  *                        
       8147 AT AT AT AT AT A- AT AT AT AT -T AT CAA 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 AT AT AT AT AT

                    
       8188 AT AT AT
          1 AT AT AT

       8194 TAGATTTAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
   1    2  0.05
   2   37  0.93
   3    1  0.03

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:9829 original size:17 final size:17

Alignment explanation


    Indices: 9785--9832  Score: 57
    Period size: 17  Copynumber: 3.0  Consensus size: 17

       9775 TCAACTTTTA

                             
       9785 ATTTGTTTAATTTAA-G
          1 ATTTGTTTAATTTAATG

              *      *       
       9801 A-CT-TTTATTTTAATG
          1 ATTTGTTTAATTTAATG

                             
       9816 ATTTGTTTAATTTAATG
          1 ATTTGTTTAATTTAATG

       9833 CTTAATTTGT


Statistics
Matches: 25,  Mismatches: 4, Indels: 5
        0.74            0.12        0.15

Matches are distributed among these distances:
  14    9  0.36
  15    3  0.12
  16    2  0.08
  17   11  0.44

ACGTcount: A:0.29, C:0.02, G:0.10, T:0.58


Consensus pattern (17 bp):   
ATTTGTTTAATTTAATG

Found at i:10144 original size:3 final size:3

Alignment explanation


    Indices: 10130--10168  Score: 69
    Period size: 3  Copynumber: 13.0  Consensus size: 3

      10120 TATTATGTTA

                     *                                         
      10130 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

      10169 GATCATCATC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:17111 original size:30 final size:30

Alignment explanation


    Indices: 17075--17135  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      17065 AAGGATATAT

                                          
      17075 TGGCCGGTTGTGGCCGGTTACCCCATGCGA
          1 TGGCCGGTTGTGGCCGGTTACCCCATGCGA

                               * *        
      17105 TGGCCGGTTGTGGCCGGTTGCTCCATGCGA
          1 TGGCCGGTTGTGGCCGGTTACCCCATGCGA

             
      17135 T
          1 T

      17136 AGCCCTTGCG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.08, C:0.28, G:0.38, T:0.26


Consensus pattern (30 bp):   
TGGCCGGTTGTGGCCGGTTACCCCATGCGA
Done.