Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011280.1 Corchorus capsularis cultivar CVL-1 contig11301, 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: 42953
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Found at i:8965 original size:211 final size:208

Alignment explanation


    Indices: 8590--9006  Score: 744
    Period size: 211  Copynumber: 2.0  Consensus size: 208

       8580 AGATAAAGGG

                                                                            *
       8590 AATAATAATAAGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTG
          1 AATAATAATAAGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTA

                                                                    *        
       8655 TGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAG
         66 TGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAG

                        *    *                                 *     *       
       8720 GGACACATGTCACCCTTCAAGACCCGCTTGTGTAGTTTTCTAAACTCCACCGCCGGTGTATTGTA
        131 GGACACATGTCAACCTTAAAGACCCGCTTGTGTAGTTTTCTAAACTCCACCACCGGTATATTGTA

                         
       8785 TAATTTGCCTAAT
        196 TAATTTGCCTAAT

                                                                             
       8798 AATAATATATATATGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGC
          1 AATAATA-ATA-A-GGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGC

                                                                             
       8863 TTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCT
         63 TTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCT

                    *                                                        
       8928 AAGGGACATATGTCAACCTTAAAGACCCGCTTGTGTAGTTTTCTAAACTCCACCACCGGTATATT
        128 AAGGGACACATGTCAACCTTAAAGACCCGCTTGTGTAGTTTTCTAAACTCCACCACCGGTATATT

                          
       8993 GTATAATTTGCCTA
        193 GTATAATTTGCCTA

       9007 TATATATAGC


Statistics
Matches: 199,  Mismatches: 7, Indels: 3
        0.95            0.03        0.01

Matches are distributed among these distances:
 208    7  0.04
 209    3  0.02
 210    1  0.01
 211  188  0.94

ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34


Consensus pattern (208 bp):   
AATAATAATAAGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTA
TGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAG
GGACACATGTCAACCTTAAAGACCCGCTTGTGTAGTTTTCTAAACTCCACCACCGGTATATTGTA
TAATTTGCCTAAT

Found at i:37707 original size:1 final size:1

Alignment explanation


    Indices: 37701--37729  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

      37691 ATGGAAACTG

                                         
      37701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      37730 CAGAAAGTAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

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


Consensus pattern (1 bp):   
A

Found at i:40005 original size:2 final size:2

Alignment explanation


    Indices: 39998--40030  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      39988 CTTACCTCAA

                                                             
      39998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      40031 ACCCAAAAGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:42630 original size:21 final size:21

Alignment explanation


    Indices: 42604--42647  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      42594 AAATACTGAA

                                  
      42604 TTGCTAAAT-ACCGCCCCATTT
          1 TTGCT-AATCACCGCCCCATTT

                  *      *       
      42625 TTGCTATTCACCGTCCCATTT
          1 TTGCTAATCACCGCCCCATTT

              
      42646 TT
          1 TT

      42648 TACGCTTTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    2  0.10
  21   18  0.90

ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41


Consensus pattern (21 bp):   
TTGCTAATCACCGCCCCATTT

Found at i:42870 original size:32 final size:33

Alignment explanation


    Indices: 42834--42908  Score: 98
    Period size: 33  Copynumber: 2.3  Consensus size: 33

      42824 CGCCCCAAGA

                            **    *          
      42834 GGGCGGCTT-ACCATGGGCAGGCCGCCCCACTG
          1 GGGCGGCTTCACCATGAACAGGACGCCCCACTG

                        *     *              
      42866 GGGCGGCTTCACTATGAATAGGACGCCCCACTG
          1 GGGCGGCTTCACCATGAACAGGACGCCCCACTG

                      
      42899 GGGCGGCTTC
          1 GGGCGGCTTC

      42909 GCCACGGCAG


Statistics
Matches: 37,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  32    9  0.24
  33   28  0.76

ACGTcount: A:0.15, C:0.33, G:0.36, T:0.16


Consensus pattern (33 bp):   
GGGCGGCTTCACCATGAACAGGACGCCCCACTG
Done.