Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010844.1 Corchorus capsularis cultivar CVL-1 contig10865, 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: 12757
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:8423 original size:33 final size:33

Alignment explanation


    Indices: 8380--8448  Score: 120
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       8370 CATGATTGAG

                 *               *           
       8380 GAATCTTTGATCCCAGATTCACTTGTTTCCATT
          1 GAATCATTGATCCCAGATTCAATTGTTTCCATT

                                             
       8413 GAATCATTGATCCCAGATTCAATTGTTTCCATT
          1 GAATCATTGATCCCAGATTCAATTGTTTCCATT

               
       8446 GAA
          1 GAA

       8449 GATGGGCGAC


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

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39


Consensus pattern (33 bp):   
GAATCATTGATCCCAGATTCAATTGTTTCCATT

Found at i:9052 original size:21 final size:22

Alignment explanation


    Indices: 9028--9070  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9018 ACGTCTGCCC

                                  
       9028 AATTATTC-AAAACCTCTGTTT
          1 AATTATTCTAAAACCTCTGTTT

                *    **           
       9049 AATTGTTCTCCAACCTCTGTTT
          1 AATTATTCTAAAACCTCTGTTT

       9071 GGATATCTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44


Consensus pattern (22 bp):   
AATTATTCTAAAACCTCTGTTT

Found at i:10159 original size:23 final size:23

Alignment explanation


    Indices: 10129--10172  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      10119 TTTGAATGGG

                         *         
      10129 AAATAAGGCTTGGTGCTCCCAAA
          1 AAATAAGGCTTGGCGCTCCCAAA

                                 
      10152 AAATAAGGCTTGGCGCTCCCA
          1 AAATAAGGCTTGGCGCTCCCA

      10173 GATATCTCCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20


Consensus pattern (23 bp):   
AAATAAGGCTTGGCGCTCCCAAA

Found at i:10859 original size:12 final size:12

Alignment explanation


    Indices: 10842--10866  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      10832 AAACAGCCAT

                        
      10842 ATATAATTTCTA
          1 ATATAATTTCTA

                        
      10854 ATATAATTTCTA
          1 ATATAATTTCTA

             
      10866 A
          1 A

      10867 AGATGAGCCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48


Consensus pattern (12 bp):   
ATATAATTTCTA

Found at i:11049 original size:27 final size:27

Alignment explanation


    Indices: 11019--11072  Score: 99
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      11009 GCCGTCTCAA

                                       
      11019 GCCAATTACGATACTGTTGACTATTGG
          1 GCCAATTACGATACTGTTGACTATTGG

                      *                
      11046 GCCAATTACGGTACTGTTGACTATTGG
          1 GCCAATTACGATACTGTTGACTATTGG

      11073 ATGATGAGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33


Consensus pattern (27 bp):   
GCCAATTACGATACTGTTGACTATTGG

Found at i:11206 original size:69 final size:69

Alignment explanation


    Indices: 11095--11236  Score: 221
    Period size: 69  Copynumber: 2.1  Consensus size: 69

      11085 TACGGCCAAG

                      *           *                                          
      11095 CCAACCTTCTGCATAATTACCGTACCTATACGGAAATAACGTATTACCTTCCCTTGAACGAACCC
          1 CCAACCTTCTACATAATTACCGAACCTATACGGAAATAACGTATTACCTTCCCTTGAACGAACCC

                
      11160 CAGT
         66 CAGT

                                *   *    *    *                       *      
      11164 CCAACCTTCTACATAATTACTGAAGCTATTCGGATATAACGTATTACCTTCCCTTGAATGAACCC
          1 CCAACCTTCTACATAATTACCGAACCTATACGGAAATAACGTATTACCTTCCCTTGAACGAACCC

                
      11229 CAGT
         66 CAGT

                
      11233 CCAA
          1 CCAA

      11237 ACATTTGAAG


Statistics
Matches: 66,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  69   66  1.00

ACGTcount: A:0.31, C:0.30, G:0.11, T:0.27


Consensus pattern (69 bp):   
CCAACCTTCTACATAATTACCGAACCTATACGGAAATAACGTATTACCTTCCCTTGAACGAACCC
CAGT
Done.