Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007362.1 Corchorus capsularis cultivar CVL-1 contig07383, 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: 50182
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:22652 original size:39 final size:40

Alignment explanation


    Indices: 22579--22659  Score: 146
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      22569 TGGTGATTCC

                                                    
      22579 AAGCTCACCTGCAACAATAAACAGTAGTAGCCATGTCAAG
          1 AAGCTCACCTGCAACAATAAACAGTAGTAGCCATGTCAAG

                      *                             
      22619 AAGCTCACCTTCAACAAT-AACAGTAGTAGCCATGTCAAG
          1 AAGCTCACCTGCAACAATAAACAGTAGTAGCCATGTCAAG

              
      22658 AA
          1 AA

      22660 ACATGCCATG


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  39   23  0.57
  40   17  0.43

ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19


Consensus pattern (40 bp):   
AAGCTCACCTGCAACAATAAACAGTAGTAGCCATGTCAAG

Found at i:25132 original size:32 final size:32

Alignment explanation


    Indices: 25087--25175  Score: 135
    Period size: 32  Copynumber: 2.8  Consensus size: 32

      25077 TTAGGGTTGT

                                            
      25087 GCCGCCC-GGCTGGGCGGCAAGGCCATGGCAA
          1 GCCGCCCAGGCTGGGCGGCAAGGCCATGGCAA

                           *        *      *
      25118 GCCGCCCAGGCTGGGTGGCAAGGCTATGGCAT
          1 GCCGCCCAGGCTGGGCGGCAAGGCCATGGCAA

                                 *    
      25150 GCCGCCCAGGCTGGGCGGCAAAGCCA
          1 GCCGCCCAGGCTGGGCGGCAAGGCCA

      25176 ATTTTTTTTA


Statistics
Matches: 51,  Mismatches: 6, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  31    7  0.14
  32   44  0.86

ACGTcount: A:0.17, C:0.34, G:0.40, T:0.09


Consensus pattern (32 bp):   
GCCGCCCAGGCTGGGCGGCAAGGCCATGGCAA

Found at i:32241 original size:21 final size:22

Alignment explanation


    Indices: 32193--32241  Score: 59
    Period size: 21  Copynumber: 2.3  Consensus size: 22

      32183 TTGTGACTTG

                                 *
      32193 GGATGGCGCGGCATAGGCTCGT
          1 GGATGGCGCGGCATAGGCTCGC

                                   
      32215 GG-TGGCGCGGCAT-GG-TACGC
          1 GGATGGCGCGGCATAGGCT-CGC

                   
      32235 GGATGGC
          1 GGATGGC

      32242 TTGGCAAGGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  19    1  0.04
  20    6  0.25
  21   15  0.62
  22    2  0.08

ACGTcount: A:0.12, C:0.22, G:0.49, T:0.16


Consensus pattern (22 bp):   
GGATGGCGCGGCATAGGCTCGC

Found at i:38167 original size:2 final size:2

Alignment explanation


    Indices: 38154--38187  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      38144 ATAGTATTAC

                   *                                          
      38154 AT AT AA AT AT AT AT AT AT 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

      38188 GTAATACTAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:48918 original size:15 final size:16

Alignment explanation


    Indices: 48900--48930  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

      48890 ATTATAGATT

                            
      48900 TTATAAATAT-ATTAA
          1 TTATAAATATAATTAA

                            
      48915 TTATAAATATAATTAA
          1 TTATAAATATAATTAA

      48931 AAAAATTAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15   10  0.67
  16    5  0.33

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (16 bp):   
TTATAAATATAATTAA
Done.