Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013076.1 Corchorus capsularis cultivar CVL-1 contig13097, 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: 20635
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:6545 original size:14 final size:14

Alignment explanation


    Indices: 6526--6559  Score: 68
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       6516 CCCAGCCGCT

                          
       6526 CCTCTCCCCTTCTC
          1 CCTCTCCCCTTCTC

                          
       6540 CCTCTCCCCTTCTC
          1 CCTCTCCCCTTCTC

                  
       6554 CCTCTC
          1 CCTCTC

       6560 TAGTTCTCAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35


Consensus pattern (14 bp):   
CCTCTCCCCTTCTC

Found at i:7417 original size:2 final size:2

Alignment explanation


    Indices: 7410--7434  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       7400 TTTTTCGGTT

                                                 
       7410 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       7435 TTGAGATTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:18958 original size:33 final size:32

Alignment explanation


    Indices: 18912--19054  Score: 137
    Period size: 32  Copynumber: 4.4  Consensus size: 32

      18902 GGAGGCTTCG

                                             
      18912 CCAC-GGGGCGGCTTCACCATGGGCAGGCCGCC
          1 CCACTGGGGCGGCTTCACCA-GGGCAGGCCGCC

                            *     ***        
      18944 CCACTGGGGCGGCTTCCCCATGAAAAGGCCGCC
          1 CCACTGGGGCGGCTTCACCA-GGGCAGGCCGCC

                                          ** 
      18977 CCACTGGGGCGGCTT-AGCCAGGGCAGGCCATC
          1 CCACTGGGGCGGCTTCA-CCAGGGCAGGCCGCC

              **            *   *           
      19009 CCGGTGGGGCGGCTTCGCCACGGCAGGCCGCC
          1 CCACTGGGGCGGCTTCACCAGGGCAGGCCGCC

              **          
      19041 CCGGTGGGGCGGCT
          1 CCACTGGGGCGGCT

      19055 CGGCTAATTT


Statistics
Matches: 92,  Mismatches: 16, Indels: 6
        0.81            0.14        0.05

Matches are distributed among these distances:
  32   50  0.54
  33   42  0.46

ACGTcount: A:0.12, C:0.38, G:0.39, T:0.11


Consensus pattern (32 bp):   
CCACTGGGGCGGCTTCACCAGGGCAGGCCGCC

Found at i:19175 original size:33 final size:33

Alignment explanation


    Indices: 19133--19244  Score: 181
    Period size: 33  Copynumber: 3.4  Consensus size: 33

      19123 GGTGCCGTCC

                                             
      19133 CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT
          1 CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT

                                             
      19166 CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT
          1 CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT

                        *         **  *      
      19199 CCCTGGGGCGGCCCTACCATGGATAGACCGCC-
          1 CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT

                          
      19231 CCCTGGGGCGGCAC
          1 CCCTGGGGCGGCAC

      19245 CGGTACTAAA


Statistics
Matches: 74,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  32   13  0.18
  33   61  0.82

ACGTcount: A:0.12, C:0.42, G:0.34, T:0.12


Consensus pattern (33 bp):   
CCCTGGGGCGGCACTACCATGGCCAGGCCGCCT

Found at i:19353 original size:32 final size:32

Alignment explanation


    Indices: 19302--19379  Score: 138
    Period size: 32  Copynumber: 2.4  Consensus size: 32

      19292 AAAAAGCCTT

                *         *                 
      19302 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
          1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA

                                            
      19334 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
          1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA

                          
      19366 GCCGTCCTAGTGGG
          1 GCCGTCCTAGTGGG

      19380 GAGGCTCCGC


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  32   44  1.00

ACGTcount: A:0.13, C:0.29, G:0.42, T:0.15


Consensus pattern (32 bp):   
GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA

Done.