Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014172.1 Corchorus capsularis cultivar CVL-1 contig14193, 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: 23057
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:5058 original size:33 final size:33

Alignment explanation


    Indices: 5005--5075  Score: 88
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4995 CGCAACACTA

                      *    *        *   *    
       5005 GCCACGCAACTTGGAGATGCCCGGCCACCACCG
          1 GCCACGCAACATGGACATGCCCGGACACAACCG

                   *             *           
       5038 GCCACGCGACATGGACATGCCTGGACACAACCG
          1 GCCACGCAACATGGACATGCCCGGACACAACCG

                 
       5071 GCCAC
          1 GCCAC

       5076 ATGATTCGGC


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   32  1.00

ACGTcount: A:0.24, C:0.41, G:0.27, T:0.08


Consensus pattern (33 bp):   
GCCACGCAACATGGACATGCCCGGACACAACCG

Found at i:9380 original size:50 final size:50

Alignment explanation


    Indices: 9300--9404  Score: 192
    Period size: 50  Copynumber: 2.1  Consensus size: 50

       9290 CCCACTATCA

                *                                             
       9300 CACTTTCATCTTTGACTCTCCATAACTGATCACAGTGCGACGCGCTAAGC
          1 CACTCTCATCTTTGACTCTCCATAACTGATCACAGTGCGACGCGCTAAGC

                                            *                 
       9350 CACTCTCATCTTTGACTCTCCATAACTGATCATAGTGCGACGCGCTAAGC
          1 CACTCTCATCTTTGACTCTCCATAACTGATCACAGTGCGACGCGCTAAGC

                 
       9400 CACTC
          1 CACTC

       9405 CCTTGTTGAC


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   53  1.00

ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28


Consensus pattern (50 bp):   
CACTCTCATCTTTGACTCTCCATAACTGATCACAGTGCGACGCGCTAAGC

Found at i:15439 original size:6 final size:6

Alignment explanation


    Indices: 15428--15456  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      15418 TTGAACTTGG

                                              
      15428 GCTCGA GCTCGA GCTCGA GCTCGA -CTCGA
          1 GCTCGA GCTCGA GCTCGA GCTCGA GCTCGA

      15457 ATTTTCCGAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.22
   6   18  0.78

ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17


Consensus pattern (6 bp):   
GCTCGA

Found at i:19294 original size:2 final size:2

Alignment explanation


    Indices: 19276--19312  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      19266 ATTGGAAAAT

                   *                                                
      19276 TA TA TG TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      19313 CACTAGCAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:20126 original size:22 final size:22

Alignment explanation


    Indices: 20101--20152  Score: 61
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      20091 AATGTTATAG

                                   
      20101 AAAATTA-CTTTGACAATTATTA
          1 AAAATTAGCTTTGACAA-TATTA

                **                
      20123 AAAAAAAGCTTTGACAATATTA
          1 AAAATTAGCTTTGACAATATTA

                    
      20145 ACAAATTA
          1 A-AAATTA

      20153 AGTAATCATA


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  22   11  0.46
  23   13  0.54

ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33


Consensus pattern (22 bp):   
AAAATTAGCTTTGACAATATTA
Done.