Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015572.1 Corchorus capsularis cultivar CVL-1 contig15593, 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: 29164
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:713 original size:2 final size:2

Alignment explanation


    Indices: 706--757  Score: 72
    Period size: 2  Copynumber: 27.0  Consensus size: 2

        696 ACCCGTGATA

                                        *  *                              
        706 AT AT AT AT AT AT -T AT -T AG AA 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 AT AT AT AT

                             
        746 AT AT AT AT AT AT
          1 AT AT AT AT AT AT

        758 TTCTAATAAT


Statistics
Matches: 45,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
   1    2  0.04
   2   43  0.96

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1953 original size:19 final size:19

Alignment explanation


    Indices: 1925--1969  Score: 81
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1915 AGGCAGCAAG

                               
       1925 CAGCAACAATATTATATAC
          1 CAGCAACAATATTATATAC

                 *             
       1944 CAGCAGCAATATTATATAC
          1 CAGCAACAATATTATATAC

                   
       1963 CAGCAAC
          1 CAGCAAC

       1970 CATTAGCAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.44, C:0.24, G:0.09, T:0.22


Consensus pattern (19 bp):   
CAGCAACAATATTATATAC

Found at i:5212 original size:16 final size:16

Alignment explanation


    Indices: 5191--5224  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       5181 GAATTGGAAG

                         *  
       5191 AAGGAATAAAAGATTA
          1 AAGGAATAAAAGAATA

                            
       5207 AAGGAATAAAAGAATA
          1 AAGGAATAAAAGAATA

              
       5223 AA
          1 AA

       5225 AATCATCTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15


Consensus pattern (16 bp):   
AAGGAATAAAAGAATA

Found at i:7295 original size:17 final size:17

Alignment explanation


    Indices: 7273--7307  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7263 TTTTTTGTTA

                             
       7273 GGGATTCACATGTGAGG
          1 GGGATTCACATGTGAGG

                             
       7290 GGGATTCACATGTGAGG
          1 GGGATTCACATGTGAGG

             
       7307 G
          1 G

       7308 AGACATATCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.23, C:0.11, G:0.43, T:0.23


Consensus pattern (17 bp):   
GGGATTCACATGTGAGG

Found at i:15544 original size:16 final size:16

Alignment explanation


    Indices: 15523--15562  Score: 53
    Period size: 16  Copynumber: 2.5  Consensus size: 16

      15513 CGACGCCATA

                            
      15523 CTTGGGTGAGCAACGC
          1 CTTGGGTGAGCAACGC

                      **   *
      15539 CTTGGGTGAGTGACGT
          1 CTTGGGTGAGCAACGC

                    
      15555 CTTGGGTG
          1 CTTGGGTG

      15563 GCGCAGGCAC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.12, C:0.17, G:0.42, T:0.28


Consensus pattern (16 bp):   
CTTGGGTGAGCAACGC

Found at i:16019 original size:36 final size:35

Alignment explanation


    Indices: 15972--16042  Score: 124
    Period size: 36  Copynumber: 2.0  Consensus size: 35

      15962 ATCTTTTACT

                                               
      15972 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
          1 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG

                                   *            
      16007 TTTCATTCACCCTTGTTTTTACACGGTGTAATCTTG
          1 TTTCA-TCACCCTTGTTTTTACAAGGTGTAATCTTG

      16043 CTTCTGCAAT


Statistics
Matches: 34,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  35    5  0.15
  36   29  0.85

ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46


Consensus pattern (35 bp):   
TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
Done.