Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013360.1 Corchorus olitorius cultivar O-4 contig13393, 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: 5354
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:108 original size:11 final size:11

Alignment explanation


    Indices: 94--127  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

         84 TAAAGGAAAA

                       
         94 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        105 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        116 AGCTAGGAAGG
          1 AGCTAGGAAGG

             
        127 A
          1 A

        128 CCCTACTCCT


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

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09


Consensus pattern (11 bp):   
AGCTAGGAAGG

Found at i:2488 original size:14 final size:15

Alignment explanation


    Indices: 2469--2498  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2459 CAATCAAAGC

                           
       2469 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       2483 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       2498 A
          1 A

       2499 TTAAAGAGAT


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

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:2883 original size:21 final size:21

Alignment explanation


    Indices: 2857--2920  Score: 83
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2847 GGAATGGCGA

                      *  *       
       2857 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCTTGACCGGTGG

                        *       *
       2878 TGGCACGGGCTTAACCGGTGA
          1 TGGCACGGGCTTGACCGGTGG

                *                
       2899 TGGCTCGGGCTTGACCGGTGG
          1 TGGCACGGGCTTGACCGGTGG

             
       2920 T
          1 T

       2921 TGCGCGACTT


Statistics
Matches: 36,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   36  1.00

ACGTcount: A:0.11, C:0.23, G:0.45, T:0.20


Consensus pattern (21 bp):   
TGGCACGGGCTTGACCGGTGG

Found at i:3073 original size:21 final size:21

Alignment explanation


    Indices: 2986--3073  Score: 56
    Period size: 21  Copynumber: 4.2  Consensus size: 21

       2976 GCTGGCTTAA

                   *         *   
       2986 CCGGGCAAGTGGCGCGGGTGG
          1 CCGGGCAGGTGGCGCGGATGG

              *           *       
       3007 CCAGGCATGGT-GCTCGGATGG
          1 CCGGGCA-GGTGGCGCGGATGG

                       *   *     **
       3028 -CGCGG-AGGAAGGCACGGATAA
          1 CCG-GGCAGG-TGGCGCGGATGG

                                 
       3049 CCGGGCAGGTGGCGCGGATGG
          1 CCGGGCAGGTGGCGCGGATGG

                
       3070 CCGG
          1 CCGG

       3074 TTGTGGTGCG


Statistics
Matches: 48,  Mismatches: 13, Indels: 12
        0.66            0.18        0.16

Matches are distributed among these distances:
  19    2  0.04
  20    2  0.04
  21   37  0.77
  22    7  0.15

ACGTcount: A:0.16, C:0.24, G:0.50, T:0.10


Consensus pattern (21 bp):   
CCGGGCAGGTGGCGCGGATGG
Done.