Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016974.1 Corchorus olitorius cultivar O-4 contig17007, 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: 36279
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1970 original size:26 final size:28

Alignment explanation


    Indices: 1941--2004  Score: 96
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       1931 AAAATTTTAG

                         *              
       1941 AAAACGCAAAA-ACACTTTTTTTT-TCA
          1 AAAACGCAAAACAAACTTTTTTTTCTCA

                           *            
       1967 AAAACGCAAAACAAATTTTTTTTTCTCA
          1 AAAACGCAAAACAAACTTTTTTTTCTCA

                      
       1995 AAAACGCAAA
          1 AAAACGCAAA

       2005 TTTTTTTTTT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  26   11  0.32
  27   10  0.29
  28   13  0.38

ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30


Consensus pattern (28 bp):   
AAAACGCAAAACAAACTTTTTTTTCTCA

Found at i:2277 original size:13 final size:13

Alignment explanation


    Indices: 2259--2283  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2249 GAAACAGGGG

                         
       2259 ATTAAAATTAACA
          1 ATTAAAATTAACA

                        
       2272 ATTAAAATTAAC
          1 ATTAAAATTAAC

       2284 TAAGAAAGCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32


Consensus pattern (13 bp):   
ATTAAAATTAACA

Found at i:9061 original size:22 final size:22

Alignment explanation


    Indices: 9012--9062  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       9002 AAATATTACC

                         *   **   
       9012 ATAATTATTTTTGGCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       9034 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       9057 A-AATTA
          1 ATAATTA

       9063 GTGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA

Found at i:16580 original size:6 final size:6

Alignment explanation


    Indices: 16565--16593  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      16555 AATCTAATAT

                                              
      16565 GAAAAA -AAAAA GAAAAA GAAAAA GAAAAA
          1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA

      16594 TAATACACAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   5    5  0.23
   6   17  0.77

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (6 bp):   
GAAAAA

Found at i:34462 original size:6 final size:6

Alignment explanation


    Indices: 34451--34482  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      34441 CACTCTTTGA

                                          *      
      34451 AAAAAT AAAAAT AAAAAT AAAAAT AATAAT AA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA

      34483 GGTTAGTAAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (6 bp):   
AAAAAT

Found at i:35631 original size:20 final size:21

Alignment explanation


    Indices: 35603--35646  Score: 63
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      35593 GTGACACTGC

                *                
      35603 CCACTTGGGTCCTCAA-GCAA
          1 CCACATGGGTCCTCAAGGCAA

                      *          
      35623 CCACATGGGTGCTCAAGGCAA
          1 CCACATGGGTCCTCAAGGCAA

               
      35644 CCA
          1 CCA

      35647 TGTGGGCGCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   14  0.67
  21    7  0.33

ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16


Consensus pattern (21 bp):   
CCACATGGGTCCTCAAGGCAA

Done.