Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012879.1 Corchorus capsularis cultivar CVL-1 contig12900, 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: 36667
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:19876 original size:3 final size:3

Alignment explanation


    Indices: 19868--19904  Score: 65
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      19858 TCTCTGCCTC

                                                      *      
      19868 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT T
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T

      19905 TATTTTATTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   32  1.00

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


Consensus pattern (3 bp):   
TCT

Found at i:24569 original size:57 final size:57

Alignment explanation


    Indices: 24481--24599  Score: 184
    Period size: 57  Copynumber: 2.1  Consensus size: 57

      24471 AAGCTCTTTC

                           *     *                  *            *  *
      24481 AACAAATGTTTTCTCTATTCATAAGACTTGAACTCGAGACTTTATTTATTTAAGGGG
          1 AACAAATGTTTTCTCCATTCACAAGACTTGAACTCGAGACCTTATTTATTTAAAGGA

                                              *                      
      24538 AACAAATGTTTTCTCCATTCACAAGACTTGAACTTGAGACCTTATTTATTTAAAGGA
          1 AACAAATGTTTTCTCCATTCACAAGACTTGAACTCGAGACCTTATTTATTTAAAGGA

                 
      24595 AACAA
          1 AACAA

      24600 GTGACAAACC


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  57   56  1.00

ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35


Consensus pattern (57 bp):   
AACAAATGTTTTCTCCATTCACAAGACTTGAACTCGAGACCTTATTTATTTAAAGGA

Found at i:25111 original size:6 final size:6

Alignment explanation


    Indices: 25100--25128  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      25090 TTTCATCTCT

                                             
      25100 AATCAA AATCAA AATCAA AATCAA AATCA
          1 AATCAA AATCAA AATCAA AATCAA AATCA

      25129 CTTTTAAACT


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

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17


Consensus pattern (6 bp):   
AATCAA

Found at i:36246 original size:29 final size:30

Alignment explanation


    Indices: 36178--36249  Score: 92
    Period size: 29  Copynumber: 2.4  Consensus size: 30

      36168 TTGAGGAGGT

                                  *   *    
      36178 AAAACGTCCCAAAATTGAAGTTTAGGGGGGC
          1 AAAACGT-CCAAAATTGAAGTTCAGGAGGGC

                *      *                  
      36209 AAAATGTCCAAGATTGAAGTTCA-GAGGGC
          1 AAAACGTCCAAAATTGAAGTTCAGGAGGGC

                        
      36238 AAAACGTCCAAA
          1 AAAACGTCCAAA

      36250 CGCTACAAGT


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  29   15  0.43
  30   14  0.40
  31    6  0.17

ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18


Consensus pattern (30 bp):   
AAAACGTCCAAAATTGAAGTTCAGGAGGGC
Done.