Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011074.1 Corchorus capsularis cultivar CVL-1 contig11095, 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: 32975
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4841 original size:22 final size:22

Alignment explanation


    Indices: 4813--4854  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4803 ATTCTGATTG

                                  
       4813 ATTGGGCAAGGGACATTTGGGC
          1 ATTGGGCAAGGGACATTTGGGC

                                
       4835 ATTGGGCAAGGGACATTTGG
          1 ATTGGGCAAGGGACATTTGG

       4855 AACAATCATC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24


Consensus pattern (22 bp):   
ATTGGGCAAGGGACATTTGGGC

Found at i:15992 original size:16 final size:17

Alignment explanation


    Indices: 15966--16006  Score: 57
    Period size: 16  Copynumber: 2.5  Consensus size: 17

      15956 TTGACAGCGC

                *        *   
      15966 AACAAAAACAAAACAAA
          1 AACAGAAACAAAAAAAA

                             
      15983 AAC-GAAACAAAAAAAA
          1 AACAGAAACAAAAAAAA

                    
      15999 AACAGAAA
          1 AACAGAAA

      16007 AACGAAAACG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  16   14  0.67
  17    7  0.33

ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00


Consensus pattern (17 bp):   
AACAGAAACAAAAAAAA

Found at i:16008 original size:11 final size:11

Alignment explanation


    Indices: 15966--16007  Score: 57
    Period size: 11  Copynumber: 3.7  Consensus size: 11

      15956 TTGACAGCGC

                       
      15966 AACAAAAACAA
          1 AACAAAAACAA

                     * 
      15977 AACAAAAACGA
          1 AACAAAAACAA

                    *  
      15988 AACAAAAAAAA
          1 AACAAAAACAA

                     
      15999 AACAGAAAA
          1 AACA-AAAA

      16008 ACGAAAACGA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  11   23  0.85
  12    4  0.15

ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:26468 original size:96 final size:96

Alignment explanation


    Indices: 26304--26494  Score: 303
    Period size: 96  Copynumber: 2.0  Consensus size: 96

      26294 GTTCAAAGGA

                  *    *          *    *                                  *  
      26304 TTCAAATTTGGTTGGAAAGGATTCACCGCCTATCTCTGAAAGAACTTCACCAGATGGGTGCTTTG
          1 TTCAAAGTTGGCTGGAAAGGATGCACCACCTATCTCTGAAAGAACTTCACCAGATGGGTGCTCTG

                                           
      26369 ATGCTGAGAAAGAGAGCCAAGATGTTGGTCC
         66 ATGCTGAGAAAGAGAGCCAAGATGTTGGTCC

                                           *                                 
      26400 TTCAAAGTTGGCTGGAAAGGATGCACCACCTGTC-CTTGAAAGAACTTCACCAGATGGGTGCTCT
          1 TTCAAAGTTGGCTGGAAAGGATGCACCACCTATCTC-TGAAAGAACTTCACCAGATGGGTGCTCT

                                  *        
      26464 GATGCTGAGAAAGAGAGCCAAGGTGTTGGTC
         65 GATGCTGAGAAAGAGAGCCAAGATGTTGGTC

      26495 AGCTTGAGCT


Statistics
Matches: 87,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  95    1  0.01
  96   86  0.99

ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25


Consensus pattern (96 bp):   
TTCAAAGTTGGCTGGAAAGGATGCACCACCTATCTCTGAAAGAACTTCACCAGATGGGTGCTCTG
ATGCTGAGAAAGAGAGCCAAGATGTTGGTCC
Done.