Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006612.1 Corchorus olitorius cultivar O-4 contig06637, 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, 633

Length: 1055
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43


Found at i:15 original size:6 final size:6

Alignment explanation


    Indices: 5--46  Score: 61
    Period size: 6  Copynumber: 7.2  Consensus size: 6

          1 CATT

                                                               
          5 TTTTCA TTTTCA TTTT-- TTTTCA TTTTTCA TTTTCA TTTTCA T
          1 TTTTCA TTTTCA TTTTCA TTTTCA -TTTTCA TTTTCA TTTTCA T

         47 CATTTTTTTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   4    4  0.12
   6   23  0.70
   7    6  0.18

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71


Consensus pattern (6 bp):   
TTTTCA

Found at i:24 original size:16 final size:17

Alignment explanation


    Indices: 3--37  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

          1 CA

                             
          3 TTTTTTCA-TTTTCATT
          1 TTTTTTCATTTTTCATT

                             
         19 TTTTTTCATTTTTCATT
          1 TTTTTTCATTTTTCATT

              
         36 TT
          1 TT

         38 CATTTTCATC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16    8  0.44
  17   10  0.56

ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77


Consensus pattern (17 bp):   
TTTTTTCATTTTTCATT

Found at i:53 original size:23 final size:24

Alignment explanation


    Indices: 1--54  Score: 76
    Period size: 23  Copynumber: 2.3  Consensus size: 24

                                 ** 
          1 CATTTTTTCATTTTCATTTTTTTT
          1 CATTTTTTCATTTTCATTTTTCAT

                                    
         25 CA-TTTTTCATTTTCA-TTTTCAT
          1 CATTTTTTCATTTTCATTTTTCAT

                    
         47 CATTTTTT
          1 CATTTTTT

         55 TTGTATGCAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  22    7  0.26
  23   18  0.67
  24    2  0.07

ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70


Consensus pattern (24 bp):   
CATTTTTTCATTTTCATTTTTCAT

Found at i:423 original size:6 final size:6

Alignment explanation


    Indices: 414--456  Score: 68
    Period size: 6  Copynumber: 7.0  Consensus size: 6

        404 CTTTTTGTTT

                                                     *       
        414 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTTG TTTTTT TTTTTG
          1 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG

        457 CATCTTTATT


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

Matches are distributed among these distances:
   6   28  0.82
   7    6  0.18

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


Consensus pattern (6 bp):   
TTTTTG

Found at i:906 original size:17 final size:16

Alignment explanation


    Indices: 873--905  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        863 ATATTTCAAG

                            
        873 TGCTTTTTTTTCATTT
          1 TGCTTTTTTTTCATTT

                             
        889 TGCTTATTTTTTC-TTT
          1 TGCTT-TTTTTTCATTT

             
        905 T
          1 T

        906 TTTTTCATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    9  0.56
  17    7  0.44

ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76


Consensus pattern (16 bp):   
TGCTTTTTTTTCATTT

Found at i:913 original size:27 final size:27

Alignment explanation


    Indices: 876--937  Score: 99
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        866 TTTCAAGTGC

                          *             
        876 TTTTTTTTCATTTTGCTTATTTTT-TCT
          1 TTTTTTTTCATTTTACTT-TTTTTCTCT

                                       
        903 TTTTTTTTCATTTTACTTTTTTTCTCT
          1 TTTTTTTTCATTTTACTTTTTTTCTCT

                    
        930 TTTTTTTT
          1 TTTTTTTT

        938 ATTATCGGGG


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  26    5  0.15
  27   28  0.85

ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81


Consensus pattern (27 bp):   
TTTTTTTTCATTTTACTTTTTTTCTCT
Done.