Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020967.1 Corchorus olitorius cultivar O-4 contig21000, 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: 16113
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30


Found at i:2541 original size:12 final size:12

Alignment explanation


    Indices: 2524--2549  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       2514 ACCCTTGCCT

                        
       2524 AAAAACTAGAAG
          1 AAAAACTAGAAG

                        
       2536 AAAAACTAGAAG
          1 AAAAACTAGAAG

              
       2548 AA
          1 AA

       2550 TCAACCTAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (12 bp):   
AAAAACTAGAAG

Found at i:3140 original size:19 final size:18

Alignment explanation


    Indices: 3107--3142  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3097 TTGAAATAAT

                              
       3107 TCTTCAAAAATCTTCAAG
          1 TCTTCAAAAATCTTCAAG

                     *        
       3125 TCTTCAAATTATCTTCAA
          1 TCTTCAAA-AATCTTCAA

       3143 ATAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39


Consensus pattern (18 bp):   
TCTTCAAAAATCTTCAAG

Found at i:8100 original size:16 final size:15

Alignment explanation


    Indices: 8062--8103  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       8052 GCAGAGGTTG

                           
       8062 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

                           
       8077 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

              *         
       8092 ATTAGAAAACAA
          1 A-AAGAAAACAA

       8104 AGCAAAGCAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14


Consensus pattern (15 bp):   
AAAGAAAACAATTAA

Found at i:8879 original size:12 final size:12

Alignment explanation


    Indices: 8862--8892  Score: 53
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       8852 ACCCTTGCCT

                        
       8862 AAAAACTAGAAG
          1 AAAAACTAGAAG

                        
       8874 AAAAACTAGAAG
          1 AAAAACTAGAAG

                   
       8886 AATAAAC
          1 AA-AAAC

       8893 CTAAAACTAA


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

Matches are distributed among these distances:
  12   14  0.78
  13    4  0.22

ACGTcount: A:0.68, C:0.10, G:0.13, T:0.10


Consensus pattern (12 bp):   
AAAAACTAGAAG

Found at i:14689 original size:28 final size:27

Alignment explanation


    Indices: 14656--14754  Score: 103
    Period size: 28  Copynumber: 3.7  Consensus size: 27

      14646 GTCACTCAAG

                                       
      14656 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCATTTTTCACATTCA

                    *                 * 
      14683 GTGGCATTATGGTCATTTTT-ACATTAA
          1 G-GGCATTTTGGTCATTTTTCACATTCA

               *              *  *     
      14710 GGGTATTTTGGTCA-TTTGCATATTCA
          1 GGGCATTTTGGTCATTTTTCACATTCA

                  **           
      14736 GGGGCAGGTTGGTCATTTT
          1 -GGGCATTTTGGTCATTTT

      14755 GAGTCCACTT


Statistics
Matches: 58,  Mismatches: 10, Indels: 7
        0.77            0.13        0.09

Matches are distributed among these distances:
  25    3  0.05
  26   16  0.28
  27   19  0.33
  28   20  0.34

ACGTcount: A:0.19, C:0.13, G:0.24, T:0.43


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTTTCACATTCA

Found at i:14738 original size:26 final size:26

Alignment explanation


    Indices: 14656--14754  Score: 99
    Period size: 27  Copynumber: 3.7  Consensus size: 26

      14646 GTCACTCAAG

                                       
      14656 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCA-TTTTCACATTCA

                    *          *     * 
      14683 GTGGCATTATGGTCATTTTTACATTAA
          1 G-GGCATTTTGGTCATTTTCACATTCA

               *             *  *     
      14710 GGGTATTTTGGTCATTTGCATATTCA
          1 GGGCATTTTGGTCATTTTCACATTCA

                  **           
      14736 GGGGCAGGTTGGTCATTTT
          1 -GGGCATTTTGGTCATTTT

      14755 GAGTCCACTT


Statistics
Matches: 57,  Mismatches: 13, Indels: 4
        0.77            0.18        0.05

Matches are distributed among these distances:
  26   19  0.33
  27   26  0.46
  28   12  0.21

ACGTcount: A:0.19, C:0.13, G:0.24, T:0.43


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTCACATTCA
Done.