Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016862.1 Corchorus olitorius cultivar O-4 contig16895, 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: 33251
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:829 original size:3 final size:3

Alignment explanation


    Indices: 821--867  Score: 94
    Period size: 3  Copynumber: 15.7  Consensus size: 3

        811 ATATTGCATA

                                                                          
        821 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

        868 AAGAACAAAT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:6536 original size:6 final size:6

Alignment explanation


    Indices: 6520--6550  Score: 53
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       6510 CCAATGGAAA

                                               
       6520 AAAAAG AAAAAAG AAAAAG AAAAAG AAAAAG
          1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG

       6551 TAAGGACTTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   18  0.75
   7    6  0.25

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:6648 original size:20 final size:20

Alignment explanation


    Indices: 6593--6649  Score: 62
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       6583 ATTTGAAGAG

                            *    
       6593 AAAAGAAAAGAAAAGAAACGA
          1 AAAAGAAAAGAAAA-ATACGA

                      **     *  
       6614 AAAA-AAAAGGGAAATAGGA
          1 AAAAGAAAAGAAAAATACGA

                             
       6633 AAAAGAAAAGAAAAATA
          1 AAAAGAAAAGAAAAATA

       6650 AGTAATAAGA


Statistics
Matches: 29,  Mismatches: 6, Indels: 3
        0.76            0.16        0.08

Matches are distributed among these distances:
  19    8  0.28
  20   17  0.59
  21    4  0.14

ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04


Consensus pattern (20 bp):   
AAAAGAAAAGAAAAATACGA

Found at i:14376 original size:2 final size:2

Alignment explanation


    Indices: 14369--14423  Score: 65
    Period size: 2  Copynumber: 27.5  Consensus size: 2

      14359 GGTTTGGATT

                                     *                            *     * 
      14369 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA GA TA GA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

               *     *         
      14411 TA GA TA AA TA TA T
          1 TA TA TA TA TA TA T

      14424 CACAATATGC


Statistics
Matches: 43,  Mismatches: 10, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:26067 original size:18 final size:18

Alignment explanation


    Indices: 26030--26067  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      26020 GCTCATCGAT

                               
      26030 ATCTCCATGATCTTCTTGC
          1 ATCTCCATGA-CTTCTTGC

                               
      26049 ATCTCCATG-CTTCCTTGC
          1 ATCTCCATGACTT-CTTGC

             
      26067 A
          1 A

      26068 GCCCTTGCAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  17    3  0.17
  18    6  0.33
  19    9  0.50

ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39


Consensus pattern (18 bp):   
ATCTCCATGACTTCTTGC

Found at i:26574 original size:26 final size:27

Alignment explanation


    Indices: 26479--26567  Score: 155
    Period size: 27  Copynumber: 3.3  Consensus size: 27

      26469 TTGGCACTTA

                                       
      26479 GGTCATTTTTACATTCAGGGGCATTTT
          1 GGTCATTTTTACATTCAGGGGCATTTT

                                       
      26506 GGTCATTTTTACATTCAGGGGCATTTT
          1 GGTCATTTTTACATTCAGGGGCATTTT

                                        
      26533 GGTCA-TTTTA-AGTTCAGGGGCATTTT
          1 GGTCATTTTTACA-TTCAGGGGCATTTT

                     
      26559 GGTCATTTT
          1 GGTCATTTT

      26568 AAGTTCACAT


Statistics
Matches: 60,  Mismatches: 0, Indels: 4
        0.94            0.00        0.06

Matches are distributed among these distances:
  25    1  0.02
  26   24  0.40
  27   35  0.58

ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45


Consensus pattern (27 bp):   
GGTCATTTTTACATTCAGGGGCATTTT

Found at i:32544 original size:27 final size:27

Alignment explanation


    Indices: 32514--32586  Score: 85
    Period size: 26  Copynumber: 2.7  Consensus size: 27

      32504 AGGGTCACCT

                                *      
      32514 AGGGGCATTTTGGTCATTTTTACACTA
          1 AGGGGCATTTTGGTCATTTTCACACTA

                               *  * * *
      32541 A-GGGCATTTTGGTCATTTGCATATTT
          1 AGGGGCATTTTGGTCATTTTCACACTA

                    *           
      32567 AGGGGCATGTTGGTCATTTT
          1 AGGGGCATTTTGGTCATTTT

      32587 AAGTCCACTT


Statistics
Matches: 38,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  26   21  0.55
  27   17  0.45

ACGTcount: A:0.19, C:0.12, G:0.26, T:0.42


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTTCACACTA

Done.