Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014949.1 Corchorus olitorius cultivar O-4 contig14982, 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: 19023
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:3036 original size:8 final size:8

Alignment explanation


    Indices: 3020--3052  Score: 57
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       3010 CAACTTCTCC

                *   
       3020 AAAACTTG
          1 AAAATTTG

                    
       3028 AAAATTTG
          1 AAAATTTG

                    
       3036 AAAATTTG
          1 AAAATTTG

                    
       3044 AAAATTTG
          1 AAAATTTG

             
       3052 A
          1 A

       3053 GGAATTTGAT


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

Matches are distributed among these distances:
   8   24  1.00

ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33


Consensus pattern (8 bp):   
AAAATTTG

Found at i:4829 original size:61 final size:62

Alignment explanation


    Indices: 4748--4874  Score: 211
    Period size: 61  Copynumber: 2.1  Consensus size: 62

       4738 TTAAAGAAAG

                                                                          
       4748 AAAATTGACCAACTTCCCATATATTATATTCGAATACAAAACCCAACACATAAAACAAAACA
          1 AAAATTGACCAACTTCCCATATATTATATTCGAATACAAAACCCAACACATAAAACAAAACA

                           *         *             *                    * 
       4810 AAAATT-ACCAACTTTCCATATATTCTATTCGAATACAATACCCAACACATAAAACAAAATA
          1 AAAATTGACCAACTTCCCATATATTATATTCGAATACAAAACCCAACACATAAAACAAAACA

                
       4871 AAAA
          1 AAAA

       4875 AATTTCCAAT


Statistics
Matches: 61,  Mismatches: 4, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  61   55  0.90
  62    6  0.10

ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23


Consensus pattern (62 bp):   
AAAATTGACCAACTTCCCATATATTATATTCGAATACAAAACCCAACACATAAAACAAAACA

Found at i:5774 original size:16 final size:16

Alignment explanation


    Indices: 5753--5788  Score: 72
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5743 CTAAAAAGCA

                            
       5753 ACTAAATATATACCTC
          1 ACTAAATATATACCTC

                            
       5769 ACTAAATATATACCTC
          1 ACTAAATATATACCTC

                
       5785 ACTA
          1 ACTA

       5789 TAGGCCATCT


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

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31


Consensus pattern (16 bp):   
ACTAAATATATACCTC

Found at i:13415 original size:16 final size:15

Alignment explanation


    Indices: 13377--13418  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      13367 ACAGAGGTTG

                           
      13377 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
      13392 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      13407 ACTAGAAAACAA
          1 AC-AGAAAACAA

      13419 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:16682 original size:21 final size:21

Alignment explanation


    Indices: 16658--16730  Score: 74
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      16648 GGCTTGGAAT

                                 
      16658 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *          * **  
      16679 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *          *      
      16700 GGTGGTGGCACGGTGAATGGCC
          1 GGTGATGGCACGG-GCATGGCC

               *     
      16722 GGTAATGGC
          1 GGTGATGGC

      16731 TTGGTAGTGG


Statistics
Matches: 41,  Mismatches: 10, Indels: 1
        0.79            0.19        0.02

Matches are distributed among these distances:
  21   30  0.73
  22   11  0.27

ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC
Done.