Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001847.1 Corchorus olitorius cultivar O-4 contig01847, 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: 8241
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:4366 original size:8 final size:8

Alignment explanation


    Indices: 4353--4396  Score: 58
    Period size: 8  Copynumber: 5.9  Consensus size: 8

       4343 ATATATATCT

                    
       4353 TATCTTAC
          1 TATCTTAC

                    
       4361 TATCTTAC
          1 TATCTTAC

               *    
       4369 TATTTTAC
          1 TATCTTAC

                    
       4377 TATC-T--
          1 TATCTTAC

                    
       4382 TATCTTAC
          1 TATCTTAC

                   
       4390 TATCTTA
          1 TATCTTA

       4397 TTACTATATA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
   5    4  0.13
   6    1  0.03
   7    1  0.03
   8   25  0.81

ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55


Consensus pattern (8 bp):   
TATCTTAC

Found at i:4366 original size:13 final size:13

Alignment explanation


    Indices: 4348--4397  Score: 64
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       4338 TGTCTATATA

                         
       4348 TATCTTATCTTAC
          1 TATCTTATCTTAC

                       *    
       4361 TATCTTACTATTTTAC
          1 TATC-T--TATCTTAC

                         
       4377 TATCTTATCTTAC
          1 TATCTTATCTTAC

                    
       4390 TATCTTAT
          1 TATCTTAT

       4398 TACTATATAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  13   19  0.59
  14    1  0.03
  15    1  0.03
  16   11  0.34

ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56


Consensus pattern (13 bp):   
TATCTTATCTTAC

Found at i:6964 original size:43 final size:44

Alignment explanation


    Indices: 6873--6975  Score: 131
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       6863 TGAATATTTT

                                 *   *     *            
       6873 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACAACCC
          1 TATGAAATTTTGATAATTACCATATGAAATTGTGATAACAACCC

                                                         
       6917 TATGAAATTTTGATAATTA-CATATGAAATTGTGAT-A-AACTCC
          1 TATGAAATTTTGATAATTACCATATGAAATTGTGATAACAAC-CC

                    *        
       6959 ATATGAAACTTTGATAA
          1 -TATGAAATTTTGATAA

       6976 CCTAACTATA


Statistics
Matches: 53,  Mismatches: 4, Indels: 5
        0.85            0.06        0.08

Matches are distributed among these distances:
  41    3  0.06
  42    3  0.06
  43   28  0.53
  44   19  0.36

ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38


Consensus pattern (44 bp):   
TATGAAATTTTGATAATTACCATATGAAATTGTGATAACAACCC

Found at i:7023 original size:21 final size:22

Alignment explanation


    Indices: 6873--7058  Score: 116
    Period size: 22  Copynumber: 8.5  Consensus size: 22

       6863 TGAATATTTT

                                    
       6873 TATGAAATTTTGATAA--TTACCC
          1 TATGAAATTTTGATAACCTT--CC

               *             ***  
       6895 TATTAAATTTTGATAACAACCC
          1 TATGAAATTTTGATAACCTTCC

                                  *
       6917 TATGAAATTTTGATAA--TTACA
          1 TATGAAATTTTGATAACCTT-CC

                     *      *     
       6938 TATGAAATTGTGATAAAC-TCC
          1 TATGAAATTTTGATAACCTTCC

                    *           ** 
       6959 ATATGAAACTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTTCC

               *       *           
       6982 TATAAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCTTCC

                                * 
       7005 TATGAAATTTTG-TAACCTTTC
          1 TATGAAATTTTGATAACCTTCC

                  *         *  *  
       7026 TATG-ATTTTTGATAATCTCCC
          1 TATGAAATTTTGATAACCTTCC

             *   *      
       7047 TGTGAGATTTTG
          1 TATGAAATTTTG

       7059 TTAATAATCC


Statistics
Matches: 125,  Mismatches: 29, Indels: 20
        0.72            0.17        0.11

Matches are distributed among these distances:
  20    6  0.05
  21   37  0.30
  22   65  0.52
  23   17  0.14

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTTCC
Done.