Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023791.1 Corchorus olitorius cultivar O-4 contig23824, 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: 14174
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:37 original size:21 final size:21

Alignment explanation


    Indices: 11--144  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

          1 CTTAGGCAAT

                         *       
         11 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
         32 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
         53 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
         74 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
         95 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        116 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        137 TCCAATGA
          1 TCCAATGA

        145 ACTTCTAGCA


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    3  0.03
  21  105  0.97

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:5939 original size:21 final size:21

Alignment explanation


    Indices: 5915--5978  Score: 74
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       5905 GGCTTGGAAT

                                 
       5915 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                           * **  
       5936 GGTGATGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *          *      
       5957 GGTGGTGGCACGGTGAATGGCC
          1 GGTGATGGCACGG-GCATGGCC

       5979 AGTTGTGGCT


Statistics
Matches: 34,  Mismatches: 8, Indels: 1
        0.79            0.19        0.02

Matches are distributed among these distances:
  21   30  0.88
  22    4  0.12

ACGTcount: A:0.16, C:0.22, G:0.45, T:0.17


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC

Found at i:10335 original size:66 final size:66

Alignment explanation


    Indices: 10228--10354  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

      10218 GATAATTCTG

                 *    *                                                      
      10228 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT

             
      10293 A
         66 A

                                  **             *        *       *       
      10294 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA

      10355 AACAAATTAT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A

Found at i:10343 original size:33 final size:33

Alignment explanation


    Indices: 10240--10354  Score: 124
    Period size: 33  Copynumber: 3.5  Consensus size: 33

      10230 CCTGATTTGA

                      **                      
      10240 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATCTGTTTTAG

            *       *       *      *  **    *
      10273 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                                    *        
      10306 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                            
      10339 GTGTTGTTTGTGATGA
          1 GTGTTGTTTGTGATGA

      10355 AACAAATTAT


Statistics
Matches: 64,  Mismatches: 17, Indels: 2
        0.77            0.20        0.02

Matches are distributed among these distances:
  33   63  0.98
  34    1  0.02

ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44


Consensus pattern (33 bp):   
GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

Found at i:10368 original size:33 final size:32

Alignment explanation


    Indices: 10260--10402  Score: 108
    Period size: 33  Copynumber: 4.3  Consensus size: 32

      10250 CAATGACATG

                *        *       *       *  
      10260 AAATCTGTTTTAGATGTTGTTAGTGATGATAC
          1 AAATTTGTTTTAGGTGTTGTTTGTGATGAAAC

                ** **    *                *  
      10292 TAAACCTAATTTAAGTGTTGTTTGTGATGACAC
          1 -AAATTTGTTTTAGGTGTTGTTTGTGATGAAAC

                                             
      10325 TAAATTTGTTTTAGGTGTTGTTTGTGATGAAAC
          1 -AAATTTGTTTTAGGTGTTGTTTGTGATGAAAC

                              * **             
      10358 AAATTATGTTTT-GGATGCTAATTGTGATGAAAAC
          1 AAATT-TGTTTTAGG-TGTTGTTTGTGATG-AAAC

                *      
      10392 AAATCTGTTTT
          1 AAATTTGTTTT

      10403 GGTTGATCAT


Statistics
Matches: 90,  Mismatches: 17, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  32    7  0.08
  33   75  0.83
  34    8  0.09

ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43


Consensus pattern (32 bp):   
AAATTTGTTTTAGGTGTTGTTTGTGATGAAAC

Found at i:13122 original size:25 final size:24

Alignment explanation


    Indices: 13086--13132  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      13076 TCCTTCTATT

                                    
      13086 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
      13109 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

      13133 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.