Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023104.1 Corchorus olitorius cultivar O-4 contig23137, 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: 11080
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34


Found at i:730 original size:2 final size:2

Alignment explanation


    Indices: 723--747  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        713 AATTGAAAAG

                                                 
        723 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        748 TTACAAAGGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:7848 original size:10 final size:10

Alignment explanation


    Indices: 7833--7857  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       7823 CAATGCTAAA

                      
       7833 AAAAAAAAAG
          1 AAAAAAAAAG

                      
       7843 AAAAAAAAAG
          1 AAAAAAAAAG

                 
       7853 AAAAA
          1 AAAAA

       7858 GAAGAAGAAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAG

Found at i:7873 original size:16 final size:16

Alignment explanation


    Indices: 7830--7860  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       7820 GCCCAATGCT

                            
       7830 AAAAAAA-AAAAAGAA
          1 AAAAAAAGAAAAAGAA

                            
       7845 AAAAAAAGAAAAAGAA
          1 AAAAAAAGAAAAAGAA

       7861 GAAGAAGGAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.47
  16    8  0.53

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (16 bp):   
AAAAAAAGAAAAAGAA

Found at i:10119 original size:41 final size:41

Alignment explanation


    Indices: 10015--10192  Score: 191
    Period size: 41  Copynumber: 4.3  Consensus size: 41

      10005 CGTGGTAATT

                        *                  * *        
      10015 CAAAGGTGACAATTTCTGGTGTCAACAGTAACTATAATTTAC
          1 CAAA-GTGACAACTTCTGGTGTCAACAGTAATTTTAATTTAC

            ***   *                                   
      10057 TGGAGTAAC-ACTTCTGGTGTCAA-AGGTAATTTTAATTTAC
          1 CAAAGTGACAACTTCTGGTGTCAACA-GTAATTTTAATTTAC

                                    *         *       
      10097 CAAAGTGACAACTTCTGGTGTCAAAAGGTAATTTCAATTTAC
          1 CAAAGTGACAACTTCTGGTGTCAACA-GTAATTTTAATTTAC

                             *    *                   
      10139 C-AAGATGACAACTTCTAGTGTTAACAGTAATTTTAATTTAC
          1 CAAAG-TGACAACTTCTGGTGTCAACAGTAATTTTAATTTAC

                  *      
      10180 CAAAGTTACAACT
          1 CAAAGTGACAACT

      10193 GTAGACACCC


Statistics
Matches: 114,  Mismatches: 17, Indels: 11
        0.80            0.12        0.08

Matches are distributed among these distances:
  39    1  0.01
  40   31  0.27
  41   43  0.38
  42   39  0.34

ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Consensus pattern (41 bp):   
CAAAGTGACAACTTCTGGTGTCAACAGTAATTTTAATTTAC

Found at i:10294 original size:28 final size:28

Alignment explanation


    Indices: 10263--10339  Score: 102
    Period size: 28  Copynumber: 2.8  Consensus size: 28

      10253 TTAGGATCAA

                        *               
      10263 CTAGGGGCATTTCGGTCATTTTCAAAAT
          1 CTAGGGGCATTTTGGTCATTTTCAAAAT

                         *       *  * * 
      10291 CTAGGGGCATTTTAGTCATTTGCATATT
          1 CTAGGGGCATTTTGGTCATTTTCAAAAT

                                  
      10319 C-AGGGGCATTTTGGTCATTTT
          1 CTAGGGGCATTTTGGTCATTTT

      10340 GGCATTTTAG


Statistics
Matches: 42,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  27   18  0.43
  28   24  0.57

ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40


Consensus pattern (28 bp):   
CTAGGGGCATTTTGGTCATTTTCAAAAT

Done.