Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015776.1 Corchorus capsularis cultivar CVL-1 contig15797, 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: 42766
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:476 original size:2 final size:2

Alignment explanation


    Indices: 469--499  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        459 GCATACAAAG

                                                          
        469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        500 AAATATCTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:17631 original size:6 final size:6

Alignment explanation


    Indices: 17617--17646  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      17607 TCCGATGCAA

                *                             
      17617 CTGACT CTGATT CTGATT CTGATT CTGATT
          1 CTGATT CTGATT CTGATT CTGATT CTGATT

      17647 GGAGCTTCGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47


Consensus pattern (6 bp):   
CTGATT

Found at i:32955 original size:180 final size:179

Alignment explanation


    Indices: 32627--32971  Score: 464
    Period size: 180  Copynumber: 1.9  Consensus size: 179

      32617 TACCTTATGA

                                *            *                       *  *    
      32627 ACAAGAAATTCTAGAAGTTTTAACATTAAAATTTCCATCAATATAACCCTGGTTAAATCCTTAGT
          1 ACAAGAAATTCTAGAAGTTTCAACATTAAAATTGCCATCAATATAACCCTGGTTAAACCCCTAGT

             *               *                                               
      32692 ACCTTTTCATTCCTACATTACCCCTACCCCTAAGCCACCTAAATTTTATATTAAGATAAGTGAGT
         66 AACTTTTCATTCCTACAATACCCCTACCCCTAAGCCACCTAAATTTTATATTAAGATAAGTGAGT

                       *                                     
      32757 CAAAGCTTTAATTGAAAACATTAC-TGGATGTGTGCTTGCTTCTTATAG
        131 CAAAGCTTTAACTGAAAACATTACTTGGATGTGTGCTTGCTTCTTATAG

                                 *                       *            *      
      32805 ACAAGAAATTCTAGAAGTTTCCACATTAAAATTGCCATCAATATATCCCTGGTTTTAACCCCCTA
          1 ACAAGAAATTCTAGAAGTTTCAACATTAAAATTGCCATCAATATAACCCTGG--TTAAACCCCTA

                            **                   **                          
      32870 GTAACTTTTCATTCCTTTAATACCCCTACCCCTAAGCTGCCTAAATTTTATATTAAGATGGATA-
         64 GTAACTTTTCATTCCTACAATACCCCTACCCCTAAGCCACCTAAATTTTATATTAAGAT--A-AG

               *          *            *            
      32934 TG-TTCAAAG-TTTCACTGAAAACATTTCTTGGATGTGTG
        126 TGAGTCAAAGCTTTAACTGAAAACATTACTTGGATGTGTG

      32972 ATTACTTGCA


Statistics
Matches: 144,  Mismatches: 17, Indels: 9
        0.85            0.10        0.05

Matches are distributed among these distances:
 178   48  0.33
 180   76  0.53
 181   16  0.11
 182    3  0.02
 183    1  0.01

ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35


Consensus pattern (179 bp):   
ACAAGAAATTCTAGAAGTTTCAACATTAAAATTGCCATCAATATAACCCTGGTTAAACCCCTAGT
AACTTTTCATTCCTACAATACCCCTACCCCTAAGCCACCTAAATTTTATATTAAGATAAGTGAGT
CAAAGCTTTAACTGAAAACATTACTTGGATGTGTGCTTGCTTCTTATAG
Done.