Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011181.1 Corchorus capsularis cultivar CVL-1 contig11202, 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: 5049
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Found at i:2941 original size:166 final size:167

Alignment explanation


    Indices: 2666--3000  Score: 469
    Period size: 166  Copynumber: 2.0  Consensus size: 167

       2656 TGAGTCATTT

                                     *             *                         
       2666 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTTAGGACAT

                      *          *            ** *               ** *   *    
       2731 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAATGTTAGTTCTCTAACT-CATCATCAATCCTT
         66 TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT

                            *                     
       2795 GATAGGGATCA-TTTATTAATTACACTACTCTATTAAA
        131 GATAGGGAT-ATTTTAGTAATTACACTACTCTATTAAA

                                                              *              
       2832 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTTAGGACAT

                        *                                                  * 
       2897 TTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCTT
         66 TTAAGTAATCGGCCAAGTAG-GAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCT

              *                   *     *         
       2961 TGGTAGGGATATTTTAGTAATTCCACTATTCTATTAAA
        130 TGATAGGGATATTTTAGTAATTACACTACTCTATTAAA

              
       2999 GT
          1 GT

       3001 TTAGCACATT


Statistics
Matches: 148,  Mismatches: 18, Indels: 5
        0.87            0.11        0.03

Matches are distributed among these distances:
 165    1  0.01
 166  105  0.71
 167   42  0.28

ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30


Consensus pattern (167 bp):   
GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTTAGGACAT
TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
GATAGGGATATTTTAGTAATTACACTACTCTATTAAA

Found at i:3108 original size:45 final size:45

Alignment explanation


    Indices: 3053--3142  Score: 144
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       3043 AGAACTTCTC

                                                         
       3053 CAGCTCATCATTAATCCGAGATAGGGATCTTTTAGTAATTCCACT
          1 CAGCTCATCATTAATCCGAGATAGGGATCTTTTAGTAATTCCACT

                 *         *  * *                        
       3098 CAGCTTATCATTAATTCGGGCTAGGGATCTTTTAGTAATTCCACT
          1 CAGCTCATCATTAATCCGAGATAGGGATCTTTTAGTAATTCCACT

       3143 ACTCTGTTAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   41  1.00

ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36


Consensus pattern (45 bp):   
CAGCTCATCATTAATCCGAGATAGGGATCTTTTAGTAATTCCACT
Done.