Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010248.1 Corchorus capsularis cultivar CVL-1 contig10269, 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: 5732
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:927 original size:332 final size:330

Alignment explanation


    Indices: 328--1162  Score: 983
    Period size: 332  Copynumber: 2.5  Consensus size: 330

        318 AATCTCAGTA

                    *     *            *           *       *  *      *       
        328 ACATTGGATTTAAAAATTTGTTTTTACAAGTATCTGAATTTTGTTTCAATATAATTATAAATTAA
          1 ACATTGGAATTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATT-A

            *  *              *             *             *                  
        393 TTTAGAAAAAATAAGAAATATGATATTAAAAGCGTGAAAAA-ACCTCCAATCTTTTTTGGCATTG
         65 GTTCGAAAAAATAAGAAAAATGATATTAAAAGTGT-AAAAACA-CTTCAATC-TTTTTGGCATTG

                             *                                     **        
        457 AATTATATA-TTTTTATAAGTATTTTAGTC-AAAAATTGA-GAAGAAATCTTGCGTGTCAATTTT
        127 AATTATATATTTTTTATGAGTATTTTA-TCAAAAAATTGAGGAA-AAATCTTGCGAATCAATTTT

             **                       *   *               **     * *        *
        519 TGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGTGTTCCAGGT
        190 TACAAAATTTTAGCCGAAATCGTGTAATAAACATCACGGTTTTTGGCAAAAAAAGCGTTCCAGGG

                *                             **       *      **             
        584 ACCCCGCTCAGTTTTGCATGATTTTTGAC-TCCATGACTACTTGAAATATTTATATTCATCTAAT
        255 ACCCAGCTCAGTTTTGCATGATTTTTGACGT-CAAAACTACTTCAAATATCCATATTCATCTAAT

                        
        648 CAAATCGCAGCC
        319 CAAATCGCAGCC

                           *         *                    *                  
        660 ACATTGGAATTAAAGGTTTGTTTTTCCGAGTATCTGAATCTTGTTTTGATTTAATTAGAAATTAG
          1 ACATTGGAATTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAG

                      *  *                      *                            
        725 TTCGGAAAAATTAGGAAAAATGATATTAGAAA-TGTCAAAACTACTTCAATCTTTTTGGCATTGA
         66 TTC-GAAAAAATAAGAAAAATGATATTA-AAAGTGTAAAAAC-ACTTCAATCTTTTTGGCATTGA

                                                       *     *               
        789 ATTATATATTTTTTATGAGTATTTTA-CAAAAAATTGAGGAAATATCTTTCGAATCAATTTTCTA
        128 ATTATATATTTTTTATGAGTATTTTATCAAAAAATTGAGGAAAAATCTTGCGAATCAATTTT-TA

                        *                       *                      *     
        853 CAAAATTTTAGCTGAAATCGTGTAATAAACATCAC-ATGTTTTGGCAAAAGAAAGCGTTTC-GGG
        192 CAAAATTTTAGCCGAAATCGTGTAATAAACATCACGGT-TTTTGGCAAAA-AAAGCGTTCCAGGG

            *                                     *     *           *        
        916 GCCCAGCTCAGTTTTGCATGATTTTTGACGTCAAAACTCCTTCAGATATCCATATTTATCTAATC
        255 ACCCAGCTCAGTTTTGCATGATTTTTGACGTCAAAACTACTTCAAATATCCATATTCATCTAATC

                 *     
        981 AAATCTCAGCC
        320 AAATCGCAGCC

                                           *                                 
        992 ACATTGGAATT-AAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
          1 ACATTGGAATTAAAG-ATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTA

                         *      *                     *               *   *  
       1056 GTTC-AAAAAATATG-AAAACGATATTAAAAGTGTAAAAAGCCCTTCAATCTTTTTGGAATTAAA
         65 GTTCGAAAAAATAAGAAAAATGATATTAAAAGTGTAAAAA-CACTTCAATCTTTTTGGCATTGAA

                                                        
       1119 TTATATATTTTTTATGAGTATTTTATCAAAAAATTGAGGAAAAA
        129 TTATATATTTTTTATGAGTATTTTATCAAAAAATTGAGGAAAAA

       1163 AATTTTCGGA


Statistics
Matches: 430,  Mismatches: 58, Indels: 32
        0.83            0.11        0.06

Matches are distributed among these distances:
 328    3  0.01
 329   63  0.15
 330   27  0.06
 331   57  0.13
 332  268  0.62
 333   12  0.03

ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38


Consensus pattern (330 bp):   
ACATTGGAATTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAG
TTCGAAAAAATAAGAAAAATGATATTAAAAGTGTAAAAACACTTCAATCTTTTTGGCATTGAATT
ATATATTTTTTATGAGTATTTTATCAAAAAATTGAGGAAAAATCTTGCGAATCAATTTTTACAAA
ATTTTAGCCGAAATCGTGTAATAAACATCACGGTTTTTGGCAAAAAAAGCGTTCCAGGGACCCAG
CTCAGTTTTGCATGATTTTTGACGTCAAAACTACTTCAAATATCCATATTCATCTAATCAAATCG
CAGCC

Found at i:5423 original size:16 final size:16

Alignment explanation


    Indices: 5402--5453  Score: 59
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       5392 AAGTCAACGT

                  *  *      
       5402 CCCGAACCTGCCCGAA
          1 CCCGAAACTACCCGAA

                   *        
       5418 CCCGAAATTACCCGAA
          1 CCCGAAACTACCCGAA

                 *  *       
       5434 CCCGAGACAACCCGAA
          1 CCCGAAACTACCCGAA

                
       5450 CCCG
          1 CCCG

       5454 CCCGAACCCG


Statistics
Matches: 30,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   30  1.00

ACGTcount: A:0.31, C:0.46, G:0.17, T:0.06


Consensus pattern (16 bp):   
CCCGAAACTACCCGAA
Done.