Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005939.1 Corchorus capsularis cultivar CVL-1 contig05957, 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, 774

Length: 1291
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34


Found at i:222 original size:119 final size:119

Alignment explanation


    Indices: 1--671  Score: 1066
    Period size: 119  Copynumber: 5.6  Consensus size: 119

                                        *  *                 *               
          1 ACGTGCTTGT-GGAGTTGCACGTGTTCAAGGTAGCATTCGGTGCTCTTCCTTAAGCATTGTTCAC
          1 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAGCATTGTTCAC

                                                   *              
         65 TCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTGC
         66 TCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

                              *                              *               
        119 ACGTGCTTGTGGGAGTTGGACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTAAGCATTGTTCAC
          1 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAGCATTGTTCAC

                   *   *                                          
        184 TCGCGCGATTGACACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC
         66 TCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

                                                  *            *          *  
        238 ACGTGCTTG-GAGGAGTTAG-ACGTGTTCAGGGGAG-AATCTGGTGCTCTTGATTAAGCATTCTT
          1 ACGTGCTTGTG-GGAGTT-GCACGTGTTCAGGGGAGCATTC-GGTGCTCTTCATTAAGCATTGTT

                                                      *              
        300 CACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTGC
         63 CACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

                                                             *               
        357 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTAAGCATTGTTCAC
          1 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAGCATTGTTCAC

                                        *                         
        422 TCGCGCGGTTGGCACTCTTCATTGAGCAATCTTCTTTTGCGCATTGGTGATTGC
         66 TCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

                                                  *                     *    
        476 ACGTGCTTAG-GGGAGTTGCACGTGTTCAGGGGAGCATCCGGTGCTCTTCATTAAGCATTCTTCA
          1 ACGTGCTT-GTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAGCATTGTTCA

                             *               *                    *
        540 CTCGCGCGGTTGGCACTTTTCATTGAGCACTCTGCTTTTGCGCATTGGTGATTGT
         65 CTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

                                                                        *    
        595 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCA-TCTGGTGCTCTTCATTAAGCATTATTCA
          1 ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTC-GGTGCTCTTCATTAAGCATTGTTCA

              *          
        659 CTAGCGCGGTTGG
         65 CTCGCGCGGTTGG

        672 TCATCATGCG


Statistics
Matches: 514,  Mismatches: 29, Indels: 19
        0.91            0.05        0.03

Matches are distributed among these distances:
 118   17  0.03
 119  491  0.96
 120    6  0.01

ACGTcount: A:0.15, C:0.22, G:0.28, T:0.34


Consensus pattern (119 bp):   
ACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAGCATTGTTCAC
TCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTGC

Found at i:496 original size:19 final size:19

Alignment explanation


    Indices: 472--509  Score: 60
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        462 GCATTGGTGA

                                
        472 TTGCACGTGCTT-AGGGGAG
          1 TTGCACGTG-TTCAGGGGAG

                               
        491 TTGCACGTGTTCAGGGGAG
          1 TTGCACGTGTTCAGGGGAG

        510 CATCCGGTGC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    2  0.11
  19   16  0.89

ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26


Consensus pattern (19 bp):   
TTGCACGTGTTCAGGGGAG

Found at i:1044 original size:24 final size:24

Alignment explanation


    Indices: 1012--1057  Score: 83
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1002 TTTTACAATT

                *                   
       1012 GCTCGCCCTTTTGACTTGTTGGTC
          1 GCTCACCCTTTTGACTTGTTGGTC

                                  
       1036 GCTCACCCTTTTGACTTGTTGG
          1 GCTCACCCTTTTGACTTGTTGG

       1058 AGATGGTCAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.07, C:0.28, G:0.24, T:0.41


Consensus pattern (24 bp):   
GCTCACCCTTTTGACTTGTTGGTC
Done.