Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013128.1 Corchorus olitorius cultivar O-4 contig13161, 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: 22642
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:1540 original size:15 final size:16

Alignment explanation


    Indices: 1510--1549  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1500 TTACTTTGTT

                            
       1510 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                     *      
       1526 TTGTTTT-TTGTTTAA
          1 TTGTTTTCTAGTTTAA

                     
       1541 TTGTTTTCT
          1 TTGTTTTCT

       1550 GTCAACCTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   14  0.64
  16    8  0.36

ACGTcount: A:0.12, C:0.05, G:0.12, T:0.70


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:3050 original size:21 final size:21

Alignment explanation


    Indices: 3021--3061  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3011 GGTGTATGAG

                                 
       3021 TGGCCGGTCCTGACTCGGTGA
          1 TGGCCGGTCCTGACTCGGTGA

                *    *  *       
       3042 TGGCTGGTCGTGGCTCGGTG
          1 TGGCCGGTCCTGACTCGGTG

       3062 GAAGATAATC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.05, C:0.24, G:0.44, T:0.27


Consensus pattern (21 bp):   
TGGCCGGTCCTGACTCGGTGA

Found at i:20168 original size:69 final size:69

Alignment explanation


    Indices: 19978--20604  Score: 914
    Period size: 69  Copynumber: 9.2  Consensus size: 69

      19968 TCATTTAACG

                  *                *                                *        
      19978 TGGCTTATGGAAAAGCCCT-TGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGCATGGAAAC
          1 TGGCTTGTGGAAAAG-CCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC

                 
      20042 GAGTT
         65 GAGTT

              *   *        *    ** **             *                          
      20047 TGACTTATGGAAAAGTC-A-AAGAATTCGGATGGAACCGAGGCTTAAACTGACTCGTATGGAAAC
          1 TGGCTTGTGGAAAAGCCTATGTGGCTT-GGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC

               * 
      20110 GAGCT
         65 GAGTT

                                            *             *                  
      20115 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGAAACCAAGGCTTAAGCTGACTCGTATGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20180 AGTT
         66 AGTT

                               *            *                        *       
      20184 TGGCTTGTGGAAAAGCCTAAGTGGCTTGGATGAAACCAAGGCTTAAACTGACTCGTACGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

              * 
      20249 AGCT
         66 AGTT

                                                                             
      20253 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20318 AGTT
         66 AGTT

                                   *        *               *       *        
      20322 TGGCTTGTGGAAAAGCCTATGTGACTTGGATGCAACCAAGGCTTAAACAGACTCGTGTGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20387 AGTT
         66 AGTT

                                         * *                    *            
      20391 TGGCTTGTGGAAAAGCCTATGTGGCTTGGCTAGAACCAAGGCTTAAACTGACACGTATGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20456 AGTT
         66 AGTT

                                                                  *    *     
      20460 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGC----A--GACTCATATGAAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20519 AGTT
         66 AGTT

                            *                                                
      20523 TGGCTTGTGGAAAAGCTTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG
          1 TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG

                
      20588 AG-T
         66 AGTT

                          
      20591 TGGCTTGTGGAAAA
          1 TGGCTTGTGGAAAA

      20605 CTCAAAGCAT


Statistics
Matches: 500,  Mismatches: 48, Indels: 21
        0.88            0.08        0.04

Matches are distributed among these distances:
  63   58  0.12
  65    1  0.00
  67    3  0.01
  68   69  0.14
  69  366  0.73
  70    3  0.01

ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25


Consensus pattern (69 bp):   
TGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG
AGTT

Found at i:21598 original size:51 final size:49

Alignment explanation


    Indices: 21505--21653  Score: 178
    Period size: 47  Copynumber: 3.0  Consensus size: 49

      21495 CCCTTCGAAC

                  *    *      *                * *        *   
      21505 AGCGAACTTTGGTCTTGGTCTCACAAATGGAATGCCACCTTATTTTGAAA
          1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA-TTTAAAA

                                                               
      21555 AGC-ATATTTTTGATCTTGGACTCACAAATGGAATGCAATCTTA--TAAAA
          1 AGCGA-A-TTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTAAAA

                        *                                     
      21603 AGCGAATTTTGACCTTGGACTCACAAATGGAATGCAATCTTATTATAAAA
          1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATT-TAAAA

             
      21653 A
          1 A

      21654 TTCTTGTTTT


Statistics
Matches: 86,  Mismatches: 7, Indels: 12
        0.82            0.07        0.11

Matches are distributed among these distances:
  47   35  0.41
  48    8  0.09
  49    2  0.02
  50   10  0.12
  51   31  0.36

ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Consensus pattern (49 bp):   
AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTAAAA

Done.