Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016418.1 Corchorus olitorius cultivar O-4 contig16451, 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: 18160
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:2127 original size:25 final size:24

Alignment explanation


    Indices: 2090--2136  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       2080 CTAGAAAATT

                                      
       2090 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       2116 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       2137 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:2994 original size:21 final size:21

Alignment explanation


    Indices: 2970--3019  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2960 CTTAGGCAAT

                                  
       2970 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGAAA-CTTGC

                   *     *       
       2991 TCCAATGTGCTTGGAACTTGC
          1 TCCAATGAGCTTGAAACTTGC

                    
       3012 TCCAATGA
          1 TCCAATGA

       3020 ACTCCTAGCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACTTGC

Found at i:5631 original size:130 final size:130

Alignment explanation


    Indices: 5395--5631  Score: 309
    Period size: 130  Copynumber: 1.8  Consensus size: 130

       5385 AACTTTATAA

                                *              *                 *           
       5395 TTGGGGCTAAAGCTTATTTATAAGTGTTCAAACTTTTTTTTCTAAAACCCTAAGATAGTGGATCT
          1 TTGGGGCTAAAGCTTATTTAAAAGTGTTCAAACTTATTTTTCTAAAACCCTAAAATAGTGGATCT

              **                              *                              
       5460 TACCATTCAAGAGCTACCCTTAAAAAATAAAACATATTTTTTTGACAAAAAAAAACATATTTTAG
         66 TAAAATTCAAGAGCTACCCTTAAAAAATAAAACACATTTTTTTGACAAAAAAAAACATATTTTAG

                       *                                  *           *      
       5525 TTGGGGCTAAATCTTATTTAAAAGTGTTCAAACTTATTTTTCTAAATCCCTAAAATAATTGG-TC
          1 TTGGGGCTAAAGCTTATTTAAAAGTGTTCAAACTTATTTTTCTAAAACCCTAAAAT-AGTGGATC

                    *    **                              
       5589 TTAAAATTTAAGATTTACCC-TAAGAAAATACTAAA-ACATTTTT
         65 TTAAAATTCAAGAGCTACCCTTAA-AAAATA--AAACACATTTTT

       5632 ATAATTGAGC


Statistics
Matches: 91,  Mismatches: 12, Indels: 7
        0.83            0.11        0.06

Matches are distributed among these distances:
 129    3  0.03
 130   74  0.81
 131   11  0.12
 132    3  0.03

ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37


Consensus pattern (130 bp):   
TTGGGGCTAAAGCTTATTTAAAAGTGTTCAAACTTATTTTTCTAAAACCCTAAAATAGTGGATCT
TAAAATTCAAGAGCTACCCTTAAAAAATAAAACACATTTTTTTGACAAAAAAAAACATATTTTAG

Found at i:17342 original size:15 final size:16

Alignment explanation


    Indices: 17322--17361  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      17312 AAAGGTTGAA

                            
      17322 AGAAAACAATTA-AAT
          1 AGAAAACAATTATAAT

                          * 
      17337 AGAAAACAATTATAGT
          1 AGAAAACAATTATAAT

                     
      17353 AGAAAACAA
          1 AGAAAACAA

      17362 AACAGAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   12  0.52
  16   11  0.48

ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17


Consensus pattern (16 bp):   
AGAAAACAATTATAAT

Done.