Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004517.1 Corchorus olitorius cultivar O-4 contig04533, 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: 1975
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1544 original size:32 final size:32

Alignment explanation


    Indices: 1503--1574  Score: 112
    Period size: 31  Copynumber: 2.3  Consensus size: 32

       1493 CTATAATATA

                                             
       1503 TAGCGGCGTTTTTCTCAGC-AGACGCCGCTAAT
          1 TAGCGGCGTTTTTCTCA-CAAGACGCCGCTAAT

                                            
       1535 TAGCGGCG-TTTTCTCACAAGACGCCGCTAAT
          1 TAGCGGCGTTTTTCTCACAAGACGCCGCTAAT

             *       
       1566 TCGCGGCGT
          1 TAGCGGCGT

       1575 CTGAAGAAGG


Statistics
Matches: 37,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  30    1  0.03
  31   28  0.76
  32    8  0.22

ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26


Consensus pattern (32 bp):   
TAGCGGCGTTTTTCTCACAAGACGCCGCTAAT

Found at i:1561 original size:161 final size:164

Alignment explanation


    Indices: 1196--1563  Score: 385
    Period size: 161  Copynumber: 2.3  Consensus size: 164

       1186 TCTGAATAAG

                                                       **    *               
       1196 AGACGCCGC-AATTTAGCGGCGTTTTGAT-AGAAAGACGCCGCCGTATTGATACATGGAGGGAGA
          1 AGACGCCGCTAA-TTAGCGGCGTTTT-ATCAGAAAGACGCCGCTATATTAATACATGGAGGGAGA

            *                *                                               
       1259 GATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCACACTAAAACAAAGGAAGCTTCCAA
         64 CATTTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTCCACACTAAAACAAAGGAAGCTTCCAA

                      *                         
       1324 CTCTAAACCTGTAATATATAGCGGCGTTTTAAAACA
        129 CTCTAAACCTATAATATATAGCGGCGTTTTAAAACA

                    *     **       *** *   *             *      *            
       1360 AGACGCCGTTAATTTTCGGCGTCAAGAGCAGTAA-ACGCCGCTATTTTAATATATGGAGGGAGAC
          1 AGACGCCGCTAATTAGCGGCGT-TTTATCAGAAAGACGCCGCTATATTAATACATGGAGGGAGAC

                                                                  *  **      
       1424 ATTTTTTTT-T-CTTTGTTTGGAGGGAAAAATTCCCTCTC-C-CTAAAACAAAGTAATTTTCCAA
         65 ATTTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTC-CACACTAAAACAAAGGAAGCTTCCAA

                 **                        ***  
       1485 CTCTACGCCTATAATATATAGCGGCGTTTT-TCTCA
        129 CTCTAAACCTATAATATATAGCGGCGTTTTAAAACA

                                       *    *            
       1520 GCAGACGCCGCTAATTAGCGGCGTTTTCTCA-CAAGACGCCGCTA
          1 --AGACGCCGCTAATTAGCGGCGTTTTATCAGAAAGACGCCGCTA

       1564 ATTCGCGGCG


Statistics
Matches: 164,  Mismatches: 33, Indels: 17
        0.77            0.15        0.08

Matches are distributed among these distances:
 160    4  0.02
 161   57  0.35
 162   45  0.27
 163    2  0.01
 164   50  0.30
 165    6  0.04

ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30


Consensus pattern (164 bp):   
AGACGCCGCTAATTAGCGGCGTTTTATCAGAAAGACGCCGCTATATTAATACATGGAGGGAGACA
TTTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTCCACACTAAAACAAAGGAAGCTTCCAACT
CTAAACCTATAATATATAGCGGCGTTTTAAAACA
Done.