Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020353.1 Corchorus olitorius cultivar O-4 contig20386, 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: 12600
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:1543 original size:22 final size:23

Alignment explanation


    Indices: 1518--1704  Score: 103
    Period size: 22  Copynumber: 8.6  Consensus size: 23

       1508 GGGAGATTAA

                  *                
       1518 CAAAATCTCATAAGGAAG-TTAT
          1 CAAAATTTCATAAGGAAGTTTAT

                  *     *     *    
       1540 CAAAA-ATCAT-TGGAAGATTA-
          1 CAAAATTTCATAAGGAAGTTTAT

                                    
       1560 CAAAATTTCAT-AGGAAGGTTTAT
          1 CAAAATTTCATAAGGAA-GTTTAT

            *             **  *    
       1583 TAAAATTTCATAA-TTAGGTTAT
          1 CAAAATTTCATAAGGAAGTTTAT

                        *          
       1605 CAAAATTTCATATGG-AGTTTAT
          1 CAAAATTTCATAAGGAAGTTTAT

              *                     
       1627 CACAATTTCAT-AGGTAA--TTAT
          1 CAAAATTTCATAAGG-AAGTTTAT

              *              * *    
       1648 CAGAATTTCAT-AGCG-TGATTAT
          1 CAAAATTTCATAAG-GAAGTTTAT

                    *   *  *   *   
       1670 CAAAATTTAATAGGGTAG-CTAT
          1 CAAAATTTCATAAGGAAGTTTAT

                         
       1692 CAAAATTTCATAA
          1 CAAAATTTCATAA

       1705 AAATATTTAA


Statistics
Matches: 128,  Mismatches: 24, Indels: 26
        0.72            0.13        0.15

Matches are distributed among these distances:
  20   10  0.08
  21   33  0.26
  22   70  0.55
  23   14  0.11
  24    1  0.01

ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35


Consensus pattern (23 bp):   
CAAAATTTCATAAGGAAGTTTAT

Found at i:1659 original size:43 final size:44

Alignment explanation


    Indices: 1601--1703  Score: 120
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       1591 CATAATTAGG

                                  *      *     *         
       1601 TTATCAAAATTTCATATG-GAGTTTATCACAATTTCATA-GGTAA
          1 TTATCAAAATTTCATA-GCGAGATTATCAAAATTTAATAGGGTAA

                  *            *                       *
       1644 TTATCAGAATTTCATAGCGTGATTATCAAAATTTAATAGGGTAG
          1 TTATCAAAATTTCATAGCGAGATTATCAAAATTTAATAGGGTAA

            *               
       1688 CTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       1704 AAAATATTTA


Statistics
Matches: 50,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  42    1  0.02
  43   31  0.62
  44   18  0.36

ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38


Consensus pattern (44 bp):   
TTATCAAAATTTCATAGCGAGATTATCAAAATTTAATAGGGTAA

Found at i:7301 original size:14 final size:16

Alignment explanation


    Indices: 7277--7318  Score: 52
    Period size: 15  Copynumber: 2.8  Consensus size: 16

       7267 GTTGAAAGAT

                *          *
       7277 TAAGCACTGAAT-TTT
          1 TAAGTACTGAATATTG

                            
       7292 TAA-TACTGAATATTG
          1 TAAGTACTGAATATTG

                        
       7307 TAAGTACTGAAT
          1 TAAGTACTGAAT

       7319 CCAAACTTTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  14    7  0.30
  15    8  0.35
  16    8  0.35

ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38


Consensus pattern (16 bp):   
TAAGTACTGAATATTG

Done.