Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012960.1 Corchorus olitorius cultivar O-4 contig12993, 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: 12661
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1517 original size:22 final size:23

Alignment explanation


    Indices: 1489--1535  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 23

       1479 GATAAACCCG

                           *       
       1489 TAACCCGAATGACCCGAGAA-AT
          1 TAACCCGAATGACCCAAGAATAT

                   *               
       1511 TAACCCGGATGACCCAAGAATAT
          1 TAACCCGAATGACCCAAGAATAT

              
       1534 TA
          1 TA

       1536 TAAACCAAAA


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

Matches are distributed among these distances:
  22   18  0.82
  23    4  0.18

ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17


Consensus pattern (23 bp):   
TAACCCGAATGACCCAAGAATAT

Found at i:8539 original size:49 final size:48

Alignment explanation


    Indices: 8440--8579  Score: 167
    Period size: 49  Copynumber: 2.9  Consensus size: 48

       8430 CGTGCCAATT

                      *         *         *       *         
       8440 AATTTTGTCAAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAGATC
          1 AATTTTGTCATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAGATC

                     *                                     *  
       8488 AATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAGTTC
          1 AATTTTGTCATAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAGATC

                                            *      *    
       8537 AATTTTGT-AGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
          1 AATTTTGTCA-TAAAAATTGAGAAAAAGTGCAATGAAAAATAAA

       8580 GGATTGCTTG


Statistics
Matches: 79,  Mismatches: 9, Indels: 8
        0.82            0.09        0.08

Matches are distributed among these distances:
  48   37  0.47
  49   42  0.53

ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27


Consensus pattern (48 bp):   
AATTTTGTCATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAGATC

Found at i:9869 original size:9 final size:9

Alignment explanation


    Indices: 9851--9888  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       9841 TTAATTCATT

                     
       9851 TAATTT-CA
          1 TAATTTCCA

                     
       9859 TAATTTCCA
          1 TAATTTCCA

                    *
       9868 TAATTTCCT
          1 TAATTTCCA

                     
       9877 TAATTTCCA
          1 TAATTTCCA

               
       9886 TAA
          1 TAA

       9889 GTAATTTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    6  0.22
   9   21  0.78

ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47


Consensus pattern (9 bp):   
TAATTTCCA
Done.