Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015110.1 Corchorus olitorius cultivar O-4 contig15143, 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: 10994
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:3581 original size:21 final size:20

Alignment explanation


    Indices: 3557--3595  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       3547 TTTTTAATGA

                 *       *       
       3557 TAATTTTTTATAATTTAAATT
          1 TAATTATTTA-AACTTAAATT

                              
       3578 TAATTATTTAAACTTAAA
          1 TAATTATTTAAACTTAAA

       3596 AAAACAAAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    7  0.44
  21    9  0.56

ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54


Consensus pattern (20 bp):   
TAATTATTTAAACTTAAATT

Found at i:8553 original size:31 final size:31

Alignment explanation


    Indices: 8490--8553  Score: 78
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       8480 AAGAAACCGG

                         *                 
       8490 AAATGGGAACTTTCCCTTCTTGTAAAACTAA
          1 AAATGGGAACTTTACCTTCTTGTAAAACTAA

                            *                
       8521 AAATGGGAACCTTTACTTTGCTTG-AAAA-TAA
          1 AAATGGGAA-CTTTACCTT-CTTGTAAAACTAA

              
       8552 AA
          1 AA

       8554 CTGGCTGATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  31   14  0.48
  32   11  0.38
  33    4  0.14

ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31


Consensus pattern (31 bp):   
AAATGGGAACTTTACCTTCTTGTAAAACTAA

Found at i:10935 original size:40 final size:41

Alignment explanation


    Indices: 10887--10977  Score: 107
    Period size: 40  Copynumber: 2.2  Consensus size: 41

      10877 GATTATCTTA

                                                       
      10887 CTTAGGGTTTAACA-TGATTTTAGGG-AATTCTTCT-ATCTCT
          1 CTTAGGGTTTAACATTG-TTTT-GGGCAATTCTTCTAATCTCT

                       *             **     *        
      10927 CTTAGGGTTTAGCATTGTTTTGGGCTCTTCTTTTAATCTCT
          1 CTTAGGGTTTAACATTGTTTTGGGCAATTCTTCTAATCTCT

                      
      10968 CTTAGGGTTT
          1 CTTAGGGTTT

      10978 GTCTATCATG


Statistics
Matches: 44,  Mismatches: 4, Indels: 5
        0.83            0.08        0.09

Matches are distributed among these distances:
  39    3  0.07
  40   23  0.52
  41   18  0.41

ACGTcount: A:0.16, C:0.15, G:0.20, T:0.48


Consensus pattern (41 bp):   
CTTAGGGTTTAACATTGTTTTGGGCAATTCTTCTAATCTCT
Done.