Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013415.1 Corchorus olitorius cultivar O-4 contig13448, 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: 23761
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:220 original size:30 final size:30

Alignment explanation


    Indices: 181--239  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        171 GTTTATTAAT

                                           
        181 GAAACTTGAAAATTAAAGACATAAAATAAAG
          1 GAAACTTGAAAATTAAAG-CATAAAATAAAG

                                    *    
        212 GAAA-TTGAAAATTAAAGCATAAATTAAA
          1 GAAACTTGAAAATTAAAGCATAAAATAAA

        240 TAACTAATCT


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

Matches are distributed among these distances:
  29   10  0.37
  30   13  0.48
  31    4  0.15

ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22


Consensus pattern (30 bp):   
GAAACTTGAAAATTAAAGCATAAAATAAAG

Found at i:16468 original size:23 final size:22

Alignment explanation


    Indices: 16424--16468  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      16414 ATAACAATTG

                *       *         
      16424 AAAAGAAAGCAATTAAACTAAA
          1 AAAACAAAGCAAGTAAACTAAA

                              *    
      16446 AAAACAAAGCAGAGTAAATTAAA
          1 AAAACAAAGCA-AGTAAACTAAA

      16469 TCTAAATCTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  22   10  0.53
  23    9  0.47

ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13


Consensus pattern (22 bp):   
AAAACAAAGCAAGTAAACTAAA

Found at i:23545 original size:26 final size:27

Alignment explanation


    Indices: 23512--23572  Score: 65
    Period size: 26  Copynumber: 2.3  Consensus size: 27

      23502 ATTGTTTTCT

                     *                  
      23512 TTAA-TTTACTTGATTGCTTT-CTT-AG
          1 TTAATTTTAATTGATTG-TTTGCTTGAG

                         *            *
      23537 TTAATTTTAATTGTTTGTTTGCTTGAT
          1 TTAATTTTAATTGATTGTTTGCTTGAG

                     
      23564 TTAATTTTA
          1 TTAATTTTA

      23573 TAATAAAAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  25    7  0.23
  26   13  0.43
  27   10  0.33

ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61


Consensus pattern (27 bp):   
TTAATTTTAATTGATTGTTTGCTTGAG
Done.