Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021619.1 Corchorus olitorius cultivar O-4 contig21652, 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: 12525
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:7753 original size:2 final size:2

Alignment explanation


    Indices: 7746--7779  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       7736 ATTTTTAATA

                                                                 
       7746 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7780 TTTTAAAGAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   28  0.93

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:10420 original size:48 final size:46

Alignment explanation


    Indices: 10345--10486  Score: 176
    Period size: 49  Copynumber: 3.0  Consensus size: 46

      10335 GAGCGTGCCA

                        *         *                 *      
      10345 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGT-AAAAATAAAAG

                                                             
      10392 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTAAAAATAAAAG

            *    *      *                                 
      10441 TTCAAATTTGTAGTAAAAATTGAGAAAAAGTGCAGTAAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTAAAAA-TAAA

      10487 GGATTGCTTT


Statistics
Matches: 84,  Mismatches: 6, Indels: 9
        0.85            0.06        0.09

Matches are distributed among these distances:
  47   20  0.24
  48   22  0.26
  49   39  0.46
  50    3  0.04

ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27


Consensus pattern (46 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTAAAAATAAAAG

Done.