Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018556.1 Corchorus olitorius cultivar O-4 contig18589, 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: 5994
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:3278 original size:48 final size:48

Alignment explanation


    Indices: 3226--3324  Score: 137
    Period size: 48  Copynumber: 2.1  Consensus size: 48

       3216 CGACTAAAGG

                             *  *    *                       
       3226 TGGCCAAAATGG-CCAATGGTAACCGTCACGACCGATAGTGACCAAAAT
          1 TGGCCAAAA-GGACCAAGGGAAACCATCACGACCGATAGTGACCAAAAT

                                                *   *       
       3274 TGGCCAAAAGGACCAAGGGAAACCATCACGACCGATGGTGGCCAAAAT
          1 TGGCCAAAAGGACCAAGGGAAACCATCACGACCGATAGTGACCAAAAT

               
       3322 TGG
          1 TGG

       3325 TCAAGGCGTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 2
        0.87            0.10        0.04

Matches are distributed among these distances:
  47    2  0.04
  48   43  0.96

ACGTcount: A:0.35, C:0.24, G:0.26, T:0.14


Consensus pattern (48 bp):   
TGGCCAAAAGGACCAAGGGAAACCATCACGACCGATAGTGACCAAAAT

Found at i:5630 original size:49 final size:49

Alignment explanation


    Indices: 5529--5670  Score: 184
    Period size: 49  Copynumber: 3.0  Consensus size: 49

       5519 GAGCATGCCA

                     *   *         *                  *      
       5529 ATCAATTTTATA-CAAAAATTGATAAAAAGTGCAA-TAAAAATTAAAAG
          1 ATCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAAAG

                       **                                     
       5576 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAA-TAAAAG
          1 ATCAATTTTGTAGTAAAAATTGAGAAAAAG-TGCAAGTAAAAAGTAAAAG

            *                                              
       5625 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
          1 ATCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAA

       5671 GGATTGCTTG


Statistics
Matches: 84,  Mismatches: 7, Indels: 7
        0.86            0.07        0.07

Matches are distributed among these distances:
  47   18  0.21
  48   22  0.26
  49   38  0.45
  50    6  0.07

ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27


Consensus pattern (49 bp):   
ATCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAAAG
Done.