Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023528.1 Corchorus olitorius cultivar O-4 contig23561, 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: 16076
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:452 original size:27 final size:26

Alignment explanation


    Indices: 414--483  Score: 79
    Period size: 27  Copynumber: 2.6  Consensus size: 26

        404 CATGTTAAGG

                *                       
        414 ATCATTCAAGTCAG-TCTCTCATTCCAA
          1 ATCAGTCAAGTCAGTTCTC-CATT-CAA

                                      
        441 ATCAGTCAAGTCAGTTCTCCATTCAA
          1 ATCAGTCAAGTCAGTTCTCCATTCAA

             *        *      
        467 AGCTAGTCAAATCAGTT
          1 ATC-AGTCAAGTCAGTT

        484 TATAACTTAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  26    5  0.13
  27   29  0.76
  28    4  0.11

ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31


Consensus pattern (26 bp):   
ATCAGTCAAGTCAGTTCTCCATTCAA

Found at i:8015 original size:13 final size:13

Alignment explanation


    Indices: 7987--8026  Score: 57
    Period size: 12  Copynumber: 3.2  Consensus size: 13

       7977 GATATCTCGG

                 *       
       7987 TATATTCGTT-GA
          1 TATATCCGTTCGA

                         
       7999 TATATCCGTTCGA
          1 TATATCCGTTCGA

                         
       8012 TATATCCG-TCGA
          1 TATATCCGTTCGA

               
       8024 TAT
          1 TAT

       8027 GTATATTAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  12   16  0.62
  13   10  0.38

ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42


Consensus pattern (13 bp):   
TATATCCGTTCGA

Found at i:13868 original size:15 final size:15

Alignment explanation


    Indices: 13841--13879  Score: 60
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      13831 CTCTGCTTTA

                            
      13841 TTTTCTAGTTTAATTG
          1 TTTTCT-GTTTAATTG

                           
      13857 TTTTCTGTTTAATTG
          1 TTTTCTGTTTAATTG

            *       
      13872 CTTTCTGT
          1 TTTTCTGT

      13880 CAATCTCTGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   16  0.73
  16    6  0.27

ACGTcount: A:0.13, C:0.10, G:0.13, T:0.64


Consensus pattern (15 bp):   
TTTTCTGTTTAATTG

Found at i:15661 original size:28 final size:29

Alignment explanation


    Indices: 15625--15702  Score: 88
    Period size: 28  Copynumber: 2.8  Consensus size: 29

      15615 TTCAAAGTAC

                *      *            *    
      15625 AAGGTTAAAACTGTAAATTTA-ACCTTCT
          1 AAGGGTAAAACGGTAAATTTATACATTCT

                                  *      
      15653 AAGGGTAAAACGGT-AATTTATTCATTCT
          1 AAGGGTAAAACGGTAAATTTATACATTCT

            *               *     
      15681 TAGGGTAAAACGGTAATTTTAT
          1 AAGGGTAAAACGGTAAATTTAT

      15703 GCCCATACAG


Statistics
Matches: 42,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  27    6  0.14
  28   30  0.71
  29    6  0.14

ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36


Consensus pattern (29 bp):   
AAGGGTAAAACGGTAAATTTATACATTCT
Done.