Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022596.1 Corchorus olitorius cultivar O-4 contig22629, 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: 3779
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32


Found at i:1190 original size:28 final size:29

Alignment explanation


    Indices: 1154--1231  Score: 88
    Period size: 28  Copynumber: 2.8  Consensus size: 29

       1144 TTCAAAGTAC

                *      *            *    
       1154 AAGGTTAAAACTGTAAATTTA-ACCTTCT
          1 AAGGGTAAAACGGTAAATTTATACATTCT

                                  *      
       1182 AAGGGTAAAACGGT-AATTTATTCATTCT
          1 AAGGGTAAAACGGTAAATTTATACATTCT

            *               *     
       1210 TAGGGTAAAACGGTAATTTTAT
          1 AAGGGTAAAACGGTAAATTTAT

       1232 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

Found at i:2030 original size:12 final size:11

Alignment explanation


    Indices: 1988--2054  Score: 55
    Period size: 12  Copynumber: 5.8  Consensus size: 11

       1978 TAAATTCCTA

                       
       1988 TTTTCTTTTCT
          1 TTTTCTTTTCT

                        
       1999 TTTTCTTTTACT
          1 TTTTCTTTT-CT

            *  *        
       2011 CTTCCTTTCTCT
          1 TTTTCTTT-TCT

                    *  
       2023 TTTTCTTTCCT
          1 TTTTCTTTTCT

               *        
       2034 TATGTCTTTT-T
          1 T-TTTCTTTTCT

                      
       2045 TTTTCCTTTT
          1 TTTT-CTTTT

       2055 TCGGGCCAGG


Statistics
Matches: 44,  Mismatches: 8, Indels: 8
        0.73            0.13        0.13

Matches are distributed among these distances:
  10    2  0.05
  11   19  0.43
  12   22  0.50
  13    1  0.02

ACGTcount: A:0.03, C:0.22, G:0.01, T:0.73


Consensus pattern (11 bp):   
TTTTCTTTTCT

Found at i:2041 original size:18 final size:17

Alignment explanation


    Indices: 1988--2053  Score: 69
    Period size: 18  Copynumber: 3.8  Consensus size: 17

       1978 TAAATTCCTA

                    *    *   
       1988 TTTTCTTTTCTTTTTCT
          1 TTTTCTTTCCTTTCTCT

               *              
       2005 TTTACTCTTCCTTTCTCT
          1 TTTTCT-TTCCTTTCTCT

                          *   
       2023 TTTTCTTTCCTTATGTCT
          1 TTTTCTTTCCTT-TCTCT

                *        
       2041 TTTTTTTTCCTTT
          1 TTTTCTTTCCTTT

       2054 TTCGGGCCAG


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  17   12  0.29
  18   29  0.71

ACGTcount: A:0.03, C:0.23, G:0.02, T:0.73


Consensus pattern (17 bp):   
TTTTCTTTCCTTTCTCT
Done.