Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017392.1 Corchorus olitorius cultivar O-4 contig17425, 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: 11767
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:1237 original size:19 final size:18

Alignment explanation


    Indices: 1204--1239  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1194 TTGAAATTAT

                              
       1204 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1222 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1240 TAAGCCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:2741 original size:17 final size:17

Alignment explanation


    Indices: 2711--2748  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       2701 ATAAAAGACA

                     *       
       2711 ATAGGAAATTAAACT-G
          1 ATAGGAAATAAAACTAG

                              
       2727 ATAGGAAAATAAAACTAG
          1 ATAGG-AAATAAAACTAG

                
       2745 ATAG
          1 ATAG

       2749 TTCATTAATG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    5  0.26
  17    9  0.47
  18    5  0.26

ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21


Consensus pattern (17 bp):   
ATAGGAAATAAAACTAG

Found at i:10133 original size:24 final size:24

Alignment explanation


    Indices: 10088--10134  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      10078 AATGAAACTT

                          *  *      
      10088 GAAAAATAAAAATATAGGATAAAG
          1 GAAAAATAAAAATAAAGCATAAAG

                 *     *           
      10112 GAAAATTAAAATTAAAGCATAAA
          1 GAAAAATAAAAATAAAGCATAAA

      10135 CTAGATAACT


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.66, C:0.02, G:0.13, T:0.19


Consensus pattern (24 bp):   
GAAAAATAAAAATAAAGCATAAAG
Done.