Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023006.1 Corchorus olitorius cultivar O-4 contig23039, 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: 8255
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28


Found at i:1205 original size:12 final size:12

Alignment explanation


    Indices: 1176--1217  Score: 50
    Period size: 12  Copynumber: 3.4  Consensus size: 12

       1166 TCATGCACCC

                 *       
       1176 AAAACAATTTATT
          1 AAAACCATTTA-T

                        
       1189 AAAACCATTTAT
          1 AAAACCATTTAT

                         
       1201 AAAA-CATTTAAT
          1 AAAACCATTT-AT

                 
       1213 AAAAC
          1 AAAAC

       1218 AGTAATAAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  11    5  0.19
  12   11  0.42
  13   10  0.38

ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31


Consensus pattern (12 bp):   
AAAACCATTTAT

Found at i:1218 original size:12 final size:12

Alignment explanation


    Indices: 1176--1227  Score: 54
    Period size: 11  Copynumber: 4.3  Consensus size: 12

       1166 TCATGCACCC

                       * 
       1176 AAAACAATTTATT
          1 AAAAC-ATTTAAT

                         
       1189 AAAACCATTT-AT
          1 AAAA-CATTTAAT

                        
       1201 AAAACATTTAAT
          1 AAAACATTTAAT

                   *    
       1213 AAAACA-GTAAT
          1 AAAACATTTAAT

                
       1224 AAAA
          1 AAAA

       1228 TAGTGCCTCA


Statistics
Matches: 35,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  11   13  0.37
  12   13  0.37
  13    8  0.23
  14    1  0.03

ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29


Consensus pattern (12 bp):   
AAAACATTTAAT

Found at i:8188 original size:28 final size:27

Alignment explanation


    Indices: 8124--8198  Score: 64
    Period size: 28  Copynumber: 2.7  Consensus size: 27

       8114 TCCGGCATTT

                                        
       8124 AAGGGCAAAACTGTAA-TTTAGTCAACC
          1 AAGGGCAAAA-TGTAATTTTAGTCAACC

             *   *                   *   
       8151 AGGGGTAAAATGGTAATTTTAG-CTGACC
          1 AAGGGCAAAAT-GTAATTTTAGTC-AACC

                       *        
       8179 AAGGGCAAAACAGTAATTTT
          1 AAGGGCAAAA-TGTAATTTT

       8199 GATATTTTAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 7
        0.75            0.12        0.14

Matches are distributed among these distances:
  26    1  0.03
  27   13  0.34
  28   24  0.63

ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25


Consensus pattern (27 bp):   
AAGGGCAAAATGTAATTTTAGTCAACC
Done.