Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012602.1 Corchorus olitorius cultivar O-4 contig12635, 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: 2670
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28


Found at i:1214 original size:15 final size:15

Alignment explanation


    Indices: 1194--1256  Score: 72
    Period size: 15  Copynumber: 4.0  Consensus size: 15

       1184 AAAAATTGGC

                  *        
       1194 ACCGTTTCAGAAACA
          1 ACCGTTGCAGAAACA

                     *     
       1209 ACCGTTGCAAAAACA
          1 ACCGTTGCAGAAACA

                     *        
       1224 TCATCCGTTTCAGAAACA
          1 --A-CCGTTGCAGAAACA

                           
       1242 ACCGTTGCAGAAACA
          1 ACCGTTGCAGAAACA

       1257 TCATCTGGTG


Statistics
Matches: 40,  Mismatches: 5, Indels: 6
        0.78            0.10        0.12

Matches are distributed among these distances:
  15   26  0.65
  16    1  0.03
  17    1  0.03
  18   12  0.30

ACGTcount: A:0.40, C:0.27, G:0.14, T:0.19


Consensus pattern (15 bp):   
ACCGTTGCAGAAACA

Found at i:1232 original size:33 final size:33

Alignment explanation


    Indices: 1195--1261  Score: 125
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       1185 AAAATTGGCA

                                             
       1195 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
          1 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT

                                   *         
       1228 CCGTTTCAGAAACAACCGTTGCAGAAACATCAT
          1 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT

             
       1261 C
          1 C

       1262 TGGTGCAGAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.37, C:0.28, G:0.13, T:0.21


Consensus pattern (33 bp):   
CCGTTTCAGAAACAACCGTTGCAAAAACATCAT

Found at i:1271 original size:33 final size:33

Alignment explanation


    Indices: 1201--1272  Score: 108
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       1191 GGCACCGTTT

                                          * *
       1201 CAGAAACAACCGTTGCAAAAACATCATCCGTTT
          1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG

                             *          *    
       1234 CAGAAACAACCGTTGCAGAAACATCATCTGGTG
          1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG

                  
       1267 CAGAAA
          1 CAGAAA

       1273 ATTGCAAATG


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18


Consensus pattern (33 bp):   
CAGAAACAACCGTTGCAAAAACATCATCCGGTG
Done.