Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019185.1 Corchorus olitorius cultivar O-4 contig19218, 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: 8231
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40


Found at i:1311 original size:20 final size:20

Alignment explanation


    Indices: 1286--1360  Score: 78
    Period size: 20  Copynumber: 3.5  Consensus size: 20

       1276 TTGGAAACAT

                                
       1286 CTTTGCAGAGATTCTTTCCA
          1 CTTTGCAGAGATTCTTTCCA

                           *        
       1306 CTTTGCAGAGCATTATTTTCAACA
          1 CTTTGCAGAG-ATT-CTTTC--CA

             *             *     
       1330 TTTTTGCAGAGATTCCTTCCA
          1 -CTTTGCAGAGATTCTTTCCA

                      
       1351 CTTTGCAGAG
          1 CTTTGCAGAG

       1361 CATTATTTTC


Statistics
Matches: 45,  Mismatches: 5, Indels: 10
        0.75            0.08        0.17

Matches are distributed among these distances:
  20   19  0.42
  21    5  0.11
  22    4  0.09
  23    3  0.07
  24    5  0.11
  25    9  0.20

ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39


Consensus pattern (20 bp):   
CTTTGCAGAGATTCTTTCCA

Found at i:1336 original size:45 final size:45

Alignment explanation


    Indices: 1281--1370  Score: 162
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       1271 CATAATTGGA

                               *                         
       1281 AACATCTTTGCAGAGATTCTTTCCACTTTGCAGAGCATTATTTTC
          1 AACATCTTTGCAGAGATTCCTTCCACTTTGCAGAGCATTATTTTC

                 *                                       
       1326 AACATTTTTGCAGAGATTCCTTCCACTTTGCAGAGCATTATTTTC
          1 AACATCTTTGCAGAGATTCCTTCCACTTTGCAGAGCATTATTTTC

       1371 TTCAATTTCA


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.24, C:0.22, G:0.13, T:0.40


Consensus pattern (45 bp):   
AACATCTTTGCAGAGATTCCTTCCACTTTGCAGAGCATTATTTTC

Found at i:6793 original size:30 final size:30

Alignment explanation


    Indices: 6759--6837  Score: 110
    Period size: 27  Copynumber: 2.7  Consensus size: 30

       6749 ATTACATCAA

                  *                       
       6759 TCATATGCATGTTTTTATTAGTTACTTTGG
          1 TCATATTCATGTTTTTATTAGTTACTTTGG

                                          
       6789 TCATATTCATG---TTATTAGTTACTTTGG
          1 TCATATTCATGTTTTTATTAGTTACTTTGG

                                  
       6816 TCATATTCATGTTCATTTATTA
          1 TCATATTCATGTT--TTTATTA

       6838 TTGGGCATAC


Statistics
Matches: 43,  Mismatches: 1, Indels: 8
        0.83            0.02        0.15

Matches are distributed among these distances:
  27   27  0.63
  30   10  0.23
  32    6  0.14

ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53


Consensus pattern (30 bp):   
TCATATTCATGTTTTTATTAGTTACTTTGG

Found at i:6811 original size:27 final size:27

Alignment explanation


    Indices: 6773--6828  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       6763 ATGCATGTTT

                                       
       6773 TTATTAGTTACTTTGGTCATATTCATG
          1 TTATTAGTTACTTTGGTCATATTCATG

                                       
       6800 TTATTAGTTACTTTGGTCATATTCATG
          1 TTATTAGTTACTTTGGTCATATTCATG

              
       6827 TT
          1 TT

       6829 CATTTATTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54


Consensus pattern (27 bp):   
TTATTAGTTACTTTGGTCATATTCATG
Done.