Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015766.1 Corchorus olitorius cultivar O-4 contig15799, 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: 5772
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30


Found at i:1122 original size:25 final size:26

Alignment explanation


    Indices: 1094--1145  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       1084 TTCTGTTTTG

                                      
       1094 TTTCCTTTTCCCTCT-TTTTTTTTCT
          1 TTTCCTTTTCCCTCTCTTTTTTTTCT

                *      * *            
       1119 TTTCTTTTTCCTTTTCTTTTTTTTCT
          1 TTTCCTTTTCCCTCTCTTTTTTTTCT

             
       1145 T
          1 T

       1146 ATATTGGGCC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   12  0.52
  26   11  0.48

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (26 bp):   
TTTCCTTTTCCCTCTCTTTTTTTTCT

Found at i:1125 original size:24 final size:25

Alignment explanation


    Indices: 1089--1141  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       1079 AAAATTTCTG

                *                    
       1089 TTTTGTTTCCTTTTCCCTCTT-TTT
          1 TTTTCTTTCCTTTTCCCTCTTCTTT

                    *     *   *      
       1113 TTTTCTTTTCTTTTTCCTTTTCTTT
          1 TTTTCTTTCCTTTTCCCTCTTCTTT

                
       1138 TTTT
          1 TTTT

       1142 TCTTATATTG


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  24   17  0.71
  25    7  0.29

ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77


Consensus pattern (25 bp):   
TTTTCTTTCCTTTTCCCTCTTCTTT

Found at i:1126 original size:12 final size:12

Alignment explanation


    Indices: 1111--1140  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       1101 TTCCCTCTTT

                        
       1111 TTTTTTCTTTTC
          1 TTTTTTCTTTTC

                 *      
       1123 TTTTTCCTTTTC
          1 TTTTTTCTTTTC

                  
       1135 TTTTTT
          1 TTTTTT

       1141 TTCTTATATT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (12 bp):   
TTTTTTCTTTTC

Found at i:5436 original size:13 final size:13

Alignment explanation


    Indices: 5418--5449  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5408 GAAATCGTTA

                   *     
       5418 AAATCAATGTCAT
          1 AAATCAAAGTCAT

                         
       5431 AAATCAAAGTCAT
          1 AAATCAAAGTCAT

                  
       5444 AAATCA
          1 AAATCA

       5450 GAGTAAAACC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25


Consensus pattern (13 bp):   
AAATCAAAGTCAT
Done.