Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010150.1 Corchorus olitorius cultivar O-4 contig10182, 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: 10654
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:1106 original size:8 final size:8

Alignment explanation


    Indices: 1090--1129  Score: 64
    Period size: 8  Copynumber: 5.1  Consensus size: 8

       1080 ATAGGGTAGG

                    
       1090 TTTTT-TT
          1 TTTTTCTT

                    
       1097 TTTTTCTT
          1 TTTTTCTT

                    
       1105 TTTTTCTT
          1 TTTTTCTT

                    
       1113 TTTTTCTT
          1 TTTTTCTT

             *      
       1121 TCTTTCTT
          1 TTTTTCTT

             
       1129 T
          1 T

       1130 CTGTGGTCTG


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   7    5  0.16
   8   26  0.84

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (8 bp):   
TTTTTCTT

Found at i:1116 original size:20 final size:20

Alignment explanation


    Indices: 1091--1131  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1081 TAGGGTAGGT

                   *       *    
       1091 TTTTTTTTTTTCTTTTTTTC
          1 TTTTTTTCTTTCTTTCTTTC

                                
       1111 TTTTTTTCTTTCTTTCTTTC
          1 TTTTTTTCTTTCTTTCTTTC

             
       1131 T
          1 T

       1132 GTGGTCTGAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (20 bp):   
TTTTTTTCTTTCTTTCTTTC

Found at i:5190 original size:24 final size:25

Alignment explanation


    Indices: 5162--5213  Score: 63
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       5152 CTGCAGCTGC

                  *                 * 
       5162 GGAAAGTGAGGAG-GAGGAG-GCGGA
          1 GGAAAGCGAGG-GTGAGGAGAGCGAA

                                     
       5186 GGAAAGCGAGGGTGAGGAGAGCGAA
          1 GGAAAGCGAGGGTGAGGAGAGCGAA

               
       5211 GGA
          1 GGA

       5214 GAAGGAGATG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  23    1  0.04
  24   16  0.67
  25    7  0.29

ACGTcount: A:0.35, C:0.06, G:0.56, T:0.04


Consensus pattern (25 bp):   
GGAAAGCGAGGGTGAGGAGAGCGAA
Done.