Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009201.1 Corchorus capsularis cultivar CVL-1 contig09222, 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: 6638
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Found at i:1047 original size:32 final size:32

Alignment explanation


    Indices: 1011--1091  Score: 83
    Period size: 31  Copynumber: 2.6  Consensus size: 32

       1001 CTCTCTAGGG

                                            
       1011 GCGGCCTGCCGTGGCAAGGCCGACCCCAGTGT
          1 GCGGCCTGCCGTGGCAAGGCCGACCCCAGTGT

                 *    *  *        *    *    
       1043 GCGGCTTG-CTTGCCAAGGCCGCCCCCTGTGT
          1 GCGGCCTGCCGTGGCAAGGCCGACCCCAGTGT

                *    * *      
       1074 GCGGTCTGCTGAGGCAAG
          1 GCGGCCTGCCGTGGCAAG

       1092 ACCGCGCCAG


Statistics
Matches: 37,  Mismatches: 11, Indels: 2
        0.74            0.22        0.04

Matches are distributed among these distances:
  31   25  0.68
  32   12  0.32

ACGTcount: A:0.11, C:0.35, G:0.37, T:0.17


Consensus pattern (32 bp):   
GCGGCCTGCCGTGGCAAGGCCGACCCCAGTGT

Found at i:1211 original size:20 final size:20

Alignment explanation


    Indices: 1186--1225  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1176 CGGCTCAGCC

                      *         
       1186 CCTAGATCTATTTTTTTACA
          1 CCTAGATCTAATTTTTTACA

                                
       1206 CCTAGATCTAATTTTTTACA
          1 CCTAGATCTAATTTTTTACA

       1226 TCCATTCCTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47


Consensus pattern (20 bp):   
CCTAGATCTAATTTTTTACA

Found at i:3682 original size:26 final size:28

Alignment explanation


    Indices: 3648--3699  Score: 72
    Period size: 26  Copynumber: 1.9  Consensus size: 28

       3638 TTTTTATTTT

                *    *                  
       3648 TTATTAATTTATATATA-TTT-ATATAA
          1 TTATGAATTAATATATACTTTGATATAA

                                      
       3674 TTATGAATTAATATATACTTTGATAT
          1 TTATGAATTAATATATACTTTGATAT

       3700 CAAAACTTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  26   15  0.68
  27    3  0.14
  28    4  0.18

ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54


Consensus pattern (28 bp):   
TTATGAATTAATATATACTTTGATATAA
Done.