Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001971.1 Corchorus capsularis cultivar CVL-1 contig01974, 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: 2636
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:1925 original size:44 final size:44

Alignment explanation


    Indices: 1875--1959  Score: 143
    Period size: 44  Copynumber: 1.9  Consensus size: 44

       1865 TTGAGAGCTT

                    *                                   
       1875 GATAATTTGATTCAAGGGTATTGGCGACTTGATCTTGAATTGAC
          1 GATAATTTAATTCAAGGGTATTGGCGACTTGATCTTGAATTGAC

                        *      *                     
       1919 GATAATTTAATTTAAGGGTCTTGGCGACTTGATCTTGAATT
          1 GATAATTTAATTCAAGGGTATTGGCGACTTGATCTTGAATT

       1960 AATAACTTGA


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  44   38  1.00

ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39


Consensus pattern (44 bp):   
GATAATTTAATTCAAGGGTATTGGCGACTTGATCTTGAATTGAC

Found at i:1977 original size:27 final size:28

Alignment explanation


    Indices: 1944--2023  Score: 78
    Period size: 27  Copynumber: 2.9  Consensus size: 28

       1934 GGGTCTTGGC

                                        
       1944 GACTTGATCTTGAATTAATAACTTGAGA
          1 GACTTGATCTTGAATTAATAACTTGAGA

              *                   *      *
       1972 G-TTTGAT-TTG-ATTCAAATATCTTG-GC
          1 GACTTGATCTTGAATT--AATAACTTGAGA

                                 *    
       1998 GACTTGATCTTGAATTAATAATTTGA
          1 GACTTGATCTTGAATTAATAACTTGA

       2024 TTCAAGGGTC


Statistics
Matches: 40,  Mismatches: 6, Indels: 12
        0.69            0.10        0.21

Matches are distributed among these distances:
  25    3  0.08
  26    5  0.12
  27   25  0.62
  28    4  0.10
  29    3  0.08

ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41


Consensus pattern (28 bp):   
GACTTGATCTTGAATTAATAACTTGAGA

Found at i:2003 original size:98 final size:98

Alignment explanation


    Indices: 1842--2049  Score: 260
    Period size: 98  Copynumber: 2.1  Consensus size: 98

       1832 AGGGTTGAAT

                             *    *                         * *              
       1842 GACTTGATCTTGAACTTGATAATTTGAGAGCTTGATAATTTGATTCAAGGGTATTGGCGACTTGA
          1 GACTTGATCTTGAACTTAATAACTTGAGAGCTT-ATAATTTGATTCAAAGATATTGGCGACTTGA

                                    *            
       1907 TCTTGAATTGACGATAATTTAATTTAAGGGTCTTGGC
         65 TCTTGAATT-A--ATAATTTAATTCAAGGGTCTTGGC

                                               *            *  *             
       1944 GACTTGATCTTGAA-TTAATAACTTGAGAG-TT-TGATTTGATTCAAATATCTTGGCGACTTGAT
          1 GACTTGATCTTGAACTTAATAACTTGAGAGCTTATAATTTGATTCAAAGATATTGGCGACTTGAT

                            *             * *
       2006 CTTGAATTAATAATTTGATTCAAGGGTCTTTGT
         66 CTTGAATTAATAATTTAATTCAAGGGTCTTGGC

                       
       2039 GACTTGATCTT
          1 GACTTGATCTT

       2050 AAACGAACAG


Statistics
Matches: 95,  Mismatches: 11, Indels: 7
        0.84            0.10        0.06

Matches are distributed among these distances:
  95   31  0.33
  97    1  0.01
  98   34  0.36
 100    2  0.02
 101   13  0.14
 102   14  0.15

ACGTcount: A:0.27, C:0.11, G:0.21, T:0.40


Consensus pattern (98 bp):   
GACTTGATCTTGAACTTAATAACTTGAGAGCTTATAATTTGATTCAAAGATATTGGCGACTTGAT
CTTGAATTAATAATTTAATTCAAGGGTCTTGGC

Found at i:2119 original size:32 final size:33

Alignment explanation


    Indices: 2082--2143  Score: 108
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       2072 CCAAATAAGC

                       *                     
       2082 TGGTG-AGATCGAAATAATGATTTCTTGAATGT
          1 TGGTGAAGATCAAAATAATGATTTCTTGAATGT

                                          
       2114 TGGTGAAGATCAAAATAATGATTTCTTGAA
          1 TGGTGAAGATCAAAATAATGATTTCTTGAA

       2144 AGCTAGCTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  32    5  0.18
  33   23  0.82

ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35


Consensus pattern (33 bp):   
TGGTGAAGATCAAAATAATGATTTCTTGAATGT

Done.