Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015302.1 Corchorus olitorius cultivar O-4 contig15335, 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: 2404
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1305 original size:28 final size:29

Alignment explanation


    Indices: 1234--1310  Score: 111
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       1224 AAATGAACTT

                   *          *          
       1234 AAAATGATCAAAATGCCCTTGAATATGCA
          1 AAAATGACCAAAATGCCCCTGAATATGCA

            *         *                  
       1263 GAAATGACCATAATGCCCCTGAATATG-A
          1 AAAATGACCAAAATGCCCCTGAATATGCA

                                
       1291 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       1311 AGGTGATCCT


Statistics
Matches: 42,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  28   19  0.45
  29   23  0.55

ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAATATGCA

Found at i:1354 original size:14 final size:14

Alignment explanation


    Indices: 1335--1364  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1325 CCAATTAAGC

                          
       1335 AACAAATTGATTTA
          1 AACAAATTGATTTA

                          
       1349 AACAAATTGATTTA
          1 AACAAATTGATTTA

              
       1363 AA
          1 AA

       1365 TAAAGGACAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33


Consensus pattern (14 bp):   
AACAAATTGATTTA

Found at i:1631 original size:35 final size:35

Alignment explanation


    Indices: 1585--1821  Score: 386
    Period size: 35  Copynumber: 6.8  Consensus size: 35

       1575 TGAGTCTATA

                                    *       *  
       1585 TTGAAGATGCTACACCGAGTCATCCGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

                  *                   *        
       1620 TTGAAGGTGCTACACCGAGTCATCTGGATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

                                       *       
       1655 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

                                      *      * 
       1690 TTGAAGATGCTACACCGAGTCATCTGGATTCAATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

                                       *       
       1725 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

                                                
       1760 TTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
          1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCAACT

                                       
       1795 TTGAAGATGCTACACCGAGTCATCTGA
          1 TTGAAGATGCTACACCGAGTCATCTGA

       1822 GAAGATGGTA


Statistics
Matches: 187,  Mismatches: 14, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
  35  186  0.99
  36    1  0.01

ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCAACT

Found at i:1916 original size:50 final size:50

Alignment explanation


    Indices: 1837--1966  Score: 188
    Period size: 50  Copynumber: 2.6  Consensus size: 50

       1827 TGGTAATGTA

                       *   * *      *                          
       1837 TCGTATGGAAATGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
          1 TCGTATGGAAAAG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC

                       *                     **               
       1888 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTTATGTTGATAATTGAC
          1 TCGTATGGAAAAGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC

                                         
       1938 TCGTATGGAAAAGAGTTTGGCTTGTGGAA
          1 TCGTATGGAAAAGAGTTTGGCTTGTGGAA

       1967 TGTTTCACTT


Statistics
Matches: 72,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  50   60  0.83
  51   12  0.17

ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32


Consensus pattern (50 bp):   
TCGTATGGAAAAGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
Done.