Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008233.1 Corchorus olitorius cultivar O-4 contig08260, 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: 2493
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:290 original size:14 final size:13

Alignment explanation


    Indices: 271--309  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        261 AAATTGTAAA

                         
        271 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
        284 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
        298 ATTTAAAAAATT
          1 ATTTAAAAAATT

        310 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:538 original size:124 final size:127

Alignment explanation


    Indices: 295--551  Score: 421
    Period size: 124  Copynumber: 2.0  Consensus size: 127

        285 ATTTAAGAAA

                                                                             
        295 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT---AATAAA

                                                                        *    
        360 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
         63 AT--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA

              
        425 AG
        126 AG

                                       *                                     
        427 TATATTTAAAAAATTCTAATATATATACGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG

                 *                                                        
        489 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

             
        551 T
          1 T

        552 TTAAACAATG


Statistics
Matches: 122,  Mismatches: 3, Indels: 8
        0.92            0.02        0.06

Matches are distributed among these distances:
 124   61  0.50
 127    5  0.04
 128    1  0.01
 132   55  0.45

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39


Consensus pattern (127 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

Found at i:1892 original size:27 final size:27

Alignment explanation


    Indices: 1854--1910  Score: 105
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1844 AGACTCTTGA

                                  *    
       1854 AATTTAATTTATATATATATTAGTAAT
          1 AATTTAATTTATATATATATTAATAAT

                                       
       1881 AATTTAATTTATATATATATTAATAAT
          1 AATTTAATTTATATATATATTAATAAT

               
       1908 AAT
          1 AAT

       1911 GAAATTTTAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (27 bp):   
AATTTAATTTATATATATATTAATAAT

Found at i:1923 original size:27 final size:27

Alignment explanation


    Indices: 1859--1917  Score: 91
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       1849 CTTGAAATTT

                             *       **
       1859 AATTTATATATATATTAGTAATAATTT
          1 AATTTATATATATATTAATAATAATGA

                                       
       1886 AATTTATATATATATTAATAATAATGA
          1 AATTTATATATATATTAATAATAATGA

                 
       1913 AATTT
          1 AATTT

       1918 TAATATTGAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49


Consensus pattern (27 bp):   
AATTTATATATATATTAATAATAATGA

Found at i:2129 original size:29 final size:30

Alignment explanation


    Indices: 2096--2160  Score: 87
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       2086 CCCATTTTGT

                     *        *           
       2096 AAGGTTAGGTACTTAAATGACCTTTT-CCA
          1 AAGGTTAGGCACTTAAATAACCTTTTACCA

                      *                    
       2125 AAGGTTAGGCCCTTAAATAACCTTTTCACCA
          1 AAGGTTAGGCACTTAAATAACCTTTT-ACCA

                 
       2156 AAGGT
          1 AAGGT

       2161 CGGGCCCCTA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  29   23  0.74
  31    8  0.26

ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Consensus pattern (30 bp):   
AAGGTTAGGCACTTAAATAACCTTTTACCA

Found at i:2167 original size:31 final size:29

Alignment explanation


    Indices: 2107--2167  Score: 77
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2097 AGGTTAGGTA

                   *               *     
       2107 CTTAAATGACCTTTTCCAAAGGTTAGGCC
          1 CTTAAATAACCTTTTCCAAAGGTCAGGCC

                                      *    
       2136 CTTAAATAACCTTTTCACCAAAGGTCGGGCC
          1 CTTAAATAACCTTTT--CCAAAGGTCAGGCC

             
       2167 C
          1 C

       2168 CTAATTGAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  29   14  0.52
  31   13  0.48

ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28


Consensus pattern (29 bp):   
CTTAAATAACCTTTTCCAAAGGTCAGGCC
Done.