Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019760.1 Corchorus olitorius cultivar O-4 contig19793, 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: 7052
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:409 original size:23 final size:24

Alignment explanation


    Indices: 380--433  Score: 76
    Period size: 24  Copynumber: 2.3  Consensus size: 24

        370 TTTGCTTAAT

                                    
        380 TTTTTAAAATTTCT-CTCAAATCA
          1 TTTTTAAAATTTCTACTCAAATCA

                    *                
        403 TTTTT-AACTTTCTAACTCAAATCA
          1 TTTTTAAAATTTCT-ACTCAAATCA

                   
        427 TTTTTAA
          1 TTTTTAA

        434 CTTTCTAAAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  22    7  0.26
  23    5  0.19
  24   14  0.52
  25    1  0.04

ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50


Consensus pattern (24 bp):   
TTTTTAAAATTTCTACTCAAATCA

Found at i:421 original size:24 final size:24

Alignment explanation


    Indices: 394--441  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        384 TAAAATTTCT

                                    
        394 CTCAAATCATTTTTAACTTTCTAA
          1 CTCAAATCATTTTTAACTTTCTAA

                                    
        418 CTCAAATCATTTTTAACTTTCTAA
          1 CTCAAATCATTTTTAACTTTCTAA

        442 ATTTTTAACT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46


Consensus pattern (24 bp):   
CTCAAATCATTTTTAACTTTCTAA

Found at i:1832 original size:96 final size:96

Alignment explanation


    Indices: 1715--1896  Score: 303
    Period size: 96  Copynumber: 1.9  Consensus size: 96

       1705 TAGCAATTCA

                            *               *  *                             
       1715 GTATAAATATTTACTCTAAAGTGGCAAATTCTGCAGCTACTGAAT-CATTCATTTCAAGATGAAG
          1 GTATAAATATTTACTCAAAAGTGGCAAATTCTACAACTACTGAATGC-TTCATTTCAAGATGAAG

                            *               
       1779 TTTTTCTAAGTTAGTTGAAAGTCTTAGCAAGG
         65 TTTTTCTAAGTTAGTTAAAAGTCTTAGCAAGG

                                       *                                     
       1811 GTATAAATATTTACTCAAAAGTGGCAACTTCTACAACTACTGAATGCTTCATTTCAAGATGAAGT
          1 GTATAAATATTTACTCAAAAGTGGCAAATTCTACAACTACTGAATGCTTCATTTCAAGATGAAGT

                                 
       1876 TTTTCTAAGTTAGTTAAAAGT
         66 TTTTCTAAGTTAGTTAAAAGT

       1897 GACTCAGCTT


Statistics
Matches: 80,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  96   79  0.99
  97    1  0.01

ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36


Consensus pattern (96 bp):   
GTATAAATATTTACTCAAAAGTGGCAAATTCTACAACTACTGAATGCTTCATTTCAAGATGAAGT
TTTTCTAAGTTAGTTAAAAGTCTTAGCAAGG

Found at i:2873 original size:18 final size:18

Alignment explanation


    Indices: 2846--2910  Score: 103
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       2836 CGATCGATAT

                 *            
       2846 CGTCATTATCATCAATAG
          1 CGTCACTATCATCAATAG

                              
       2864 CGTCACTATCATCAATAG
          1 CGTCACTATCATCAATAG

                    *        *
       2882 CGTCACTAGCATCAATAT
          1 CGTCACTATCATCAATAG

                       
       2900 CGTCACTATCA
          1 CGTCACTATCA

       2911 CTATCATCCA


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   43  1.00

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


Consensus pattern (18 bp):   
CGTCACTATCATCAATAG

Found at i:4079 original size:21 final size:21

Alignment explanation


    Indices: 4055--4096  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4045 GGAACCATGG

                                 
       4055 CATATATGTTTGGAATAGATT
          1 CATATATGTTTGGAATAGATT

                                 
       4076 CATATATGTTTGGAATAGATT
          1 CATATATGTTTGGAATAGATT

       4097 ACGTTTTGAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43


Consensus pattern (21 bp):   
CATATATGTTTGGAATAGATT

Found at i:5140 original size:15 final size:15

Alignment explanation


    Indices: 5116--5145  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       5106 AAAGGAAGTG

                 *         
       5116 ATTTATACAAAAAGA
          1 ATTTAGACAAAAAGA

                           
       5131 ATTTAGACAAAAAGA
          1 ATTTAGACAAAAAGA

       5146 GAAGCAACTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23


Consensus pattern (15 bp):   
ATTTAGACAAAAAGA

Found at i:5200 original size:24 final size:21

Alignment explanation


    Indices: 5136--5187  Score: 86
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       5126 AAAGAATTTA

                          *      
       5136 GACAAAAAGAGAAGCAACTTG
          1 GACAAAAAGAGAAGTAACTTG

              *                  
       5157 GATAAAAAGAGAAGTAACTTG
          1 GACAAAAAGAGAAGTAACTTG

                      
       5178 GACAAAAAGA
          1 GACAAAAAGA

       5188 ATCGAAGTGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.56, C:0.10, G:0.23, T:0.12


Consensus pattern (21 bp):   
GACAAAAAGAGAAGTAACTTG
Done.