Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017947.1 Corchorus olitorius cultivar O-4 contig17980, 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: 10477
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1671 original size:61 final size:61

Alignment explanation


    Indices: 1596--1718  Score: 237
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       1586 CTGGTGTCAC

                                                              *          
       1596 TAAGTTTAACCAAATGTTTTATAGAAATAAACTTAGGACAAATAAAGAAAGAGTTATTATT
          1 TAAGTTTAACCAAATGTTTTATAGAAATAAACTTAGGACAAATAAAGAAAAAGTTATTATT

                                                                         
       1657 TAAGTTTAACCAAATGTTTTATAGAAATAAACTTAGGACAAATAAAGAAAAAGTTATTATT
          1 TAAGTTTAACCAAATGTTTTATAGAAATAAACTTAGGACAAATAAAGAAAAAGTTATTATT

             
       1718 T
          1 T

       1719 GATACATCGT


Statistics
Matches: 61,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  61   61  1.00

ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33


Consensus pattern (61 bp):   
TAAGTTTAACCAAATGTTTTATAGAAATAAACTTAGGACAAATAAAGAAAAAGTTATTATT

Found at i:6397 original size:26 final size:26

Alignment explanation


    Indices: 6332--6430  Score: 90
    Period size: 27  Copynumber: 3.7  Consensus size: 26

       6322 GTCACTCAAG

                                   * * 
       6332 GGGCATTTTGGTCATTATTCACATTCA
          1 GGGCATTTTGGTCATT-TTCACACTAA

                    *          *       
       6359 GTGGCATTATGGTCATTTTTACACTAA
          1 G-GGCATTTTGGTCATTTTCACACTAA

                             *  * *   *
       6386 GGGCATTTTGGTCATTTACATATTCAG
          1 GGGCATTTTGGTCATTTTCACACT-AA

                  *           
       6413 GGGCATGTTGGTCATTTT
          1 GGGCATTTTGGTCATTTT

       6431 GAGTCCACTT


Statistics
Matches: 58,  Mismatches: 12, Indels: 4
        0.78            0.16        0.05

Matches are distributed among these distances:
  26   18  0.31
  27   26  0.45
  28   14  0.24

ACGTcount: A:0.21, C:0.15, G:0.22, T:0.41


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTCACACTAA

Found at i:6610 original size:25 final size:26

Alignment explanation


    Indices: 6575--6623  Score: 82
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       6565 TATTTTTGCG

                                      
       6575 TTCATTGTAGCTCAAAGCTAATTTCA
          1 TTCATTGTAGCTCAAAGCTAATTTCA

                            *       
       6601 TTCA-TGTAGCTCAAATCTAATTT
          1 TTCATTGTAGCTCAAAGCTAATTT

       6624 AATATTGCAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  25   18  0.82
  26    4  0.18

ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41


Consensus pattern (26 bp):   
TTCATTGTAGCTCAAAGCTAATTTCA

Found at i:10322 original size:40 final size:40

Alignment explanation


    Indices: 10264--10477  Score: 313
    Period size: 40  Copynumber: 5.4  Consensus size: 40

      10254 GTCTTGTCTA

                    *    *             *            
      10264 GTTTAAATACCCAGTTTGCCCTTCCCCGCCGGAAGGTGTT
          1 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

                                                    
      10304 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT
          1 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

                *                     *             
      10344 GTTTGAATTCCCAATTTGCCCTTCCCAACCGGAAGGTGTT
          1 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

                    *    * *            *           
      10384 GTTTAAATACCCAGTCTGCCCTTCCCCATCGGAAGGTGTT
          1 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

                     *   *             *            
      10424 GTTTAAA-TACCAGTTTGCCCTTCCCCGCCGGAAGGTGTT
          1 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

                           
      10463 GTTTAAATTCCCAAT
          1 GTTTAAATTCCCAAT


Statistics
Matches: 155,  Mismatches: 18, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
  39   34  0.22
  40  121  0.78

ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32


Consensus pattern (40 bp):   
GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT

Done.