Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024700.1 Corchorus olitorius cultivar O-4 contig24733, 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: 28498
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:6490 original size:29 final size:30

Alignment explanation


    Indices: 6430--6509  Score: 90
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       6420 GCTAAATACC

                 *                         
       6430 CAAAAAAATCCCTTATGTTTCACTTTCGGGA
          1 CAAAATAATCCCTTATGTTT-ACTTTCGGGA

                                 *   *    
       6461 CAAAATAATCCCTTATGTTT-TTTTTGGGA
          1 CAAAATAATCCCTTATGTTTACTTTCGGGA

                *    *     *    
       6490 CAAATTAATTCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

       6510 CAAAAGTGAG


Statistics
Matches: 43,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  29   24  0.56
  31   19  0.44

ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTACTTTCGGGA

Found at i:18707 original size:11 final size:11

Alignment explanation


    Indices: 18691--18720  Score: 51
    Period size: 11  Copynumber: 2.6  Consensus size: 11

      18681 CTGTTTCAAA

                       
      18691 AAAAAAAAAAG
          1 AAAAAAAAAAG

                       
      18702 AAAAAAAAAAG
          1 AAAAAAAAAAG

                    
      18713 AAAGAAAA
          1 AAA-AAAA

      18721 GGGTACGTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   14  0.78
  12    4  0.22

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAAG

Found at i:18708 original size:15 final size:15

Alignment explanation


    Indices: 18688--18720  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      18678 AACCTGTTTC

                           
      18688 AAAAAAAAAAAAAGA
          1 AAAAAAAAAAAAAGA

                     *     
      18703 AAAAAAAAAGAAAGA
          1 AAAAAAAAAAAAAGA

               
      18718 AAA
          1 AAA

      18721 GGGTACGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (15 bp):   
AAAAAAAAAAAAAGA

Found at i:20917 original size:16 final size:17

Alignment explanation


    Indices: 20893--20925  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

      20883 ACGGTGTACG

                             
      20893 TATAAATTATAT-TTAA
          1 TATAAATTATATATTAA

                *            
      20909 TATATATTATATATTAA
          1 TATAAATTATATATTAA

      20926 CAAATAAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (17 bp):   
TATAAATTATATATTAA

Found at i:25457 original size:125 final size:127

Alignment explanation


    Indices: 25248--25545  Score: 394
    Period size: 125  Copynumber: 2.4  Consensus size: 127

      25238 AAACTAAACG

                                     *                        *              
      25248 AATTTTAAGCTCGTTTAATTTGCC-ACT-AGAATTTTCACTTTGGAACGAGATTTGGAACCCACA
          1 AATTTTAAGCTCGTTTAATTTGCCGCCTAAGAATTTTCACTTTGGAACGACATTTGGAACCCACA

                                     *     *       *   *            *     
      25311 TTAAAAGTCCGTTCTGAAAGCCGTTTCAAAAGAAAATTGGAAATTTTG-AAAAAATTGAACA
         66 TTAAAAGTCCGTTCTGAAAGCCGTTCCAAAACAAAATTGAAAAATTTGAAAAAAATGGAACA

                       *                    *     *                          
      25372 AATTTTAAGCTTGTTTAATTTGCCGCCTAAG-TTTTTCGCTTTGGAACGACATTTGGAACCCACA
          1 AATTTTAAGCTCGTTTAATTTGCCGCCTAAGAATTTTCACTTTGGAACGACATTTGGAACCCACA

                *                          *    *                          
      25436 TTAATAG-CCTGTTCTGAAAGCCGTTCCAAATCAAATTTGAAAAATTTGAAAAAAATGGAACA
         66 TTAAAAGTCC-GTTCTGAAAGCCGTTCCAAAACAAAATTGAAAAATTTGAAAAAAATGGAACA

                    *              *                          
      25498 AATTTTAAACTCGTTTAATTTGCTGCCTAA-AATTTTCA-TTTAGGAACG
          1 AATTTTAAGCTCGTTTAATTTGCCGCCTAAGAATTTTCACTTT-GGAACG

      25546 GATTTTGGCA


Statistics
Matches: 150,  Mismatches: 18, Indels: 10
        0.84            0.10        0.06

Matches are distributed among these distances:
 124   25  0.17
 125   73  0.49
 126   52  0.35

ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Consensus pattern (127 bp):   
AATTTTAAGCTCGTTTAATTTGCCGCCTAAGAATTTTCACTTTGGAACGACATTTGGAACCCACA
TTAAAAGTCCGTTCTGAAAGCCGTTCCAAAACAAAATTGAAAAATTTGAAAAAAATGGAACA

Found at i:26234 original size:13 final size:13

Alignment explanation


    Indices: 26216--26245  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      26206 GGAGGGTTGA

                         
      26216 TGCAATTATCATT
          1 TGCAATTATCATT

                         
      26229 TGCAATTATCATT
          1 TGCAATTATCATT

                
      26242 TGCA
          1 TGCA

      26246 CCCGATTGCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43


Consensus pattern (13 bp):   
TGCAATTATCATT
Done.