Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013872.1 Corchorus olitorius cultivar O-4 contig13905, 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: 14136
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:11412 original size:21 final size:21

Alignment explanation


    Indices: 11382--11421  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      11372 CTAAAAACAG

                 *               
      11382 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
      11403 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

      11422 CTGGTCTGTT


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:11480 original size:21 final size:21

Alignment explanation


    Indices: 11454--11495  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11444 AAAATTCAGA

                                 
      11454 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

                                 
      11475 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

      11496 GTCTGTTGAA


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:0.24, C:0.38, G:0.19, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGGACTTG

Found at i:11504 original size:71 final size:71

Alignment explanation


    Indices: 11383--11567  Score: 325
    Period size: 71  Copynumber: 2.6  Consensus size: 71

      11373 TAAAAACAGG

                                                   *             *           
      11383 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA

                  
      11448 TTCAGA
         66 TTCAGA

                *                                                            
      11454 ACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA

                  
      11519 TTCAGA
         66 TTCAGA

                      *                                
      11525 ACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGACTTG
          1 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG

      11568 TTGTGAAAAT


Statistics
Matches: 108,  Mismatches: 5, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  71   86  0.80
  72   22  0.20

ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19


Consensus pattern (71 bp):   
ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
TTCAGA

Found at i:11555 original size:22 final size:22

Alignment explanation


    Indices: 11525--11567  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      11515 AAAATTCAGA

                *     *           
      11525 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
      11547 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

      11568 TTGTGAAAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Found at i:12451 original size:15 final size:15

Alignment explanation


    Indices: 12431--12462  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      12421 CCTTGGGGGT

                           
      12431 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                    *      
      12446 TCAAAATCGACAAGC
          1 TCAAAATCAACAAGC

              
      12461 TC
          1 TC

      12463 CACTTAGTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:13163 original size:33 final size:33

Alignment explanation


    Indices: 13060--13189  Score: 120
    Period size: 33  Copynumber: 3.9  Consensus size: 33

      13050 CCTGATTTGA

                      **                      
      13060 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATCTGTTTTAG

            *       *   *   *      *  **    *
      13093 ATGTTGTTAGTGTTGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                                    *        
      13126 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                            *               
      13159 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
          1 GTGTTGTTTGTGATGACACTAAA-TCTGTTTT

      13190 GGATGCTAAT


Statistics
Matches: 74,  Mismatches: 21, Indels: 4
        0.75            0.21        0.04

Matches are distributed among these distances:
  32    3  0.04
  33   70  0.95
  34    1  0.01

ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45


Consensus pattern (33 bp):   
GTGTTGTTTGTGATGACACTAAATCTGTTTTAG
Done.