Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019030.1 Corchorus olitorius cultivar O-4 contig19063, 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: 12049
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:279 original size:47 final size:48

Alignment explanation


    Indices: 209--304  Score: 185
    Period size: 47  Copynumber: 2.0  Consensus size: 48

        199 AACTCGGTGT

                                                            
        209 AACAAATGCTTACTTATTTGTTAGTCTTTTCGATGCAGACTTTTATGG
          1 AACAAATGCTTACTTATTTGTTAGTCTTTTCGATGCAGACTTTTATGG

                                                            
        257 AACAAATGCTT-CTTATTTGTTAGTCTTTTCGATGCAGACTTTTATGG
          1 AACAAATGCTTACTTATTTGTTAGTCTTTTCGATGCAGACTTTTATGG

             
        304 A
          1 A

        305 GGAGTTTGAC


Statistics
Matches: 48,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  47   37  0.77
  48   11  0.23

ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44


Consensus pattern (48 bp):   
AACAAATGCTTACTTATTTGTTAGTCTTTTCGATGCAGACTTTTATGG

Found at i:2562 original size:19 final size:20

Alignment explanation


    Indices: 2538--2590  Score: 65
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       2528 ATAATAACTG

                                 
       2538 TTTGGTGTAATGAT-TCCAA-
          1 TTTGGTGTAATGATAT-CAAT

                        *       
       2557 TTTGGTGTAATGGTATCAAT
          1 TTTGGTGTAATGATATCAAT

                          
       2577 TTTGAGTGTAATGA
          1 TTTG-GTGTAATGA

       2591 AAATTTTCTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  19   16  0.55
  20    5  0.17
  21    8  0.28

ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43


Consensus pattern (20 bp):   
TTTGGTGTAATGATATCAAT

Found at i:3096 original size:30 final size:30

Alignment explanation


    Indices: 3035--3111  Score: 93
    Period size: 29  Copynumber: 2.6  Consensus size: 30

       3025 TGACACCAAA

                                 *    *   
       3035 TTATAAGTAGAGGGACCAAATTGACAGTTT
          1 TTATAAGTAGAGGGACCAAATCGACACTTT

                      *               *    
       3065 TTATAA-TAGGGGGACCAAATCGATCCCTTT
          1 TTATAAGTAGAGGGACCAAATCGA-CACTTT

              *              
       3095 TTGTAAGTAGAGGGACC
          1 TTATAAGTAGAGGGACC

       3112 TGTACGGTAT


Statistics
Matches: 39,  Mismatches: 6, Indels: 3
        0.81            0.12        0.06

Matches are distributed among these distances:
  29   15  0.38
  30   15  0.38
  31    9  0.23

ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29


Consensus pattern (30 bp):   
TTATAAGTAGAGGGACCAAATCGACACTTT

Found at i:11177 original size:13 final size:13

Alignment explanation


    Indices: 11159--11188  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      11149 ATACTATGTT

                         
      11159 CTTACCTGGAGCC
          1 CTTACCTGGAGCC

                         
      11172 CTTACCTGGAGCC
          1 CTTACCTGGAGCC

                
      11185 CTTA
          1 CTTA

      11189 AGCCTTGTAC


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:0.17, C:0.37, G:0.20, T:0.27


Consensus pattern (13 bp):   
CTTACCTGGAGCC

Found at i:11353 original size:57 final size:58

Alignment explanation


    Indices: 11261--11375  Score: 178
    Period size: 57  Copynumber: 2.0  Consensus size: 58

      11251 TTGTCCAACC

                                     *                                
      11261 ATTTTCCAAACTCGATATACAAACATAAGCCTGCGGCGAAACGCGAGCCC-AACCTAG
          1 ATTTTCCAAACTCGATATACAAACACAAGCCTGCGGCGAAACGCGAGCCCAAACCTAG

                               * *        *              *            
      11318 ATTTTCCAAACTCGATATATAGACACAAGCTTGCGGCGAAACGCGGGCCCAAACCTAG
          1 ATTTTCCAAACTCGATATACAAACACAAGCCTGCGGCGAAACGCGAGCCCAAACCTAG

      11376 TAACATATCT


Statistics
Matches: 52,  Mismatches: 5, Indels: 1
        0.90            0.09        0.02

Matches are distributed among these distances:
  57   45  0.87
  58    7  0.13

ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18


Consensus pattern (58 bp):   
ATTTTCCAAACTCGATATACAAACACAAGCCTGCGGCGAAACGCGAGCCCAAACCTAG
Done.