Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015131.1 Corchorus olitorius cultivar O-4 contig15164, 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: 26855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:9127 original size:68 final size:68

Alignment explanation


    Indices: 9049--9180  Score: 264
    Period size: 68  Copynumber: 1.9  Consensus size: 68

       9039 AAAAGCTAAT

                                                                             
       9049 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAGA
          1 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAGA

               
       9114 AAC
         66 AAC

                                                                            
       9117 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAG
          1 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAG

       9181 GTATATAATT


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  68   64  1.00

ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27


Consensus pattern (68 bp):   
TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAGA
AAC

Found at i:9184 original size:13 final size:13

Alignment explanation


    Indices: 9166--9191  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9156 ATAACGTCAA

                         
       9166 AGGTATATAATTC
          1 AGGTATATAATTC

                         
       9179 AGGTATATAATTC
          1 AGGTATATAATTC

       9192 GGAAACACTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (13 bp):   
AGGTATATAATTC

Found at i:11753 original size:29 final size:29

Alignment explanation


    Indices: 11719--11775  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      11709 ACCTTCCCGA

                                           
      11719 AAAG-TTGGGACCCTTATTTG-GCATTTTTT
          1 AAAGTTTGGG-CCCTTATTTGAG-ATTTTTT

                    *                   
      11748 AAAGTTTGTGCCCTTATTTGAGATTTTT
          1 AAAGTTTGGGCCCTTATTTGAGATTTTT

      11776 GGCAAAGTTC


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  29   20  0.80
  30    5  0.20

ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47


Consensus pattern (29 bp):   
AAAGTTTGGGCCCTTATTTGAGATTTTTT

Found at i:23475 original size:21 final size:22

Alignment explanation


    Indices: 23435--23475  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      23425 GACAAACTCG

                           *      
      23435 TAACCCGAATAACCCGAGAAAA
          1 TAACCCGAATAACCCAAGAAAA

                      *         
      23457 TAACCCG-ATGACCCAAGAA
          1 TAACCCGAATAACCCAAGAA

      23476 TATTATAAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10


Consensus pattern (22 bp):   
TAACCCGAATAACCCAAGAAAA

Found at i:25858 original size:27 final size:27

Alignment explanation


    Indices: 25822--25895  Score: 78
    Period size: 28  Copynumber: 2.7  Consensus size: 27

      25812 TCCGGCATTT

                                 *     
      25822 AAGGGCAAAACTGTAATTTAGTCAACC
          1 AAGGGCAAAACTGTAATTTAGCCAACC

             *   *                   *   
      25849 AGGGGTAAAA-TGGTAATTTTAGCCTACC
          1 AAGGGCAAAACT-GTAA-TTTAGCCAACC

                       *       
      25877 AAGGGCAAAACAGTAATTT
          1 AAGGGCAAAACTGTAATTT

      25896 TGACATCTTA


Statistics
Matches: 37,  Mismatches: 7, Indels: 6
        0.74            0.14        0.12

Matches are distributed among these distances:
  26    1  0.03
  27   15  0.41
  28   21  0.57

ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24


Consensus pattern (27 bp):   
AAGGGCAAAACTGTAATTTAGCCAACC

Done.