Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023039.1 Corchorus olitorius cultivar O-4 contig23072, 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: 5622
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31


Found at i:918 original size:35 final size:35

Alignment explanation


    Indices: 870--1055  Score: 221
    Period size: 35  Copynumber: 5.3  Consensus size: 35

        860 ATCAACCCAA

                    *                          
        870 AAAACTTCCTGAAAGGAGATCAACTCTGATCACCG
          1 AAAACTTCTTGAAAGGAGATCAACTCTGATCACCG

                   *      *              *   **
        905 AAAACTTTTTGAAATGAGATCAACTCTGACCA-TA
          1 AAAACTTCTTGAAAGGAGATCAACTCTGATCACCG

                 *         *                 ***
        939 AAAACATCTTGAAAATGAGATCAACTCTGATCATAA
          1 AAAACTTCTTG-AAAGGAGATCAACTCTGATCACCG

                    *                          
        975 AAAACTTCCTGAAAGGAGATCAACTCTGATCACCG
          1 AAAACTTCTTGAAAGGAGATCAACTCTGATCACCG

                          *                 *  
       1010 AAAACTTCTTGAAACGAGATCAACTCTGATCATCG
          1 AAAACTTCTTGAAAGGAGATCAACTCTGATCACCG

               *       
       1045 AAAGCTTCTTG
          1 AAAACTTCTTG

       1056 GAATGACCGC


Statistics
Matches: 129,  Mismatches: 20, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  34    9  0.07
  35  110  0.85
  36   10  0.08

ACGTcount: A:0.39, C:0.22, G:0.15, T:0.25


Consensus pattern (35 bp):   
AAAACTTCTTGAAAGGAGATCAACTCTGATCACCG

Found at i:1090 original size:54 final size:54

Alignment explanation


    Indices: 1026--1134  Score: 182
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1016 TCTTGAAACG

                         *        *                  *            
       1026 AGATCAACTCTGATCATCGAAAGCTTCTTGGAATGACCGCACTGGATCATCTGA
          1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA

                             *                                    
       1080 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
          1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA

             
       1134 A
          1 A

       1135 CACCTGTTTC


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  54   51  1.00

ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26


Consensus pattern (54 bp):   
AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA

Found at i:2245 original size:21 final size:21

Alignment explanation


    Indices: 2221--2281  Score: 55
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       2211 AAATCCCCTT

                                 
       2221 CCTTAAACTGCCTCGGACGTA
          1 CCTTAAACTGCCTCGGACGTA

                                 *
       2242 CCTTCAAA-T-CC-C---C-TT
          1 CCTT-AAACTGCCTCGGACGTA

                                 
       2257 CCTTAAACTGCCTCGGACGTA
          1 CCTTAAACTGCCTCGGACGTA

                
       2278 CCTT
          1 CCTT

       2282 CTTTAAAAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 16
        0.62            0.04        0.33

Matches are distributed among these distances:
  14    3  0.10
  15    6  0.20
  16    3  0.10
  17    1  0.03
  19    1  0.03
  20    3  0.10
  21   10  0.33
  22    3  0.10

ACGTcount: A:0.21, C:0.38, G:0.13, T:0.28


Consensus pattern (21 bp):   
CCTTAAACTGCCTCGGACGTA

Found at i:2257 original size:36 final size:36

Alignment explanation


    Indices: 2210--2282  Score: 146
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       2200 TCTTAAACAC

                                                
       2210 CAAATCCCCTTCCTTAAACTGCCTCGGACGTACCTT
          1 CAAATCCCCTTCCTTAAACTGCCTCGGACGTACCTT

                                                
       2246 CAAATCCCCTTCCTTAAACTGCCTCGGACGTACCTT
          1 CAAATCCCCTTCCTTAAACTGCCTCGGACGTACCTT

             
       2282 C
          1 C

       2283 TTTAAAAAAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   37  1.00

ACGTcount: A:0.22, C:0.40, G:0.11, T:0.27


Consensus pattern (36 bp):   
CAAATCCCCTTCCTTAAACTGCCTCGGACGTACCTT
Done.