Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022198.1 Corchorus olitorius cultivar O-4 contig22231, 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: 14667
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:8224 original size:52 final size:52

Alignment explanation


    Indices: 8146--8417  Score: 331
    Period size: 52  Copynumber: 5.3  Consensus size: 52

       8136 TGTTTGAATG

                      * *      *            *                    
       8146 CTTTGAAAACCTAATGGGAGCTTTCCCGCTTTTAAAAGACCTAATATGATA-A
          1 CTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACCTAATATGA-ACA

                                 *          *                   * 
       8198 CTTTGAAAACTTGATGGGAACCTTCCCAG-TTCGAAAAGACCTAA-ATTGAATA
          1 CTTTGAAAACTTGATGGGAACTTTCCC-GCTTTGAAAAGACCTAATA-TGAACA

             *                   *     *                         
       8250 CCTTGAAAACTTGATGGGAACCTTCCCACTTTGAAAAGACCTAA-ATTGAACA
          1 CTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACCTAATA-TGAACA

                                                *        *      
       8302 CTTTGAAAACTT-ATGGGAACTTTCCCGCTTTGAAATGACCTAATTTGAACA
          1 CTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACCTAATATGAACA

                 *                     *                 *      
       8353 CTTTGGAAACTT-ATGGGAACTTTCCCACTTTGAAAAGACCTAATTTGAACA
          1 CTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACCTAATATGAACA

                          
       8404 CTTTGAAAACTTGA
          1 CTTTGAAAACTTGA

       8418 AAGGAAATTC


Statistics
Matches: 195,  Mismatches: 19, Indels: 12
        0.86            0.08        0.05

Matches are distributed among these distances:
  51   95  0.49
  52   99  0.51
  53    1  0.01

ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30


Consensus pattern (52 bp):   
CTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACCTAATATGAACA

Found at i:8342 original size:51 final size:51

Alignment explanation


    Indices: 8146--8415  Score: 339
    Period size: 51  Copynumber: 5.2  Consensus size: 51

       8136 TGTTTGAATG

                        *      *            *                     
       8146 CTTTGAAAACCTAATGGGAGCTTTCCCGCTTTTAAAAGACCT-AATATGATA-A
          1 CTTTGAAAA-CTTATGGGAACTTTCCCGCTTTGAAAAGACCTAAAT-TGA-ACA

                                 *          *                  * 
       8198 CTTTGAAAACTTGATGGGAACCTTCCCAG-TTCGAAAAGACCTAAATTGAATA
          1 CTTTGAAAACTT-ATGGGAACTTTCCC-GCTTTGAAAAGACCTAAATTGAACA

             *                   *     *                        
       8250 CCTTGAAAACTTGATGGGAACCTTCCCACTTTGAAAAGACCTAAATTGAACA
          1 CTTTGAAAACTT-ATGGGAACTTTCCCGCTTTGAAAAGACCTAAATTGAACA

                                               *       *       
       8302 CTTTGAAAACTTATGGGAACTTTCCCGCTTTGAAATGACCTAATTTGAACA
          1 CTTTGAAAACTTATGGGAACTTTCCCGCTTTGAAAAGACCTAAATTGAACA

                 *                    *                *       
       8353 CTTTGGAAACTTATGGGAACTTTCCCACTTTGAAAAGACCTAATTTGAACA
          1 CTTTGAAAACTTATGGGAACTTTCCCGCTTTGAAAAGACCTAAATTGAACA

                        
       8404 CTTTGAAAACTT
          1 CTTTGAAAACTT

       8416 GAAAGGAAAT


Statistics
Matches: 195,  Mismatches: 18, Indels: 11
        0.87            0.08        0.05

Matches are distributed among these distances:
  51   97  0.50
  52   94  0.48
  53    4  0.02

ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Consensus pattern (51 bp):   
CTTTGAAAACTTATGGGAACTTTCCCGCTTTGAAAAGACCTAAATTGAACA

Found at i:8462 original size:15 final size:16

Alignment explanation


    Indices: 8437--8466  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       8427 CTTTTTGATT

                            
       8437 TTTTTGAATTTTGAAC
          1 TTTTTGAATTTTGAAC

                           
       8453 TTTTTG-ATTTTGAA
          1 TTTTTGAATTTTGAA

       8467 AACCTTTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.23, C:0.03, G:0.13, T:0.60


Consensus pattern (16 bp):   
TTTTTGAATTTTGAAC

Found at i:11417 original size:15 final size:14

Alignment explanation


    Indices: 11397--11435  Score: 62
    Period size: 15  Copynumber: 2.8  Consensus size: 14

      11387 TCCATTTCCC

                           
      11397 CTTTCTTTTTATTTT
          1 CTTTCTTTTT-TTTT

                          
      11412 CTTTCTTTTTTTTT
          1 CTTTCTTTTTTTTT

                       
      11426 CTTT-TTTTTT
          1 CTTTCTTTTTT

      11436 CCTCTTTTGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    6  0.25
  14    8  0.33
  15   10  0.42

ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85


Consensus pattern (14 bp):   
CTTTCTTTTTTTTT

Found at i:13417 original size:20 final size:22

Alignment explanation


    Indices: 13383--13423  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      13373 CTCAAATCAC

                      *           
      13383 AAAAGGTAAGCTTGAA-CTAAA
          1 AAAAGGTAAGATTGAAGCTAAA

                                 
      13404 AAAAGGTAA-ATTGAAGCTAA
          1 AAAAGGTAAGATTGAAGCTAA

      13424 CATAAAGTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    5  0.28
  21   13  0.72

ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20


Consensus pattern (22 bp):   
AAAAGGTAAGATTGAAGCTAAA

Done.