Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024034.1 Corchorus olitorius cultivar O-4 contig24067, 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: 17219
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31


Found at i:2944 original size:13 final size:13

Alignment explanation


    Indices: 2926--2960  Score: 70
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       2916 TTCTAGCAAC

                         
       2926 TCTCCAACTTGTT
          1 TCTCCAACTTGTT

                         
       2939 TCTCCAACTTGTT
          1 TCTCCAACTTGTT

                     
       2952 TCTCCAACT
          1 TCTCCAACT

       2961 CTTTTGTTTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   22  1.00

ACGTcount: A:0.17, C:0.34, G:0.06, T:0.43


Consensus pattern (13 bp):   
TCTCCAACTTGTT

Found at i:5874 original size:25 final size:24

Alignment explanation


    Indices: 5837--5883  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       5827 CTAGAAAATT

                                      
       5837 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       5863 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       5884 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:13475 original size:21 final size:21

Alignment explanation


    Indices: 13449--13496  Score: 60
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      13439 GCAGGCTTGA

                                 
      13449 CCGGGCAGGCGGCGCGGATGG
          1 CCGGGCAGGCGGCGCGGATGG

                   * *   *   *   
      13470 CCGGGCATGTGGCTCGGGTGG
          1 CCGGGCAGGCGGCGCGGATGG

                  
      13491 CCGGGC
          1 CCGGGC

      13497 TGTGGCCGGG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.06, C:0.29, G:0.54, T:0.10


Consensus pattern (21 bp):   
CCGGGCAGGCGGCGCGGATGG

Found at i:15513 original size:31 final size:29

Alignment explanation


    Indices: 15462--15532  Score: 81
    Period size: 31  Copynumber: 2.3  Consensus size: 29

      15452 AGGAAAATAT

                                    *      
      15462 TTTTTTTTCTTTTCTAAAAACGCAGAAACAA
          1 TTTTTTTT-TTTTCTAAAAACGCAAAAAC-A

                                   *       
      15493 TTTTTCTTTTTTT-TAGAAAACGTAAAAACA
          1 TTTTT-TTTTTTTCTA-AAAACGCAAAAACA

                      
      15523 TTTTTTTTTT
          1 TTTTTTTTTT

      15533 CAAAAACACA


Statistics
Matches: 36,  Mismatches: 2, Indels: 6
        0.82            0.05        0.14

Matches are distributed among these distances:
  29    5  0.14
  30    8  0.22
  31   20  0.56
  32    3  0.08

ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52


Consensus pattern (29 bp):   
TTTTTTTTTTTTCTAAAAACGCAAAAACA

Found at i:15575 original size:15 final size:15

Alignment explanation


    Indices: 15533--15575  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      15523 TTTTTTTTTT

                    *      
      15533 CAAAAACACAAAACA
          1 CAAAAACAAAAAACA

                  **      *
      15548 CAAAAATTAAAAACG
          1 CAAAAACAAAAAACA

                         
      15563 CAAAAACAAAAAA
          1 CAAAAACAAAAAA

      15576 TCTCTTTTCT


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.74, C:0.19, G:0.02, T:0.05


Consensus pattern (15 bp):   
CAAAAACAAAAAACA

Found at i:15576 original size:22 final size:22

Alignment explanation


    Indices: 15534--15574  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      15524 TTTTTTTTTC

                                  
      15534 AAAAACACAAAACACAAAAATT
          1 AAAAACACAAAACACAAAAATT

                  *             
      15556 AAAAACGCAAAA-ACAAAAA
          1 AAAAACACAAAACACAAAAA

      15575 ATCTCTTTTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.76, C:0.17, G:0.02, T:0.05


Consensus pattern (22 bp):   
AAAAACACAAAACACAAAAATT

Found at i:16870 original size:16 final size:15

Alignment explanation


    Indices: 16832--16873  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      16822 ATAGAGATTG

                   *     * 
      16832 ACAGAAAGCAATTTA
          1 ACAGAAAACAATTAA

                           
      16847 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      16862 ACTAGAAAACAA
          1 AC-AGAAAACAA

      16874 AGCAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.