Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018868.1 Corchorus olitorius cultivar O-4 contig18901, 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: 35579
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:8547 original size:31 final size:31

Alignment explanation


    Indices: 8509--8572  Score: 128
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       8499 ATTTTGTGAC

                                           
       8509 CTTTCAAGGTGCTCTCAGCTTTACCGTATAT
          1 CTTTCAAGGTGCTCTCAGCTTTACCGTATAT

                                           
       8540 CTTTCAAGGTGCTCTCAGCTTTACCGTATAT
          1 CTTTCAAGGTGCTCTCAGCTTTACCGTATAT

              
       8571 CT
          1 CT

       8573 ATAGACATTG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.19, C:0.27, G:0.16, T:0.39


Consensus pattern (31 bp):   
CTTTCAAGGTGCTCTCAGCTTTACCGTATAT

Found at i:17544 original size:72 final size:71

Alignment explanation


    Indices: 17412--17544  Score: 185
    Period size: 72  Copynumber: 1.9  Consensus size: 71

      17402 ATATACATAG

                                  *    *            *   *                    
      17412 TTTTACAAATGTTTCATATGGATCAATGAACACTTAACATGATTTAATCCAATTGAGGTGACCAC
          1 TTTTACAAATGTTTCATATGGACCAATAAACACTTAACATAATTAAATCCAATTGAGGTGACCAC

                  
      17477 CCCAAT
         66 CCCAAT

                  *               *                          *      *     
      17483 TTTTACTAATGTTTCATATGGGCCCAATAAACACTTAACATAATTAAATTCAATTGGGGTGA
          1 TTTTACAAATGTTTCATAT-GGACCAATAAACACTTAACATAATTAAATCCAATTGAGGTGA

      17545 GCACTCACAA


Statistics
Matches: 53,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  71   18  0.34
  72   35  0.66

ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Consensus pattern (71 bp):   
TTTTACAAATGTTTCATATGGACCAATAAACACTTAACATAATTAAATCCAATTGAGGTGACCAC
CCCAAT

Found at i:18000 original size:137 final size:137

Alignment explanation


    Indices: 17825--18096  Score: 411
    Period size: 137  Copynumber: 2.0  Consensus size: 137

      17815 GGTAACTTTT

                                                                  *    *   * 
      17825 GGGCCTGCGACAATGCCCAATTGCTTTGAATAATGTGTTTTGATAGATTTG-GATTTAAGTAAGG
          1 GGGCCTGCGACAATGCCCAATTGCTTTGAATAATGTGTTTTGATAGATTTGAG-CTTAAATAAAG

                                  *                                  **      
      17889 ATTCGACCCAATCTTCAAAACTCTATGGTTGAACTAAGACGTGACAAAAGGTTAGTCGGAAATTC
         65 ATTCGACCCAATCTTCAAAACTATATGGTTGAACTAAGACGTGACAAAAGGTTAGTCACAAATTC

                    
      17954 AAACTTCA
        130 AAACTTCA

                *                        *                *                  
      17962 GGGCTTGCGACAATGCCCAATTGCTTTGAGTAATGTGTTTTGATAGGTTTGAGCTTAAATAAAGA
          1 GGGCCTGCGACAATGCCCAATTGCTTTGAATAATGTGTTTTGATAGATTTGAGCTTAAATAAAGA

                 **                *        *                                
      18027 TTCGAGTCAATCTTCAAAACTATGTGGTTGAATTAAGACGTGACAAAAGGTTAGTCACAAATTCA
         66 TTCGACCCAATCTTCAAAACTATATGGTTGAACTAAGACGTGACAAAAGGTTAGTCACAAATTCA

                 
      18092 AACTT
        131 AACTT

      18097 TAAAGAGCTT


Statistics
Matches: 121,  Mismatches: 13, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 137  120  0.99
 138    1  0.01

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31


Consensus pattern (137 bp):   
GGGCCTGCGACAATGCCCAATTGCTTTGAATAATGTGTTTTGATAGATTTGAGCTTAAATAAAGA
TTCGACCCAATCTTCAAAACTATATGGTTGAACTAAGACGTGACAAAAGGTTAGTCACAAATTCA
AACTTCA

Found at i:35550 original size:14 final size:14

Alignment explanation


    Indices: 35533--35563  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      35523 TAAAAAGATA

                      *   
      35533 AAAAAAAAACGCAG
          1 AAAAAAAAACCCAG

                          
      35547 AAAAAAAAACCCAG
          1 AAAAAAAAACCCAG

               
      35561 AAA
          1 AAA

      35564 TAGATGGCGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAACCCAG
Done.