Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022118.1 Corchorus olitorius cultivar O-4 contig22151, 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: 22336
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:2781 original size:199 final size:192

Alignment explanation


    Indices: 2429--2821  Score: 644
    Period size: 199  Copynumber: 2.0  Consensus size: 192

       2419 TAATTTATTT

                      *                                                 *    
       2429 ATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAATATAGCAAA
          1 ATTTTTTAATGAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAATATACCAAA

                                                                             
       2494 GGCTTTATTCTAATCAATATATCAAGAATATTAGAATTAATTAGAGACACGTGTCGAGATTTGGA
         66 GGCTTTATTCTAATCAATATATCAAGAATATTAGAATTAATTAGAGACACGTGTCGAGATTTGGA

                 *                                                        
       2559 GGCCTTAACATTTAAAGAGTTTCCATATTTATAGTGTACATTATTATCATTATATATATATG
        131 GGCCTCAACATTTAAAGAGTTTCCATATTTATAGTGTACATTATTATCATTATATATATATG

                                                                             
       2621 ATTTTTTAATGAAAATCTTAAAAATTTGTAAGAGAAATTATTGTT-TTCTCTTAAAATATACCAA
          1 ATTTTTTAATGAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTT-TCTTAAAATATACCAA

                    *     *                                                  
       2685 AGGCATTTTTTCTAGTCAATATATCAATATAATGAATATTAGAATTAATTAGAGACACGTGTCGA
         65 AGGC-TTTATTCTAATCAATATATC-----AA-GAATATTAGAATTAATTAGAGACACGTGTCGA

                                                  *           *              
       2750 GATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATAT
        123 GATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTATAGTGTACATTATTATCATTATATAT

                 
       2815 ATATG
        188 ATATG

              
       2820 AT
          1 AT

       2822 ATATGATTTT


Statistics
Matches: 186,  Mismatches: 7, Indels: 9
        0.92            0.03        0.04

Matches are distributed among these distances:
 191    2  0.01
 192   63  0.34
 193   18  0.10
 198    2  0.01
 199  101  0.54

ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40


Consensus pattern (192 bp):   
ATTTTTTAATGAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAATATACCAAA
GGCTTTATTCTAATCAATATATCAAGAATATTAGAATTAATTAGAGACACGTGTCGAGATTTGGA
GGCCTCAACATTTAAAGAGTTTCCATATTTATAGTGTACATTATTATCATTATATATATATG

Found at i:3964 original size:60 final size:60

Alignment explanation


    Indices: 3886--4016  Score: 165
    Period size: 60  Copynumber: 2.2  Consensus size: 60

       3876 GCTATTTGCT

                                   *      *          ** *              * 
       3886 TAAATAAGGGCCTAACGTT-TGCCAAAATATTCAAATAAGGGTCTGATTTTTTAATTTGGC
          1 TAAATAAGGGCCTAACGTTAT-CAAAAATACTCAAATAAGGACCCGATTTTTTAATTTGAC

                                        *                *              
       3946 TAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGACCCGGTTTTTTAATTTGAC
          1 TAAATAAGGGCCTAACGTTATCAAAAATACTCAAATAAGGACCCGATTTTTTAATTTGAC

            *          
       4006 CAAATAAGGGC
          1 TAAATAAGGGC

       4017 TTGGTGTCAG


Statistics
Matches: 61,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  60   60  0.98
  61    1  0.02

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (60 bp):   
TAAATAAGGGCCTAACGTTATCAAAAATACTCAAATAAGGACCCGATTTTTTAATTTGAC

Found at i:16867 original size:43 final size:44

Alignment explanation


    Indices: 16819--16903  Score: 145
    Period size: 43  Copynumber: 2.0  Consensus size: 44

      16809 AGGATTATTT

                                                        
      16819 AAAGAAGATCCACATATGTGGAGGATTATTATCAAA-AAGATTG
          1 AAAGAAGATCCACATATGTGGAGGATTATTATCAAAGAAGATTG

                         *          *                 
      16862 AAAGAAGATCCACGTATGTGGAGGGTTATTATCAAAGAAGAT
          1 AAAGAAGATCCACATATGTGGAGGATTATTATCAAAGAAGAT

      16904 CAAAGGAGGA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  43   34  0.87
  44    5  0.13

ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25


Consensus pattern (44 bp):   
AAAGAAGATCCACATATGTGGAGGATTATTATCAAAGAAGATTG

Found at i:19069 original size:22 final size:22

Alignment explanation


    Indices: 19044--19096  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 22

      19034 GAAGTTCGTG

                               *  
      19044 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGACTTATTGAAGACAA

                                * 
      19066 TTTGAAGA--T-TTGAAGACCA
          1 TTTGAAGACTTATTGAAGACAA

                         
      19085 -TTGAAGACTTAT
          1 TTTGAAGACTTAT

      19097 CTCAAGAAGC


Statistics
Matches: 26,  Mismatches: 2, Indels: 7
        0.74            0.06        0.20

Matches are distributed among these distances:
  18    7  0.27
  19    8  0.31
  20    2  0.08
  21    1  0.04
  22    8  0.31

ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36


Consensus pattern (22 bp):   
TTTGAAGACTTATTGAAGACAA
Done.