Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024834.1 Corchorus olitorius cultivar O-4 contig24867, 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: 19875
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:539 original size:17 final size:17

Alignment explanation


    Indices: 519--553  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        509 TCGAAATCAA

                         *   
        519 ACCCGAGCCCGAATCCG
          1 ACCCGAGCCCGAACCCG

                             
        536 ACCCGAGCCCGAACCCG
          1 ACCCGAGCCCGAACCCG

             
        553 A
          1 A

        554 ACCCTACCCG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.26, C:0.49, G:0.23, T:0.03


Consensus pattern (17 bp):   
ACCCGAGCCCGAACCCG

Found at i:546 original size:23 final size:23

Alignment explanation


    Indices: 520--574  Score: 65
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        510 CGAAATCAAA

                 *      *          
        520 CCCGAGCCCGAATCCGACCCGAG
          1 CCCGAACCCGAACCCGACCCGAG

                           *       
        543 CCCGAACCCGAACCCTACCCGAG
          1 CCCGAACCCGAACCCGACCCGAG

            * *      
        566 ACTGAACCC
          1 CCCGAACCC

        575 AAAAATACCC


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  23   27  1.00

ACGTcount: A:0.25, C:0.49, G:0.20, T:0.05


Consensus pattern (23 bp):   
CCCGAACCCGAACCCGACCCGAG

Found at i:667 original size:12 final size:12

Alignment explanation


    Indices: 650--674  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        640 AGCTATGAAT

                        
        650 TTGGTTATCCTC
          1 TTGGTTATCCTC

                        
        662 TTGGTTATCCTC
          1 TTGGTTATCCTC

             
        674 T
          1 T

        675 ATGTGTAATC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.24, G:0.16, T:0.52


Consensus pattern (12 bp):   
TTGGTTATCCTC

Found at i:12476 original size:11 final size:11

Alignment explanation


    Indices: 12433--12470  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      12423 TTTCTATATA

                *      
      12433 AAATAAATTAT
          1 AAATTAATTAT

                        
      12444 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      12455 AAATTAATTAT
          1 AAATTAATTAT

                 
      12466 AAATT
          1 AAATT

      12471 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:18347 original size:42 final size:43

Alignment explanation


    Indices: 18296--18389  Score: 120
    Period size: 45  Copynumber: 2.2  Consensus size: 43

      18286 AGTGCATTAT

                                                  *    
      18296 CTAA-ATTCTA-CTACATCTCTAGAGAATTCATCAAAATAAAG
          1 CTAATATTCTACCTACATCTCTAGAGAATTCATCAAAAAAAAG

                            *          * *               
      18337 CTAATATTCTACTCCTCCATCTCTAGATACTTCATCAAAAAAAAG
          1 CTAATATTCTA--CCTACATCTCTAGAGAATTCATCAAAAAAAAG

                    
      18382 CTAATATT
          1 CTAATATT

      18390 AATTGTTGCT


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   35  0.78

ACGTcount: A:0.40, C:0.22, G:0.05, T:0.32


Consensus pattern (43 bp):   
CTAATATTCTACCTACATCTCTAGAGAATTCATCAAAAAAAAG
Done.