Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024518.1 Corchorus olitorius cultivar O-4 contig24551, 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: 16156
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:14215 original size:2 final size:2

Alignment explanation


    Indices: 14208--14249  Score: 57
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      14198 ATAATATGTA

                                                                         
      14208 AT AT AT AT AT AGT AT AT AGT AT AT AGT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT AT A

      14250 ATTAATAAAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   2   31  0.84
   3    6  0.16

ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:14223 original size:7 final size:6

Alignment explanation


    Indices: 14208--14249  Score: 57
    Period size: 7  Copynumber: 6.5  Consensus size: 6

      14198 ATAATATGTA

                                                            
      14208 ATATAT ATATAGT ATATAGT ATATAGT ATATAT ATATAT ATA
          1 ATATAT ATATA-T ATATA-T ATATA-T ATATAT ATATAT ATA

      14250 ATTAATAAAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   6   15  0.43
   7   20  0.57

ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45


Consensus pattern (6 bp):   
ATATAT

Found at i:14506 original size:37 final size:38

Alignment explanation


    Indices: 14456--14533  Score: 131
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      14446 CCGTCAAATT

                                                  
      14456 TACCAGATTTGGTTCCAA-CCAACTTAATTGATATCTC
          1 TACCAGATTTGGTTCCAACCCAACTTAATTGATATCTC

                                   *         *    
      14493 TACCAGATTTGGTTCCAACCCAATTTAATTGATTTCTC
          1 TACCAGATTTGGTTCCAACCCAACTTAATTGATATCTC

               
      14531 TAC
          1 TAC

      14534 AAGCTGCCTC


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  37   18  0.47
  38   20  0.53

ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37


Consensus pattern (38 bp):   
TACCAGATTTGGTTCCAACCCAACTTAATTGATATCTC

Found at i:14649 original size:23 final size:23

Alignment explanation


    Indices: 14611--14666  Score: 78
    Period size: 23  Copynumber: 2.4  Consensus size: 23

      14601 TCACACCAAT

                              *     
      14611 ACCAGAAAAAAAAAGTTTTTTCAC
          1 ACCAG-AAAAAAAAGTTTGTTCAC

                      *            
      14635 ACCAGAAAAATAAGTTTGTTCAC
          1 ACCAGAAAAAAAAGTTTGTTCAC

                      
      14658 ACCA-AAAAA
          1 ACCAGAAAAA

      14667 CCCTCTCCCA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  22    5  0.17
  23   20  0.67
  24    5  0.17

ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21


Consensus pattern (23 bp):   
ACCAGAAAAAAAAGTTTGTTCAC
Done.