Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015375.1 Corchorus olitorius cultivar O-4 contig15408, 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: 7874
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:971 original size:56 final size:56

Alignment explanation


    Indices: 885--992  Score: 189
    Period size: 56  Copynumber: 1.9  Consensus size: 56

        875 GGCCCTTTTC

                                                                    
        885 TCATGATTTCCTATCTAGTCATTATGAGTTACCATTCTCAAAATTGGGCCAATTTA
          1 TCATGATTTCCTATCTAGTCATTATGAGTTACCATTCTCAAAATTGGGCCAATTTA

                               *            *      *            
        941 TCATGATTTCCTATCTAGTTATTATGAGTTACTATTCTCGAAATTGGGCCAA
          1 TCATGATTTCCTATCTAGTCATTATGAGTTACCATTCTCAAAATTGGGCCAA

        993 GAAAAATTTG


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  56   49  1.00

ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40


Consensus pattern (56 bp):   
TCATGATTTCCTATCTAGTCATTATGAGTTACCATTCTCAAAATTGGGCCAATTTA

Found at i:4528 original size:24 final size:24

Alignment explanation


    Indices: 4501--4562  Score: 79
    Period size: 24  Copynumber: 2.6  Consensus size: 24

       4491 CTCCCTTTAA

                         * *        
       4501 GAACATATTCGATCAGATGTTCAC
          1 GAACATATTCGATAAAATGTTCAC

                      *            *
       4525 GAACATATTCAATAAAATGTTCAT
          1 GAACATATTCGATAAAATGTTCAC

                  *       
       4549 GAACATGTTCGATA
          1 GAACATATTCGATA

       4563 TGGTATTCAC


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31


Consensus pattern (24 bp):   
GAACATATTCGATAAAATGTTCAC

Found at i:4759 original size:23 final size:23

Alignment explanation


    Indices: 4708--4759  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       4698 AATGTAATAT

                                   
       4708 TTGTTCGTGAACATGTTCTATTA
          1 TTGTTCGTGAACATGTTCTATTA

            **                       
       4731 GCGTTCGT-AAGCATGTTCGT-TTA
          1 TTGTTCGTGAA-CATGTTC-TATTA

                  
       4754 TTGTTC
          1 TTGTTC

       4760 ACGTACGAAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  22    2  0.09
  23   20  0.87
  24    1  0.04

ACGTcount: A:0.17, C:0.15, G:0.21, T:0.46


Consensus pattern (23 bp):   
TTGTTCGTGAACATGTTCTATTA
Done.