Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023579.1 Corchorus olitorius cultivar O-4 contig23612, 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: 3268
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33


Found at i:740 original size:76 final size:77

Alignment explanation


    Indices: 643--794  Score: 236
    Period size: 76  Copynumber: 2.0  Consensus size: 77

        633 TCACTTTCCA

                                       **                                    
        643 CAAAGCGATCAAATTTATTATTCGCTTTTGATCAAGACCCAAGCGATCAATTTCATTATTCGCTT
          1 CAAAGCGATCAAATTTATTATTCGCTTGGGATCAAGACCCAAGCGATCAATTTCATTATTCGCTT

                        
        708 AGAACCAAGACC
         66 AGAACCAAGACC

                             *                      *                        
        720 CAAA-CGATC-AATTTCTTTATTCGCTTGGGATCAAGACCTAAGCGATCAATTTCATTATTCGCT
          1 CAAAGCGATCAAATTT-ATTATTCGCTTGGGATCAAGACCCAAGCGATCAATTTCATTATTCGCT

               *        
        783 TAGGACCAAGAC
         65 TAGAACCAAGAC

        795 TAATAAATTT


Statistics
Matches: 69,  Mismatches: 5, Indels: 3
        0.90            0.06        0.04

Matches are distributed among these distances:
  75    5  0.07
  76   60  0.87
  77    4  0.06

ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30


Consensus pattern (77 bp):   
CAAAGCGATCAAATTTATTATTCGCTTGGGATCAAGACCCAAGCGATCAATTTCATTATTCGCTT
AGAACCAAGACC

Found at i:793 original size:38 final size:38

Alignment explanation


    Indices: 645--794  Score: 203
    Period size: 38  Copynumber: 3.9  Consensus size: 38

        635 ACTTTCCACA

                                      **  *        
        645 AAGCGATCAAATTT-ATTATTCGCTTTTGATCAAGACCC
          1 AAGCGATC-AATTTCATTATTCGCTTAGGACCAAGACCC

                                       *          
        683 AAGCGATCAATTTCATTATTCGCTTAGAACCAAGACCC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

              *           *          *   *       *
        721 AAACGATCAATTTCTTTATTCGCTTGGGATCAAGACCT
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                                                
        759 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGAC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGAC

        795 TAATAAATTT


Statistics
Matches: 97,  Mismatches: 14, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  37    5  0.05
  38   92  0.95

ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31


Consensus pattern (38 bp):   
AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

Found at i:1859 original size:57 final size:57

Alignment explanation


    Indices: 1785--1901  Score: 198
    Period size: 57  Copynumber: 2.1  Consensus size: 57

       1775 CTTTGGTTTT

                *                                          *         
       1785 TTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAATTTAGCGAAC
          1 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC

                                                        *          * 
       1842 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
          1 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC

               
       1899 TTT
          1 TTT

       1902 GTAAGTAGTT


Statistics
Matches: 56,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  57   56  1.00

ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42


Consensus pattern (57 bp):   
TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC
Done.