Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018848.1 Corchorus olitorius cultivar O-4 contig18881, 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: 9179
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:2913 original size:51 final size:50

Alignment explanation


    Indices: 2812--2913  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       2802 GTTCTTCATA

                                                     * **     
       2812 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            * *                  
       2862 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATATAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
       2913 T
          1 T

       2914 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   36  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:8666 original size:29 final size:31

Alignment explanation


    Indices: 8634--8700  Score: 111
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       8624 ATGCAATTTG

                                           
       8634 GGATATAACGTTAC-AAAA-CAAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                                 *         
       8663 GGATATAACGTTACGAAAAGCGAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                   
       8694 GGATATA
          1 GGATATA

       8701 GTCCGTTAGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  30    4  0.11
  31   17  0.49

ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21


Consensus pattern (31 bp):   
GGATATAACGTTACGAAAAGCAAGCAATTAA

Found at i:8899 original size:32 final size:31

Alignment explanation


    Indices: 8830--8911  Score: 119
    Period size: 32  Copynumber: 2.6  Consensus size: 31

       8820 CCCTAACTAA

                                   **      
       8830 TTATATCCTTAATTGCTTGAAATCGAAAACG
          1 TTATATCCTTAATTGCTTGAAATAAAAAACG

             *      *                       
       8861 TCATATCCCTAATTGCTTGAAATAAAAAAACG
          1 TTATATCCTTAATTGCTTGAAAT-AAAAAACG

                               
       8893 TTATATCCTTAATTGCTTG
          1 TTATATCCTTAATTGCTTG

       8912 TTTTGTAACG


Statistics
Matches: 44,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  31   21  0.48
  32   23  0.52

ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37


Consensus pattern (31 bp):   
TTATATCCTTAATTGCTTGAAATAAAAAACG

Found at i:8956 original size:31 final size:31

Alignment explanation


    Indices: 8887--8972  Score: 95
    Period size: 29  Copynumber: 2.8  Consensus size: 31

       8877 TTGAAATAAA

                                      **** 
       8887 AAAACGTTATATCCTTAATTGCTTG-TTTTG
          1 AAAACGTTATATCCTTAATTGCTTGCGGCAG

             *                             
       8917 -TAACGTTATATCCTTAATTGCTTGCGGCAG
          1 AAAACGTTATATCCTTAATTGCTTGCGGCAG

                           *    *     
       8947 AAAACGTTATATCCTAAATTACTTGC
          1 AAAACGTTATATCCTTAATTGCTTGC

       8973 TTATCCTCTA


Statistics
Matches: 46,  Mismatches: 8, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  29   23  0.50
  30    1  0.02
  31   22  0.48

ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40


Consensus pattern (31 bp):   
AAAACGTTATATCCTTAATTGCTTGCGGCAG
Done.