Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001624.1 Corchorus olitorius cultivar O-4 contig01624, 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, 740

Length: 1234
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:783 original size:101 final size:100

Alignment explanation


    Indices: 585--788  Score: 381
    Period size: 101  Copynumber: 2.0  Consensus size: 100

        575 TCTAATATTT

                         *                                   *               
        585 AAAGGACCGTCTTTCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTGAAAGGACCGTCTTCC
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCC

                                               
        650 GCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
         66 GCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                                             
        685 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGACCGTCTTC
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-AAAAGGACCGTCTTC

                                                
        750 CGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
         65 CGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

               
        786 AAA
          1 AAA

        789 AGGTAATGCA


Statistics
Matches: 101,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 100   48  0.48
 101   53  0.52

ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34


Consensus pattern (100 bp):   
AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCC
GCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

Found at i:791 original size:51 final size:50

Alignment explanation


    Indices: 585--788  Score: 381
    Period size: 50  Copynumber: 4.1  Consensus size: 50

        575 TCTAATATTT

                         *                                   *
        585 AAAGGACCGTCTTTCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTG
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                              
        635 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                               
        685 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAA
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-A

                                                              
        736 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
          1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

               
        786 AAA
          1 AAA

        789 AGGTAATGCA


Statistics
Matches: 151,  Mismatches: 2, Indels: 2
        0.97            0.01        0.01

Matches are distributed among these distances:
  50  101  0.67
  51   50  0.33

ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34


Consensus pattern (50 bp):   
AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

Found at i:875 original size:50 final size:50

Alignment explanation


    Indices: 800--979  Score: 292
    Period size: 50  Copynumber: 3.6  Consensus size: 50

        790 GGTAATGCAC

                                            * * *               
        800 CGTATGGAAACG-GATGT-GGCTTGTGGAAAAGCATGTGTTGATAATTGACT
          1 CGTATGGAAACGAG-T-TCGGCTTGTGGAAAACCCTATGTTGATAATTGACT

                                                              
        850 CGTATGGAAACGAGTTCGGCTTGTGGAAAACCCTATGTTGATAATTGACT
          1 CGTATGGAAACGAGTTCGGCTTGTGGAAAACCCTATGTTGATAATTGACT

                                                              
        900 CGTATGGAAACGAGTTCGGCTTGTGGAAAACCCTATGTTGATAATTGACT
          1 CGTATGGAAACGAGTTCGGCTTGTGGAAAACCCTATGTTGATAATTGACT

                                  *       
        950 CGTATGGAAACGAGTTCGGCTTATGGAAAA
          1 CGTATGGAAACGAGTTCGGCTTGTGGAAAA

        980 GCCAAAGCAT


Statistics
Matches: 124,  Mismatches: 4, Indels: 4
        0.94            0.03        0.03

Matches are distributed among these distances:
  49    1  0.01
  50  122  0.98
  51    1  0.01

ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29


Consensus pattern (50 bp):   
CGTATGGAAACGAGTTCGGCTTGTGGAAAACCCTATGTTGATAATTGACT

Done.