Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024613.1 Corchorus olitorius cultivar O-4 contig24646, 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: 17011
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32

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


Found at i:673 original size:29 final size:28

Alignment explanation


    Indices: 630--736  Score: 88
    Period size: 29  Copynumber: 3.8  Consensus size: 28

        620 AAATGAACTT

                   *                     
        630 AAAATGATCAAAATGCCCCTAAATATGCA
          1 AAAATGACCAAAATGCCCCTAAATATG-A

            *         *         *   *   
        659 GAAATGACCATAATGCCCCTGAATGTGA
          1 AAAATGACCAAAATGCCCCTAAATATGA

                          *   *  *** * * 
        687 AAAATGACCAAAATACCCTTGGGTTTTTA
          1 AAAATGACCAAAATGCCCCT-AAATATGA

                                 
        716 AAAATGACCAAAATGCCCCTA
          1 AAAATGACCAAAATGCCCCTA

        737 GGTGATCCTA


Statistics
Matches: 61,  Mismatches: 16, Indels: 3
        0.76            0.20        0.04

Matches are distributed among these distances:
  28   17  0.28
  29   44  0.72

ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTAAATATGA

Found at i:3688 original size:21 final size:19

Alignment explanation


    Indices: 3664--3702  Score: 51
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       3654 TTACTCCTTC

                                 
       3664 CTCTTCCCCGAAAAACTCTTT
          1 CTCTT-CCC-AAAAACTCTTT

                 *            
       3685 CTCTTTCCAAAAACTCTT
          1 CTCTTCCCAAAAACTCTT

       3703 CAGTTATTTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   10  0.59
  20    2  0.12
  21    5  0.29

ACGTcount: A:0.26, C:0.36, G:0.03, T:0.36


Consensus pattern (19 bp):   
CTCTTCCCAAAAACTCTTT

Found at i:9788 original size:62 final size:62

Alignment explanation


    Indices: 9717--9837  Score: 242
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       9707 CATATGTAAG

                                                                          
       9717 TCTGCATAAGAATTTAGAATTTAGGATTTGATTGTTTTTGGATTGATCTTTTATTTCCCTAA
          1 TCTGCATAAGAATTTAGAATTTAGGATTTGATTGTTTTTGGATTGATCTTTTATTTCCCTAA

                                                                       
       9779 TCTGCATAAGAATTTAGAATTTAGGATTTGATTGTTTTTGGATTGATCTTTTATTTCCC
          1 TCTGCATAAGAATTTAGAATTTAGGATTTGATTGTTTTTGGATTGATCTTTTATTTCCC

       9838 CAATTTTTGA


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  62   59  1.00

ACGTcount: A:0.25, C:0.10, G:0.17, T:0.49


Consensus pattern (62 bp):   
TCTGCATAAGAATTTAGAATTTAGGATTTGATTGTTTTTGGATTGATCTTTTATTTCCCTAA

Found at i:14343 original size:27 final size:27

Alignment explanation


    Indices: 14296--14394  Score: 137
    Period size: 27  Copynumber: 3.6  Consensus size: 27

      14286 GTCATCTATG

                                 **     
      14296 GGGCATTTTGGGTCATTTGCATGTCCAA
          1 GGGCATTTT-GGTCATTTGCACATCCAA

                                      *
      14324 GGGCATTTTGGTCATTTGCACATCCAG
          1 GGGCATTTTGGTCATTTGCACATCCAA

                             *         
      14351 GGGCATTTTGGTCATTTCCACATCC-A
          1 GGGCATTTTGGTCATTTGCACATCCAA

                              
      14377 GGAGCATTTTGGTCATTT
          1 GG-GCATTTTGGTCATTT

      14395 TAAGCTCACT


Statistics
Matches: 65,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  26    2  0.03
  27   54  0.83
  28    9  0.14

ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTGCACATCCAA
Done.