Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010249.1 Corchorus olitorius cultivar O-4 contig10281, 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: 5602
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34


Found at i:1063 original size:25 final size:24

Alignment explanation


    Indices: 1026--1072  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1016 TTGAAAAATT

                                      
       1026 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1052 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1073 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:1872 original size:21 final size:21

Alignment explanation


    Indices: 1848--1901  Score: 83
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1838 CTTAGGCAAT

                                  
       1848 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGAAA-CTTGC

                         *       
       1869 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGAAACTTGC

                        
       1890 TCCAATGAGCTT
          1 TCCAATGAGCTT

       1902 CTAGCATTTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  20    3  0.10
  21   28  0.90

ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACTTGC

Found at i:2282 original size:17 final size:16

Alignment explanation


    Indices: 2228--2278  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       2218 GCTCACCCCC

                   *         
       2228 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATC-A

                             
       2245 AGATCACCAGTGATGCA
          1 AGATCACCAGTGAT-CA

                    *       
       2262 AGATCACCGGTGATCA
          1 AGATCACCAGTGATCA

             
       2278 A
          1 A

       2279 AGATTACATG


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22


Consensus pattern (16 bp):   
AGATCACCAGTGATCA

Found at i:3641 original size:11 final size:12

Alignment explanation


    Indices: 3616--3645  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       3606 GAATATTACC

                        
       3616 AAATTTAATGCA
          1 AAATTTAATGCA

                      * 
       3628 AAATTTAATGAA
          1 AAATTTAATGCA

                  
       3640 AAATTT
          1 AAATTT

       3646 CAATATAGTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37


Consensus pattern (12 bp):   
AAATTTAATGCA
Done.