Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009923.1 Corchorus olitorius cultivar O-4 contig09955, 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: 3789
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37


Found at i:143 original size:27 final size:26

Alignment explanation


    Indices: 93--143  Score: 66
    Period size: 26  Copynumber: 1.9  Consensus size: 26

         83 TTGGCCCCGC

                             * *      
         93 TTTTTTTGAATTTGCCCCTTATAATT
          1 TTTTTTTGAATTTGCCCATGATAATT

                   *                 
        119 TTTTTTTTAATTTGACCCATGATAA
          1 TTTTTTTGAATTTG-CCCATGATAA

        144 AACTTACTAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  26   13  0.62
  27    8  0.38

ACGTcount: A:0.24, C:0.14, G:0.08, T:0.55


Consensus pattern (26 bp):   
TTTTTTTGAATTTGCCCATGATAATT

Found at i:2576 original size:2 final size:2

Alignment explanation


    Indices: 2569--2603  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2559 CATTATTACT

                                                                
       2569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2604 TATTGTTTCT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:3782 original size:28 final size:32

Alignment explanation


    Indices: 3703--3789  Score: 85
    Period size: 28  Copynumber: 2.8  Consensus size: 32

       3693 TATAAAATTC

                             *                  
       3703 AGACTCGATAACTCAGATTCGAAAAGAACTGAGACT
          1 AGACTCGA-AAC-C-GACTCGAAAA-AACTGAGACT

                       *                    
       3739 AGACTCGAAACTGACTCGAAAAAAC-GA-ACT
          1 AGACTCGAAACCGACTCGAAAAAACTGAGACT

                                    
       3769 -GACTC-AAACCGACTC-AAAAAA
          1 AGACTCGAAACCGACTCGAAAAAA


Statistics
Matches: 48,  Mismatches: 3, Indels: 9
        0.80            0.05        0.15

Matches are distributed among these distances:
  27    6  0.12
  28    9  0.19
  29    5  0.10
  30    3  0.06
  31    2  0.04
  32    3  0.06
  33    9  0.19
  35    3  0.06
  36    8  0.17

ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15


Consensus pattern (32 bp):   
AGACTCGAAACCGACTCGAAAAAACTGAGACT
Done.