Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016963.1 Corchorus olitorius cultivar O-4 contig16996, 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: 5461
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29


Found at i:160 original size:15 final size:15

Alignment explanation


    Indices: 140--168  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        130 GCATTTGAAC

                           
        140 ATTGACTTCCAAGCA
          1 ATTGACTTCCAAGCA

                          
        155 ATTGACTTCCAAGC
          1 ATTGACTTCCAAGC

        169 TACTCAACAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28


Consensus pattern (15 bp):   
ATTGACTTCCAAGCA

Found at i:3191 original size:21 final size:21

Alignment explanation


    Indices: 3161--3208  Score: 69
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3151 TCTCATTTTG

                 *        *   *  
       3161 TTGTTAAGCCAATTTCCCTAC
          1 TTGTTGAGCCAATTGCCCCAC

                                 
       3182 TTGTTGAGCCAATTGCCCCAC
          1 TTGTTGAGCCAATTGCCCCAC

                  
       3203 TTGTTG
          1 TTGTTG

       3209 CTCAAGATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.19, C:0.27, G:0.17, T:0.38


Consensus pattern (21 bp):   
TTGTTGAGCCAATTGCCCCAC

Found at i:3270 original size:21 final size:22

Alignment explanation


    Indices: 3244--3285  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       3234 GTGGATTTAT

                                  
       3244 TGCATTGAGAAAGTTG-TTGAG
          1 TGCATTGAGAAAGTTGATTGAG

                                 
       3265 TGCATTGAGAAAGTTGATTGA
          1 TGCATTGAGAAAGTTGATTGA

       3286 ACTTTGCTGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   16  0.80
  22    4  0.20

ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33


Consensus pattern (22 bp):   
TGCATTGAGAAAGTTGATTGAG
Done.