Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001177.1 Corchorus olitorius cultivar O-4 contig01177, 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, 873

Length: 1456
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Found at i:1005 original size:191 final size:194

Alignment explanation


    Indices: 588--1168  Score: 1132
    Period size: 191  Copynumber: 3.0  Consensus size: 194

        578 GATTAGTGGG

                                                                             
        588 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT
          1 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT

                                                                             
        653 TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAAGGAATTTATTTTCTTCTTTCACT
         66 TATCATTACTAGATACCTGATCGAAAGGTCCATACC-AAAAAGGAATTTATTTTCTTCTTTCACT

                                                                             
        718 TGGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA
        130 TGGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA

                                                                             
        783 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT
          1 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT

                                                                             
        848 TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAGG-ATTTA-TTTC-TCTTTCACTT
         66 TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAGGAATTTATTTTCTTCTTTCACTT

                                                                            
        910 GGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA
        131 GGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA

                                                                             
        974 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT
          1 TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT

                                                                             
       1039 TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAGGAATTTATTTTCTTCTTTCACTT
         66 TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAGGAATTTATTTTCTTCTTTCACTT

                                                                            
       1104 GGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA
        131 GGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA

             
       1168 T
          1 T

       1169 CCATGCGGTA


Statistics
Matches: 383,  Mismatches: 0, Indels: 7
        0.98            0.00        0.02

Matches are distributed among these distances:
 191  182  0.48
 192    9  0.02
 193    9  0.02
 194   82  0.21
 195  101  0.26

ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33


Consensus pattern (194 bp):   
TGGAGAAAATAGGCATTGGAAGAGCTTACCCATAATAAGGGTTCGACGTGACTTGATTTCGGATT
TATCATTACTAGATACCTGATCGAAAGGTCCATACCAAAAAGGAATTTATTTTCTTCTTTCACTT
GGTGAACCAACATGTTAGTCTCTTTTTCTTTTTAATGTAATGGTATAGGCTAGAAGGAAAGCGA

Found at i:1269 original size:36 final size:36

Alignment explanation


    Indices: 1228--1300  Score: 137
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       1218 AATTGAACGC

                                                
       1228 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
          1 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA

                    *                           
       1264 ATGGGTTCTTCAGCTTAAATACTCAAATCAGGATTA
          1 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA

             
       1300 A
          1 A

       1301 AATTTTGGTA


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Consensus pattern (36 bp):   
ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
Done.