Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008100.1 Corchorus olitorius cultivar O-4 contig08127, 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, 685

Length: 1142
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA 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 TA TA T

         40 TTCTTTTGCT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:824 original size:31 final size:32

Alignment explanation


    Indices: 789--848  Score: 79
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        779 TGACTATAGC

                                             
        789 GGCG-TTTGAAATG-AAGACGCCGCCATTTAGT
          1 GGCGTTTTGAAA-GAAAGACGCCGCCATTTAGT

                      *             *    
        820 GGCGTTTTGATAGAAAGACGCCGCTATTT
          1 GGCGTTTTGAAAGAAAGACGCCGCCATTT

        849 TAATATATGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  31    5  0.20
  32   20  0.80

ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28


Consensus pattern (32 bp):   
GGCGTTTTGAAAGAAAGACGCCGCCATTTAGT

Found at i:1054 original size:164 final size:163

Alignment explanation


    Indices: 783--1122  Score: 531
    Period size: 164  Copynumber: 2.1  Consensus size: 163

        773 TGAAATTGAC

                                           *          * *  *                 
        783 TATAGCGGCGTTTGAAATGAAGACGCCGCCATTTAGTGGCGTTTTGATAGAAAGACGCCGCTATT
          1 TATAGCGGCGTTTGAAATGAAGACGCCGCCAATTAGTGGCGTCTAGAAAGAAAGACGCCGCTATT

                                                                             
        848 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
         66 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCC-CTAA

                      *                       
        913 AACAAAGAAAGTTTACAACTCTACACCTATAATA
        130 AACAAAGAAAATTTACAACTCTACACCTATAATA

                            *   *                               *            
        947 TATAGCGGCGTTTGGACAT-CAGACGCCGCCAATTAGTGGCGTCTAGAAAAGGAA-ACGCCGCTA
          1 TATAGCGGCGTTT-GAAATGAAGACGCCGCCAATTAGTGGCGTCTAG-AAAGAAAGACGCCGCTA

                                                                        *    
       1010 TTTTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCTCCTA
         64 TTTTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCCTA

                   *       *         *         
       1075 AAACAAATAAAATTTTCAACTCTACGCCTATAATA
        129 AAACAAAGAAAATTTACAACTCTACACCTATAATA

                         
       1110 TATAGCGGCGTTT
          1 TATAGCGGCGTTT

       1123 TCTCACCAGA


Statistics
Matches: 162,  Mismatches: 12, Indels: 5
        0.91            0.07        0.03

Matches are distributed among these distances:
 163   47  0.29
 164  106  0.65
 165    9  0.06

ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Consensus pattern (163 bp):   
TATAGCGGCGTTTGAAATGAAGACGCCGCCAATTAGTGGCGTCTAGAAAGAAAGACGCCGCTATT
TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCCTAAA
ACAAAGAAAATTTACAACTCTACACCTATAATA
Done.