Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010628.1 Corchorus olitorius cultivar O-4 contig10660, 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, 697

Length: 1162
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30


Found at i:137 original size:49 final size:48

Alignment explanation


    Indices: 72--200  Score: 154
    Period size: 49  Copynumber: 2.7  Consensus size: 48

         62 TACTTTTCAC

                                 **                 *       
         72 TGCACTTTTTATCAATTTTTACTACAAAATTGAACTTTTATTTTTACT
          1 TGCACTTTTTATCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

                       *                      *               
        120 TGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTT-CAT
          1 TGCA-CTTTTTATCAATTTTTAAGACAAAATTGAACTTTTAATTTTAC-T

            **                   *           
        169 CACACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TGCACTTTTTATCAATTTTTAAGACAAAATTGA

        201 TTGGCACGCT


Statistics
Matches: 70,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  47   11  0.16
  48   20  0.29
  49   39  0.56

ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50


Consensus pattern (48 bp):   
TGCACTTTTTATCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

Found at i:1066 original size:15 final size:15

Alignment explanation


    Indices: 1025--1074  Score: 73
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       1015 TGCTAGGGTG

                    *      
       1025 AATGGTGCAAACAAC
          1 AATGGTGCGAACAAC

                           
       1040 AATGGTGCGAACAAC
          1 AATGGTGCGAACAAC

                   *      *
       1055 AATGGTGTGAACAAT
          1 AATGGTGCGAACAAC

                 
       1070 AATGG
          1 AATGG

       1075 AAATGGTGCA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   32  1.00

ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18


Consensus pattern (15 bp):   
AATGGTGCGAACAAC
Done.