Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006461.1 Corchorus olitorius cultivar O-4 contig06486, 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, 638

Length: 1064
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:911 original size:30 final size:30

Alignment explanation


    Indices: 826--1064  Score: 343
    Period size: 30  Copynumber: 7.9  Consensus size: 30

        816 TTGGAAATTT

                         *              *  *
        826 ATCATGACAACTTATGGTGTCAATTGAATAAA
          1 ATCATGACAACTTCTGGTGTCAATTG--CAAG

              *      *    **  *           
        858 ATTATGACATCTTCAAGTATCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                         *                
        888 ATCATGACAACTTATGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                         *
        918 ATCATGACAACTTCTGGTGTCAATTGCAAC
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                         *
        948 ATCATGACAACTTCTGGTGTCAATTGCAAC
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                         *
        978 ATCATGACAACTTCTGGTGTCAATTGCAAA
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                          
       1008 ATCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                         
       1038 AGCATGACAACTTCTGGTGTCAATTGC
          1 ATCATGACAACTTCTGGTGTCAATTGC


Statistics
Matches: 188,  Mismatches: 19, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
  30  168  0.89
  32   20  0.11

ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Consensus pattern (30 bp):   
ATCATGACAACTTCTGGTGTCAATTGCAAG

Found at i:954 original size:60 final size:60

Alignment explanation


    Indices: 758--1064  Score: 344
    Period size: 60  Copynumber: 5.0  Consensus size: 60

        748 TTTGAAAGGT

                            *              *  *  *      *    ***    *    *
        758 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGG
          1 AAAATCATGACAACTTATGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGC

                                              *  *  *      *    **  *        
        820 AAATTTATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGC
          1 AAA---ATCATGACAACTTATGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGC

              *                                                         
        885 AAGATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGC

              *             *               *                           
        945 AACATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGC

                            *                 *                         
       1005 AAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGC


Statistics
Matches: 223,  Mismatches: 19, Indels: 8
        0.89            0.08        0.03

Matches are distributed among these distances:
  60  138  0.62
  62   29  0.13
  65   56  0.25

ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Consensus pattern (60 bp):   
AAAATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGC

Found at i:986 original size:90 final size:90

Alignment explanation


    Indices: 758--1064  Score: 346
    Period size: 90  Copynumber: 3.3  Consensus size: 90

        748 TTTGAAAGGT

                                           *  *  *      *      **    *    *  
        758 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCA-AATGTCTATTGGAA
          1 AAAATCATGACAACTTCTGGTGTCAATTG--CAACATCATGACAACTT-ATGGTGTCAATTGCAA

                             *              *
        822 ATTTATCATGACAACTTATGGTGTCAATTGAAT
         63 A---ATCATGACAACTTCTGGTGTCAATTG--C

                 *      *    **  *          *                             *  
        855 AAAATTATGACATCTTCAAGTATCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGAT
          1 AAAATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTATGGTGTCAATTGCAAAAT

                                     
        920 CATGACAACTTCTGGTGTCAATTGC
         66 CATGACAACTTCTGGTGTCAATTGC

              *                                           *                  
        945 AACATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAAAAT
          1 AAAATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTATGGTGTCAATTGCAAAAT

                                     
       1010 CATGACAACTTCTGGTGTCAATTGC
         66 CATGACAACTTCTGGTGTCAATTGC

              * *                         
       1035 AAGAGCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTCTGGTGTCAATTGC


Statistics
Matches: 182,  Mismatches: 27, Indels: 9
        0.83            0.12        0.04

Matches are distributed among these distances:
  90  109  0.60
  92   25  0.14
  94    1  0.01
  95   23  0.13
  97   24  0.13

ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Consensus pattern (90 bp):   
AAAATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTATGGTGTCAATTGCAAAAT
CATGACAACTTCTGGTGTCAATTGC
Done.