Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009713.1 Corchorus olitorius cultivar O-4 contig09745, 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: 4288
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Found at i:478 original size:48 final size:48

Alignment explanation


    Indices: 404--501  Score: 133
    Period size: 48  Copynumber: 2.0  Consensus size: 48

        394 ATTCTATGTA

                 *    *    *                       * *      
        404 ATAAGTGTGGTCGATCTGCAATGGAAACAAGTGAATCTGTGCTCAAAG
          1 ATAAGCGTGGCCGATATGCAATGGAAACAAGTGAATCTGGGATCAAAG

                             *                  *           
        452 ATAAGCGTGGCCGATATTCAATGGAAACAAGTGAATTTGGGATCAAAG
          1 ATAAGCGTGGCCGATATGCAATGGAAACAAGTGAATCTGGGATCAAAG

              
        500 AT
          1 AT

        502 CCAGCGCAAG


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  48   43  1.00

ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24


Consensus pattern (48 bp):   
ATAAGCGTGGCCGATATGCAATGGAAACAAGTGAATCTGGGATCAAAG

Found at i:1563 original size:40 final size:41

Alignment explanation


    Indices: 1518--1596  Score: 133
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1508 TTCCAAACAG

                                         *           
       1518 ATGTTTACAAGCAAAAT-AAAGATATCATCAATATCTACAT
          1 ATGTTTACAAGCAAAATAAAAGATATCATAAATATCTACAT

                       *                           
       1558 ATGTTTACAAGTAAAATAAAAGATATCATAAATATCTAC
          1 ATGTTTACAAGCAAAATAAAAGATATCATAAATATCTAC

       1597 TCTTGTGGAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  40   16  0.44
  41   20  0.56

ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30


Consensus pattern (41 bp):   
ATGTTTACAAGCAAAATAAAAGATATCATAAATATCTACAT

Found at i:3156 original size:48 final size:48

Alignment explanation


    Indices: 3099--3193  Score: 129
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       3089 TTCTATGTAA

                *         *                                  
       3099 TAAGTGTGGCCGATCTGCAATGGAAACAAGTGAA-TCTGGGATCAAAGG
          1 TAAGCGTGGCCGATATGCAATGGAAACAAGTGAATTC-GGGATCAAAGG

                            *         *  *                 
       3147 TAAGCGTGGCCGATATTCAATGGAAATAATTGAATTCGGGATCAAAG
          1 TAAGCGTGGCCGATATGCAATGGAAACAAGTGAATTCGGGATCAAAG

       3194 ATCCAGCCCA


Statistics
Matches: 41,  Mismatches: 5, Indels: 2
        0.85            0.10        0.04

Matches are distributed among these distances:
  48   39  0.95
  49    2  0.05

ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23


Consensus pattern (48 bp):   
TAAGCGTGGCCGATATGCAATGGAAACAAGTGAATTCGGGATCAAAGG
Done.