Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015906.1 Corchorus olitorius cultivar O-4 contig15939, 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: 26315
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Found at i:17525 original size:45 final size:45

Alignment explanation


    Indices: 17461--17555  Score: 127
    Period size: 45  Copynumber: 2.1  Consensus size: 45

      17451 ATGCCCTAAA

                    *                  *        *    * * 
      17461 AGCCAAACTCTAAACTGCATATAAACTTAGCATCAATCATTTAGC
          1 AGCCAAACCCTAAACTGCATATAAACTAAGCATCAAACATTCAAC

                          *         *                    
      17506 AGCCAAACCCTAAAGTGCATATAATCTAAGCATCAAACATTCAAC
          1 AGCCAAACCCTAAACTGCATATAAACTAAGCATCAAACATTCAAC

                 
      17551 AGCCA
          1 AGCCA

      17556 CTCACTTATA


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

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.42, C:0.26, G:0.09, T:0.22


Consensus pattern (45 bp):   
AGCCAAACCCTAAACTGCATATAAACTAAGCATCAAACATTCAAC

Found at i:19583 original size:88 final size:88

Alignment explanation


    Indices: 19392--19653  Score: 363
    Period size: 88  Copynumber: 3.0  Consensus size: 88

      19382 AGAAAGCTAG

                                       *       **   *                 *      
      19392 AAATGCCTACAGAGTACAAAAGGGTTCAAAAGGAATTATTTACAGCAAAC---TA-ACCAAACAT
          1 AAATGCCTACAGAGTACAAAAGGGTTCGAAAGGAACAATTAACAGCAAACTGATATACAAAACAT

                       *           
      19453 CTAATTATCCAGAAAAAAAATAC
         66 CTAATTATCCAAAAAAAAAATAC

                 *     *                                *                    
      19476 AAATGTCTACAAAGTACAAAAGGGTTCGAAAGGAACAATTAACAACAAACTGATATACAAAACAT
          1 AAATGCCTACAGAGTACAAAAGGGTTCGAAAGGAACAATTAACAGCAAACTGATATACAAAACAT

                                   
      19541 CTAATTATCCAAAAAAAAAATAC
         66 CTAATTATCCAAAAAAAAAATAC

                     *    *                       * *            *           
      19564 AAATGCCTATAGAGCACAAAAGGGTTCGAAAGGAACAACTGACAGCAAACTGACATACAAAACAT
          1 AAATGCCTACAGAGTACAAAAGGGTTCGAAAGGAACAATTAACAGCAAACTGATATACAAAACAT

                                   
      19629 CTAATTATCC-AAAAAAAAATAC
         66 CTAATTATCCAAAAAAAAAATAC

               
      19651 AAA
          1 AAA

      19654 ACAACTAATT


Statistics
Matches: 157,  Mismatches: 17, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
  84   43  0.27
  87   17  0.11
  88   97  0.62

ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18


Consensus pattern (88 bp):   
AAATGCCTACAGAGTACAAAAGGGTTCGAAAGGAACAATTAACAGCAAACTGATATACAAAACAT
CTAATTATCCAAAAAAAAAATAC
Done.