Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000770.1 Corchorus olitorius cultivar O-4 contig00770, 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, 683

Length: 1139
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34


Found at i:652 original size:95 final size:96

Alignment explanation


    Indices: 523--993  Score: 557
    Period size: 95  Copynumber: 4.9  Consensus size: 96

        513 AGAGTGAATT

                            *   *  *                    *                    
        523 TTTACAGATAAGTGTATAGGGTCCATAATT-ATCAATATTTTGTATGATATACG-AAAATATTAC
          1 TTTACAGATAAGTGTAAAGGATCTA-AATTAATCAATATTTTGTGTGATATACGAAAAATATTAC

                                       **   
        586 AATTAAGGTAAAGCACTGACGTGTCGTTTATA
         65 AATTAAGGTAAAGCACTGACGTGTCGTGGATA

                                                     *                *      
        618 TTTACAGATAAGTGTAAAGGATCTAAATTAATCAATATTTTTTGTGATATACGAAAAACATTACA
          1 TTTACAGATAAGTGTAAAGGATCTAAATTAATCAATATTTTGTGTGATATACGAAAAATATTACA

                         *                 
        683 ATTAAGGTAAAGCGCTGACGTGTCGTGGA-A
         66 ATTAAGGTAAAGCACTGACGTGTCGTGGATA

                                                                             
        713 TTTTACAGATAAGTGTAAAGGAT-TCATAA-TAATCAATA-TTTGTGTGATGA-ACGAAAAATAT
          1 -TTTACAGATAAGTGTAAAGGATCT-A-AATTAATCAATATTTTGTGTGAT-ATACGAAAAATAT

                                              *
        774 TACAATTAAGGTAAAGCACTGACGTGTCGTGGATT
         62 TACAATTAAGGTAAAGCACTGACGTGTCGTGGATA

                              **                *                *    *      
        809 TTTACAGATAAGTGTAAACAATCTAAATTAATCAATCTTTTGTGTGA-ATTACTAAAACTATTAC
          1 TTTACAGATAAGTGTAAAGGATCTAAATTAATCAATATTTTGTGTGATA-TACGAAAAATATTAC

                           *           *     
        873 AATTAAGGTAAA-CAGTGACGTGTCGTTGACT-
         65 AATTAAGGTAAAGCACTGACGTGTCGTGGA-TA

                         *      *    *         *     *    *             *  * 
        904 TTTACAGATAAGTTTAAAGGGTCTAGATTAATCAAAATTTTATGTGTTATACGAAAAATAATAAA
          1 TTTACAGATAAGTGTAAAGGATCTAAATTAATCAATATTTTGTGTGATATACGAAAAATATTACA

                     *    *    *     
        969 ATTAAGGTAGAGCAATGACCTGTCG
         66 ATTAAGGTAAAGCACTGACGTGTCG

        994 GCGTTTTTGA


Statistics
Matches: 325,  Mismatches: 36, Indels: 29
        0.83            0.09        0.07

Matches are distributed among these distances:
  94    7  0.02
  95  200  0.62
  96  116  0.36
  97    2  0.01

ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33


Consensus pattern (96 bp):   
TTTACAGATAAGTGTAAAGGATCTAAATTAATCAATATTTTGTGTGATATACGAAAAATATTACA
ATTAAGGTAAAGCACTGACGTGTCGTGGATA

Found at i:874 original size:191 final size:190

Alignment explanation


    Indices: 522--993  Score: 598
    Period size: 191  Copynumber: 2.5  Consensus size: 190

        512 CAGAGTGAAT

                               *   *      *             *                    
        522 TTTTACAGATAAGTGTATAGGGTCCATAATTATCAATATTTTGTATGATATACG-AAAATATTAC
          1 TTTTACAGATAAGTGTA-AAGGTTCATAATAATCAATATTTTGTGTGATATACGAAAAATATTAC

                                       **                     **             
        586 AATTAAGGTAAAGCACTGACGTGTCGTTTATATTTACAGATAAGTGTAAAGGATCTAAATTAATC
         65 AATTAAGGTAAAGCACTGACGTGTCGTGGATATTTACAGATAAGTGTAAACAATCTAAATTAATC

                    *                                                      
        651 AATATTTTTTGTGATATACGAAAAACATTACAATTAAGGTAAAGC-GCTGACGTGTCGTGGAA
        130 AATATTTTGTGTGATATACGAAAAACATTACAATTAAGGTAAA-CAG-TGACGTGTCGTGGAA

                                                                             
        713 TTTTACAGATAAGTGTAAAGGATTCATAATAATCAATA-TTTGTGTGATGA-ACGAAAAATATTA
          1 TTTTACAGATAAGTGTAAAGG-TTCATAATAATCAATATTTTGTGTGAT-ATACGAAAAATATTA

                                            *                                
        776 CAATTAAGGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAACAATCTAAATTAAT
         64 CAATTAAGGTAAAGCACTGACGTGTCGTGGATATTTACAGATAAGTGTAAACAATCTAAATTAAT

                *                 *                                     *  *
        841 CAATCTTTTGTGTGA-ATTAC-TAAAACTATTACAATTAAGGTAAACAGTGACGTGTCGTTGAC
        129 CAATATTTTGTGTGATA-TACGAAAAAC-ATTACAATTAAGGTAAACAGTGACGTGTCGTGGAA

                          *      *               *     *    *             *  
        903 TTTTACAGATAAGTTTAAAGGGTC-TAGATTAATCAAAATTTTATGTGTTATACGAAAAATAATA
          1 TTTTACAGATAAGTGTAAAGGTTCATA-A-TAATCAATATTTTGTGTGATATACGAAAAATATTA

            *          *    *    *     
        967 AAATTAAGGTAGAGCAATGACCTGTCG
         64 CAATTAAGGTAAAGCACTGACGTGTCG

        994 GCGTTTTTGA


Statistics
Matches: 247,  Mismatches: 24, Indels: 20
        0.85            0.08        0.07

Matches are distributed among these distances:
 188    2  0.01
 189    3  0.01
 190   64  0.26
 191  178  0.72

ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33


Consensus pattern (190 bp):   
TTTTACAGATAAGTGTAAAGGTTCATAATAATCAATATTTTGTGTGATATACGAAAAATATTACA
ATTAAGGTAAAGCACTGACGTGTCGTGGATATTTACAGATAAGTGTAAACAATCTAAATTAATCA
ATATTTTGTGTGATATACGAAAAACATTACAATTAAGGTAAACAGTGACGTGTCGTGGAA
Done.