Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006093.1 Corchorus olitorius cultivar O-4 contig06118, 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, 720

Length: 1200
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39


Found at i:272 original size:141 final size:139

Alignment explanation


    Indices: 8--515  Score: 576
    Period size: 141  Copynumber: 3.7  Consensus size: 139

          1 ATAAATA

                                      *                                      
          8 AATTAGTAATTATGTT-GTCAAAAATGTAAATTGATTGAACATGCTAAATAAATAAATGAATCAA
          1 AATTAGTAATTATGTTAG-CAAAAA-ATAAATTGATTGAACATGCTAAATAAATAAATGAATCAA

                                 *               *         * *    *       *  
         72 GTTAGTCGTTAATCAACTTTGTCAATCAAAGTTATAATTGATTGATGGTGATTTGATTTTGCTAT
         64 GTTAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACT-ATTGATGATTA-TTAATTTTGCCAT

               *         
        137 AAACAAAAGAATC
        127 AAATAAAAGAATC

                                                     *                     * 
        150 AATTAGTAATTATGTTAGCAAAAAATAAATTGATTGAACATACTAAATAAATAAATGAATCAAAT
          1 AATTAGTAATTATGTTAGCAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGT

                       *                                                   * 
        215 TAGTCGTTAATTAACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTAAATTTTGCCATGA
         66 TAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACT-ATTGATGATTATT-AATTTTGCCATAA

                 *     
        280 ATAAATGAATC
        129 ATAAAAGAATC

                                         * *   *               *       *     
        291 AATTAGTAATTATGTTAGC-AAAAATAAACTAATTCAACATGCTAAATAAACAAATGAACCAAGT
          1 AATTAGTAATTATGTTAGCAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGT

                  *                                      **                  
        355 TAGTC-CTAAGTCAACTTTGCCAATCAAAG-T-T-AC------T-CCTA-TAATTTTGCCATAAA
         66 TAGTCGTTAA-TCAACTTTGCCAATCAAAGTTATAACTATTGATGATTATTAATTTTGCCATAAA

              * *     
        408 TAGACGAATC
        130 TAAAAGAATC

                        *                       *                            
        418 AATTAGTAATTACGTTAGCAAAAAAATAAAATTGATAGAACATGCTAAATAAATAAATGAATCAA
          1 AATTAGTAATTATGTTAGC-AAAAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAA

                 *     * *  *                
        483 GTTAGCCGTTAGTTAATTTTGCCAATCAAAGTT
         64 GTTAGTCGTTAATCAACTTTGCCAATCAAAGTT

        516 GTAATCAAAG


Statistics
Matches: 318,  Mismatches: 40, Indels: 27
        0.83            0.10        0.07

Matches are distributed among these distances:
 127   39  0.12
 128    1  0.00
 129    8  0.03
 130   55  0.17
 131    3  0.01
 137    2  0.01
 138    1  0.00
 139    4  0.01
 140   63  0.20
 141  119  0.37
 142   22  0.07
 143    1  0.00

ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33


Consensus pattern (139 bp):   
AATTAGTAATTATGTTAGCAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGT
TAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACTATTGATGATTATTAATTTTGCCATAAAT
AAAAGAATC

Found at i:435 original size:127 final size:129

Alignment explanation


    Indices: 267--515  Score: 342
    Period size: 130  Copynumber: 1.9  Consensus size: 129

        257 ATGATTATTA

                       *      *                 *                      *     
        267 AATTTTGCCATGAATAAATGAATCAATTAGTAATTATGTTAGC-AAAAAT-AAACTAATTCAACA
          1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAATAAAACTAATACAACA

                                                                             
        330 TGCTAAATAAACAAATGAACCAAGTTAGTCC-TAAGTCAACTTTGCCAATCAAAGTTACTCCTAT
         66 TGCTAAATAAACAAATGAACCAAGTTAG-CCGTAAGTCAACTTTGCCAATCAAAGTTACTCCTAT

                            *                                      * *   *   
        394 AATTTTGCCATAAATAGACGAATCAATTAGTAATTACGTTAGCAAAAAAATAAAATTGATAGAAC
          1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGC-AAAAAATAAAACTAATACAAC

                        *       *            *   *  *                
        459 ATGCTAAATAAATAAATGAATCAAGTTAGCCGTTAGTTAATTTTGCCAATCAAAGTT
         65 ATGCTAAATAAACAAATGAACCAAGTTAGCCGTAAGTCAACTTTGCCAATCAAAGTT

        516 GTAATCAAAG


Statistics
Matches: 105,  Mismatches: 13, Indels: 5
        0.85            0.11        0.04

Matches are distributed among these distances:
 127   39  0.37
 129    8  0.08
 130   58  0.55

ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30


Consensus pattern (129 bp):   
AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAATAAAACTAATACAACA
TGCTAAATAAACAAATGAACCAAGTTAGCCGTAAGTCAACTTTGCCAATCAAAGTTACTCCTAT

Done.