Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022140.1 Corchorus olitorius cultivar O-4 contig22173, 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: 2509
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35


Found at i:713 original size:13 final size:13

Alignment explanation


    Indices: 686--736  Score: 59
    Period size: 13  Copynumber: 3.9  Consensus size: 13

        676 CCCAACAGCC

                  *       
        686 TTTTTCCTCTCTTT
          1 TTTTTCTTCT-TTT

                         
        700 TTTTT-TTCTTTT
          1 TTTTTCTTCTTTT

                       * 
        712 TTTTTCTTCTTCT
          1 TTTTTCTTCTTTT

              *         
        725 TTCTTCTTCTTT
          1 TTTTTCTTCTTT

        737 AGCCGGAAAC


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  12    8  0.25
  13   19  0.59
  14    5  0.16

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (13 bp):   
TTTTTCTTCTTTT

Found at i:1720 original size:109 final size:106

Alignment explanation


    Indices: 1499--1957  Score: 396
    Period size: 109  Copynumber: 4.3  Consensus size: 106

       1489 AATCATTATT

                     *            *         *  *     **       *      *     * 
       1499 ATTG-AAATGTATTCTTATA-AAGTTTTAGAATAAGAAAATTGACGAAGTCCACTAAGTTTAGTC
          1 ATTGAAAATATATTCTTATAGAGGTTTTAGAAAAAAAAAATCAACGAAGTTCACTAAATTTAGCC

             *                  *    *                
       1562 CTAAATAAAAAAATTAATTCGTTTAAAAGG-TAAGTCATTAA
         66 CCAAATAAAAAAATTAATTCATTT-TAAGGATAAGTCATTAA

                     *              *                     *                 *
       1603 ATTGAAAATGTATTCTTATAGAGTTTTTTAGAAAAAAAAAATCAACTAA-TATCACTAAATTTAA
          1 ATTGAAAATATATTCTTATAGAG-GTTTTAGAAAAAAAAAATCAACGAAGT-TCACTAAATTTAG

            *  *                                 *       
       1667 TCCTAAATAATAAAAAATTAATTCATTTTAAGGATAAATCATTAA
         64 CCCCAAAT-A-AAAAAATTAATTCATTTTAAGGATAAGTCATTAA

                             *        *                 *   *      *  *      
       1712 ATTGAAAATATATTCTTGTAG-GGTTCTAGAAAAAAAAAATCAATGAATTTCA-TTAAGTTAGCC
          1 ATTGAAAATATATTCTTATAGAGGTTTTAGAAAAAAAAAATCAACGAAGTTCACTAAATTTAGCC

                *       **          *     * *         
       1775 CCAACTAAAAATTTTTAATTCATTATAAGGGTTAGTCATTAA
         66 CCAAATAAAAA-AATTAATTCATTTTAAGGATAAGTCATTAA

                *                 *                     *           *        
       1817 ATTGGAAATATATTCTTATATATAGGGTTTTAGAAAAAAAAAATTAACGAAGTTCATTAAATTTA
          1 ATTGAAAATATATTC-T-TATAGA-GGTTTTAGAAAAAAAAAATCAACGAAGTTCACTAAATTTA

                      * * **                             
       1882 GCCCCAAAT-TATATTTTAATTCATTTTAAGGATAAGGT-ATTAA
         63 GCCCCAAATAAAAAAATTAATTCATTTTAAGGATAA-GTCATTAA

                          *            *      
       1925 ATTGAAAATATATTATTATAGA-GTTTCAGAAAA
          1 ATTGAAAATATATTCTTATAGAGGTTTTAGAAAA

       1958 GACATTAATG


Statistics
Matches: 290,  Mismatches: 50, Indels: 30
        0.78            0.14        0.08

Matches are distributed among these distances:
 104   18  0.06
 105   54  0.19
 106   19  0.07
 107   65  0.22
 108   44  0.15
 109   76  0.26
 110   14  0.05

ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36


Consensus pattern (106 bp):   
ATTGAAAATATATTCTTATAGAGGTTTTAGAAAAAAAAAATCAACGAAGTTCACTAAATTTAGCC
CCAAATAAAAAAATTAATTCATTTTAAGGATAAGTCATTAA

Found at i:1817 original size:105 final size:104

Alignment explanation


    Indices: 1555--2013  Score: 372
    Period size: 109  Copynumber: 4.3  Consensus size: 104

       1545 GTCCACTAAG

                 *  *         **       *    *                         *      
       1555 TTTAGTCCTAAATAAAAAAATTAATTCGTTTAAAAGG-TAAGTCATTAAATTGAAAATGTATTCT
          1 TTTAGCCCCAAATAAAAATTTTAATTCATTT-TAAGGATAAGTCATTAAATTGAAAATATATTCT

                    *                          *     *  
       1619 TATAGAGTTTTTTAGAAAAAAAAAATCAACT-AATATCACTAAA
         65 TATAG-G-GTTTTAGAAAAAAAAAATCAA-TGAATTTCA-TTAA

                **  *           **                    *                      
       1662 TTTAATCCTAAATAATAAAAAATTAATTCATTTTAAGGATAAATCATTAAATTGAAAATATATTC
          1 TTTAGCCCCAAAT-A-AAAATTTTAATTCATTTTAAGGATAAGTCATTAAATTGAAAATATATTC

              *       *                              
       1727 TTGTAGGGTTCTAGAAAAAAAAAATCAATGAATTTCATTAA
         64 TTATAGGGTTTTAGAAAAAAAAAATCAATGAATTTCATTAA

            *          *                   *     * *             *           
       1768 GTTAGCCCCAACTAAAAATTTTTAATTCATTATAAGGGTTAGTCATTAAATTGGAAATATATTCT
          1 TTTAGCCCCAAATAAAAA-TTTTAATTCATTTTAAGGATAAGTCATTAAATTGAAAATATATTC-

                                        *  *   *         
       1833 TATATATAGGGTTTTAGAAAAAAAAAATTAACGAAGTTCATTAAA
         64 --T-TATAGGGTTTTAGAAAAAAAAAATCAATGAATTTCATT-AA

                          * *                                              * 
       1878 TTTAGCCCCAAAT-TATATTTTAATTCATTTTAAGGATAAGGT-ATTAAATTGAAAATATATTAT
          1 TTTAGCCCCAAATAAAAATTTTAATTCATTTTAAGGATAA-GTCATTAAATTGAAAATATATTCT

                 *    *        * *  *         *   *  
       1941 TATAGAGTTTCAG--AAAAGACATTAATGAATTTTACTAAA
         65 TATAGGGTTTTAGAAAAAAAAAATCAATGAATTTCA-TTAA

            *     *      * *                  
       1980 CTTAGCTCCAAATTATAATTTTAATTCATTTTAA
          1 TTTAGCCCCAAATAAAAATTTTAATTCATTTTAA

       2014 AAGTAGATTA


Statistics
Matches: 290,  Mismatches: 49, Indels: 30
        0.79            0.13        0.08

Matches are distributed among these distances:
 102   29  0.10
 103   18  0.06
 104   15  0.05
 105   40  0.14
 106   12  0.04
 107   37  0.13
 108   44  0.15
 109   82  0.28
 110   13  0.04

ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37


Consensus pattern (104 bp):   
TTTAGCCCCAAATAAAAATTTTAATTCATTTTAAGGATAAGTCATTAAATTGAAAATATATTCTT
ATAGGGTTTTAGAAAAAAAAAATCAATGAATTTCATTAA

Done.