Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010442.1 Corchorus olitorius cultivar O-4 contig10474, 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: 2818
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37


Found at i:1125 original size:461 final size:461

Alignment explanation


    Indices: 1--1408  Score: 2122
    Period size: 461  Copynumber: 3.0  Consensus size: 461

                                                             *               
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTT

               **              *               *                             
         66 GGGATTATCGGGGCCCATTGGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTT
         66 GGGCCTATCGGGGCCCATTAGTGT-CGTTTTGAATAGTCTTCGATTTGGCAACCCTCAATGCTTT

                    *   *        *                                           
        130 TCTTTCCAATGTCTATGGCCTTACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTA
        130 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTA

                                              *                        *     
        195 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCAACGACCATTAGTTCCGTTTTGAATCGTCTT
        195 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGACCATTAGTTCCGTTTTGAATAGTCTT

            *                                       *                        
        260 TGATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA
        260 AGATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATAGCCTAACTATAATCA-TTTGGTGA

                   *                *             *          *  *      *     
        325 GATTAGTCCATTGTGAAGTTTTTAACTCATTTGGAACAATTGTTATTTTTGGACTATCGGGGCCC
        324 GATTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCC

                               *                              *        *     
        390 ATTAGTTCTGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCCTTTTTTTTCCATTTTTTAT
        389 ATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG-CTTTTCTTTCCATTGTTTAT

                     
        455 GGCCTAACT
        453 GGCCTAACT

                                      *                              *       
        464 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTTTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTT

                                   *                                         
        529 GGGCCTATCGGGGCCCATTAGTGACGTTTTGAATAGTCTTCGATTT-GCAACCCTCAATGCTTTT
         66 GGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATAGTCTTCGATTTGGCAACCCTCAATGCTTTT

                                                                        *   *
        593 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTATTAA
        131 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAG

                                       *                       *            *
        658 CTCATTTGGAACACTTGTTATTTTGGGACTATCGACGACCATTAGTTCCGTATTGAATAGTCTTC
        196 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGACCATTAGTTCCGTTTTGAATAGTCTTA

                               *                                       *  * *
        723 GATTTGGCAACCCTCAATGATTTTCGTTCCATTGTTTATAGCCTAACTATAATCATTTAAGTAAA
        261 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATAGCCTAACTATAATCATTT-GGTGAG

                                                          *                  
        788 ATTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTCTGGGCCTATCGAGGCCCA
        325 ATTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCA

              *    *                                               *         
        853 TTGGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGG
        390 TTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                   
        918 CCTAACT
        455 CCTAACT

                                          *                  *        *      
        925 ATAATCATTTTGGTGAGATTAGTCCATTGTTAAGTTTTTAGCTCATTTGGAACACTTGGTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTT

            *        *** *                                  *                
        990 AGGCCTATCAACGACCATTAGTGTCGTTTTGAATAGTCTTCG-TTTGGAAACCCTCAATGCTTTT
         66 GGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATAGTCTTCGATTTGGCAACCCTCAATGCTTTT

                                                              *              
       1054 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
        131 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAG

                                           *  ** *      * ***                
       1119 CTCATTTGGAACACTTGTTATTTTGGGCCTAACGGGGCCCATTACTGATGTTTTGAATCA-TCTT
        196 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGACCATTAGTTCCGTTTTGAAT-AGTCTT

                                      *  **          *                       
       1183 AGATTTGGCAACCCTCAATGCTTTTCTTTATATTGTTTATATCCTAACTATAATCATATTGGTGA
        260 AGATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATAGCCTAACTATAATCAT-TTGGTGA

                   ** *                                          *        *  
       1248 GATTAGTTTACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACC
        324 GATTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCC

                                                   *                         
       1313 ATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTTAATGCTTTTCTTTCCATTGTTTATG
        389 ATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATG

                    
       1378 GCCTAACT
        454 GCCTAACT

               *          *   *    
       1386 ATATTCATTTTGGTAAGACTAGT
          1 ATAATCATTTTGGTGAGATTAGT

       1409 TGATGCGCCA


Statistics
Matches: 857,  Mismatches: 83, Indels: 12
        0.90            0.09        0.01

Matches are distributed among these distances:
 460    3  0.00
 461  457  0.53
 462  295  0.34
 463  102  0.12

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42


Consensus pattern (461 bp):   
ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTT
GGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATAGTCTTCGATTTGGCAACCCTCAATGCTTTT
CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAG
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGACCATTAGTTCCGTTTTGAATAGTCTTA
GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATAGCCTAACTATAATCATTTGGTGAGA
TTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCAT
TAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACT

Found at i:1409 original size:154 final size:154

Alignment explanation


    Indices: 1--1408  Score: 2066
    Period size: 154  Copynumber: 9.1  Consensus size: 154

                                                             *               
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

               **     *        *                                             
         66 GGGATTATCGGGGCCCATTGGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

                   *   *        *   
        131 CTTTCCAATGTCTATGGCCTTACT
        131 CTTTCCATTGTTTATGGCCTAACT

                                                                             
        155 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

                     * * *                          *                        
        220 GGGCCTATCAACGACCATTAGTTCCGTTTTGAATCGTCTTTGATTTGGCAACCCTCAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

             *                      
        285 CGTTCCATTGTTTATGGCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

                                                    *             *          
        309 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAACTCATTTGGAACAATTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

            *  *      *             *          *                             
        374 TGGACTATCGGGGCCCATTAGTTCTGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCCTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG-CTTT

             *        *              
        439 TTTTTCCATTTTTTATGGCCTAACT
        130 TCTTTCCATTGTTTATGGCCTAACT

                                      *                      *       *       
        464 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTTTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

                      *           **          *                              
        529 GGGCCTATCGGGGCCCATTAGTGACGTTTTGAATAGTCTTCGATTT-GCAACCCTCAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

                                    
        593 CTTTCCATTGTTTATGGCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

                                                *   *                        
        617 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTATTAACTCATTTGGAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

               *       * *             *      *                         *    
        682 GGGACTATCGACGACCATTAGTTCCGTATTGAATAGTCTTCGATTTGGCAACCCTCAATGATTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

             *             *        
        747 CGTTCCATTGTTTATAGCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

                      **  * *      *                                       * 
        771 ATAATCATTTAAGTAAAATTAGTACATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTCT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

                               *                                             
        836 GGGCCTATCGAGGCCCATTGGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

                   *                
        901 CTTTCCAATGTTTATGGCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

                                          *                           *      
        925 ATAATCATTTTGGTGAGATTAGTCCATTGTTAAGTTTTTAGCTCATTTGGAACACTTGGTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

            *        * * *                     *             *               
        990 AGGCCTATCAACGACCATTAGTGT-CGTTTTGAATAGTCTTCG-TTTGGAAACCCTCAATGCTTT
         66 GGGCCTATCGAGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTT

                                     
       1053 TCTTTCCATTGTTTATGGCCTAACT
        130 TCTTTCCATTGTTTATGGCCTAACT

                                      *                                      
       1078 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

                   *  *         * ***          *    *                        
       1143 GGGCCTAACGGGGCCCATTACTGATGTTTTGAATCATCTTAGATTTGGCAACCCTCAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

                **         **       
       1208 CTTTATATTGTTTATATCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

                    *              ** *                                      
       1232 ATAATCATATTGGTGAGATTAGTTTACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
          1 ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT

                *        *          *                              *         
       1297 GGGCATATCGAGGACCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTTAATGCTTTT
         66 GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

                                    
       1362 CTTTCCATTGTTTATGGCCTAACT
        131 CTTTCCATTGTTTATGGCCTAACT

               *          *   *    
       1386 ATATTCATTTTGGTAAGACTAGT
          1 ATAATCATTTTGGTGAGATTAGT

       1409 TGATGCGCCA


Statistics
Matches: 1118,  Mismatches: 131, Indels: 10
        0.89            0.10        0.01

Matches are distributed among these distances:
 153  261  0.23
 154  731  0.65
 155  126  0.11

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42


Consensus pattern (154 bp):   
ATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
GGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT
CTTTCCATTGTTTATGGCCTAACT

Found at i:2106 original size:29 final size:29

Alignment explanation


    Indices: 1971--2097  Score: 245
    Period size: 29  Copynumber: 4.4  Consensus size: 29

       1961 CAGAGCCGCC

                                         
       1971 CCCCCTTCTTGCCTATATAAAGGCACCAA
          1 CCCCCTTCTTGCCTATATAAAGGCACCAA

                                         
       2000 CCCCCTTCTTGCCTATATAAAGGCACCAA
          1 CCCCCTTCTTGCCTATATAAAGGCACCAA

                                         
       2029 CCCCCTTCTTGCCTATATAAAGGCACCAA
          1 CCCCCTTCTTGCCTATATAAAGGCACCAA

                                         
       2058 CCCCCTTCTTGCCTATATAAAGGCACCAA
          1 CCCCCTTCTTGCCTATATAAAGGCACCAA

                 *     
       2087 CCCCCCTCTTG
          1 CCCCCTTCTTG

       2098 TAAACATAAG


Statistics
Matches: 97,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  29   97  1.00

ACGTcount: A:0.25, C:0.40, G:0.10, T:0.24


Consensus pattern (29 bp):   
CCCCCTTCTTGCCTATATAAAGGCACCAA
Done.