Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008946.1 Corchorus olitorius cultivar O-4 contig08973, 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, 703

Length: 1173
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41


Found at i:352 original size:154 final size:154

Alignment explanation


    Indices: 2--1173  Score: 1861
    Period size: 154  Copynumber: 7.6  Consensus size: 154

          1 A

                    *            *       *             *  *                  
          2 TCGATTTGACAAACCACAATGATTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                        *                        *           
         67 AGATTAGTCCATTGTGAAG-TTTTAGCTTA-TTTGAACACTTGTTATTTTGGGACATTC-GGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

                         *      *   
        129 CATTAGTTCGGTTCTGAATCGTCT
        131 CATTAGTTCGGTTTTGAATCATCT

             *      *                *                                    *  
        153 TGGATTT-TCAAACCACAATGCTTGATCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGT
          1 TCGATTTGGCAAACCACAATGCTT-TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGT

                        *             *                                 *    
        217 AAGATTAGTCCACTGTGAAGTTTTTAACTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGC
         65 AAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGC

            *               *  *     
        282 TCATTAGTTCGGTTTTAAACCATCT
        130 CCATTAGTTCGGTTTTGAATCATCT

                                                                             
        307 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                              *                              *               
        372 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTC-GGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

               *                *   
        436 CATAAGTTCGGTTTTGAATCTTCT
        131 CATTAGTTCGGTTTTGAATCATCT

                                         *             *  *                  
        460 TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                        *                        *     *     
        525 AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTCGGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

                         *      *   
        590 CATTAGTTCGGTTCTGAATCGTCT
        131 CATTAGTTCGGTTTTGAATCATCT

                    **                                                       
        614 TCGATTTGTTAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                                            *                
        679 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTATGGGCCATTCAGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

                                    
        744 CATTAGTTCGGTTTTGAATCATCT
        131 CATTAGTTCGGTTTTGAATCATCT

                                   *                   *  *             *    
        768 TCGATTTGGCAAACCACAATGCTCTTCTTTCCATTGTTTATGGGCTCACTATAATCATTTAGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                                             *       *       
        833 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTGGGGCCATGCAGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

                                    
        898 CATTAGTTCGGTTTTGAATCATCT
        131 CATTAGTTCGGTTTTGAATCATCT

             *                     *                   *  *                  
        922 TTGATTTGGCAAACCACAATGCTCTTCTTTCCATTGTTTATGGGCTCAC-ATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                                                             
        986 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC

                                  * 
       1051 CATTAGTTCGGTTTTGAATCATAT
        131 CATTAGTTCGGTTTTGAATCATCT

                                               *                             
       1075 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                   *             *            
       1140 AGATTAGACCATTGTGAAGTTATTAGCTCATTTT
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTT


Statistics
Matches: 942,  Mismatches: 72, Indels: 11
        0.92            0.07        0.01

Matches are distributed among these distances:
 150   14  0.01
 151   60  0.06
 152    8  0.01
 153  312  0.33
 154  533  0.57
 155   15  0.02

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41


Consensus pattern (154 bp):   
TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC
CATTAGTTCGGTTTTGAATCATCT

Found at i:560 original size:307 final size:308

Alignment explanation


    Indices: 2--1173  Score: 1836
    Period size: 307  Copynumber: 3.8  Consensus size: 308

          1 A

                    *            *       *             *  *                  
          2 TCGATTTGACAAACCACAATGATTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                               *        *                    *   *           
         67 AGATTAGTCCATTGTG-AAGTTTTAGCTTA-TTTGAACACTTGTTATTTTGGGACATTC-GGGCC
         66 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTCAGGGCC

                         *      *    *      *                *               
        129 CATTAGTTCGGTTCTGAATCGTCTTGGATTT-TCAAACCACAATGCTTGATCTTTCCATTGTTTA
        131 CATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTT-TTCTTTCCATTGTTTA

                                 *              *             *              
        193 TGGCCTAACTATAATCATTTTTGTAAGATTAGTCCACTGTGAAGTTTTTAACTCATTTTGAACAC
        195 TGGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACAC

                                    *               *  *     
        258 TTGTTATTTTGGGCCATTCGGGGCTCATTAGTTCGGTTTTAAACCATCT
        260 TTGTTATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCATCT

                                                                             
        307 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                                                                             
        372 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTC-GGGCC
         66 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTCAGGGCC

               *                *                                *           
        436 CATAAGTTCGGTTTTGAATCTTCTTCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTAT
        131 CATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT

              *  *                                              *            
        501 GGGCTCACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACT
        196 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                        *                        *      *   
        566 TGTTATTTTGGGACATTCGGGGCCCATTAGTTCGGTTCTGAATCGTCT
        261 TGTTATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCATCT

                    **                                                       
        614 TCGATTTGTTAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                              *                                              
        679 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTA-TTATGGGCCATTCAGGGC
         66 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTA-GGGCCATTCAGGGC

                                                            *                
        743 CCATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTCTTCTTTCCATTGTTTA
        130 CCATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTA

               *  *             *                                            
        808 TGGGCTCACTATAATCATTTAGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACAC
        195 TGGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACAC

                     *       * *                             
        873 TTGTTATTTGGGGCCATGCAGGGCCCATTAGTTCGGTTTTGAATCATCT
        260 TTGTTATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCATCT

             *                     *                   *  *                  
        922 TTGATTTGGCAAACCACAATGCTCTTCTTTCCATTGTTTATGGGCTCAC-ATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA

                              *                              *               
        986 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC
         66 AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTCAGGGCC

                                  *                                    *     
       1051 CATTAGTTCGGTTTTGAATCATATTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTATTTAT
        131 CATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT

                                           *             *            
       1116 GGCCTAACTATAATCATTTTGGTAAGATTAGACCATTGTGAAGTTATTAGCTCATTTT
        196 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTT


Statistics
Matches: 803,  Mismatches: 58, Indels: 10
        0.92            0.07        0.01

Matches are distributed among these distances:
 305   76  0.09
 306   14  0.02
 307  482  0.60
 308  231  0.29

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41


Consensus pattern (308 bp):   
TCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTA
AGATTAGTCCATTGTGAAATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTCAGGGCC
CATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT
GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT
TGTTATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCATCT

Found at i:861 original size:461 final size:461

Alignment explanation


    Indices: 2--1173  Score: 1976
    Period size: 461  Copynumber: 2.5  Consensus size: 461

          1 A

                    *            *                                           
          2 TCGATTTGACAAACCACAATGATTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA

                                                                             
         67 AGATTAGTCCATTGTGAAG-TTTTAGCTTA-TTTGAACACTTGTTATTTTGGGACATTCGGGCCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTCGGGCCC

                                    *                       *                
        130 ATTAGTTCGGTTCTGAATCGTCTTGGATTT-TCAAACCACAATGCTTGATCTTTCCATTGTTTAT
        131 ATTAGTTCGGTTCTGAATCGTCTTCGATTTGTCAAACCACAATGCTT-TTCTTTCCATTGTTTAT

                                *              *             *               
        194 GGCCTAACTATAATCATTTTTGTAAGATTAGTCCACTGTGAAGTTTTTAACTCATTTTGAACACT
        195 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                   *          *    *                                         
        259 TGTTATTTTGGGCCATTCGGGGCTCATTAGTTCGGTTTTAAACCATCTTCGATTTGGCAAACCAC
        260 TGTTATTATGGGCCATTCAGGGCCCATTAGTTCGGTTTTAAACCATCTTCGATTTGGCAAACCAC

                  *                                    *                     
        324 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGA
        325 AATGCTCTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCATTGTGA

                                                    *                        
        389 AATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATTC-GGGCCCATAAGTTCGGTTTTGA
        390 AATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATGCAGGGCCCATAAGTTCGGTTTTGA

               *   
        453 ATCTTCT
        455 ATCATCT

                                                                             
        460 TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA

                                                                             
        525 AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTCGGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTC-GGGCC

                                             *                               
        590 CATTAGTTCGGTTCTGAATCGTCTTCGATTTGTTAAACCACAATGCTTTTCTTTCCATTGTTTAT
        130 CATTAGTTCGGTTCTGAATCGTCTTCGATTTGTCAAACCACAATGCTTTTCTTTCCATTGTTTAT

                                                                             
        655 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT
        195 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                                                   *  *                      
        720 TGTTATTATGGGCCATTCAGGGCCCATTAGTTCGGTTTTGAATCATCTTCGATTTGGCAAACCAC
        260 TGTTATTATGGGCCATTCAGGGCCCATTAGTTCGGTTTTAAACCATCTTCGATTTGGCAAACCAC

                                      *  *                                   
        785 AATGCTCTTCTTTCCATTGTTTATGGGCTCACTATAATCATTTAGGTAAGATTAGTCCATTGTGA
        325 AATGCTCTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCATTGTGA

             *                              *                  *             
        850 AGTTTTTAGCTCATTTTGAACACTTGTTATTTGGGGCCATGCAGGGCCCATTAGTTCGGTTTTGA
        390 AATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATGCAGGGCCCATAAGTTCGGTTTTGA

                   
        915 ATCATCT
        455 ATCATCT

             *                     *     *                                   
        922 TTGATTTGGCAAACCACAATGCTCTTCTTTCCATTGTTTATGGGCTCAC-ATAATCATTTTGGTA
          1 TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA

                                        *                        *           
        986 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCAGGGCC
         66 AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTC-GGGCC

                         *      * *         *                          *     
       1051 CATTAGTTCGGTTTTGAATCATATTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTATTTAT
        130 CATTAGTTCGGTTCTGAATCGTCTTCGATTTGTCAAACCACAATGCTTTTCTTTCCATTGTTTAT

                                           *             *            
       1116 GGCCTAACTATAATCATTTTGGTAAGATTAGACCATTGTGAAGTTATTAGCTCATTTT
        195 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTT


Statistics
Matches: 673,  Mismatches: 36, Indels: 7
        0.94            0.05        0.01

Matches are distributed among these distances:
 458   82  0.12
 459   10  0.01
 460   28  0.04
 461  465  0.69
 462   88  0.13

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41


Consensus pattern (461 bp):   
TCGATTTGGCAAACCACAATGCTTTTCTTACCATTGTTTATGGGCTCACTATAATCATTTTGGTA
AGATTAGTCCATTGTGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGACATTCGGGCCC
ATTAGTTCGGTTCTGAATCGTCTTCGATTTGTCAAACCACAATGCTTTTCTTTCCATTGTTTATG
GCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTT
GTTATTATGGGCCATTCAGGGCCCATTAGTTCGGTTTTAAACCATCTTCGATTTGGCAAACCACA
ATGCTCTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCATTGTGAA
ATTTTTAGCTCATTTTGAACACTTGTTATTTAGGGCCATGCAGGGCCCATAAGTTCGGTTTTGAA
TCATCT
Done.