Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011925.1 Corchorus olitorius cultivar O-4 contig11958, 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, 907

Length: 1512
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22


Found at i:394 original size:154 final size:154

Alignment explanation


    Indices: 1--1503  Score: 2281
    Period size: 154  Copynumber: 9.8  Consensus size: 154

                                           *    *      *                     
          1 ACTAATGGT-CTCCGATAGGCCCAAAATAACGAGTGCTCCAAAGGAGCTAAAAACTTCACAGTGG
          1 ACTAATGGTCCT-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                                      *              *                       
         65 ACTAATCTCACCAAAATGATTATAGTCAGGCCATAAA-AATAGAAAGAAAAGCATTGAGGTTTGC
         65 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC

                  *                  
        129 CAAATCAAAGACGATTCAAAACGTC
        130 CAAATCGAAGACGATTCAAAACGTC

                    *           **                     *                     
        154 ACTAATGGGCCTCGATA-GCAAAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                     *   *                     *             
        218 CTAATCTCACCAAAATGATTATAGTCAGGACATAAACAATGGAAAGAAAAGAATTGAGGTTTGCC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                                    
        283 AAATCGAAGACGATTCAAAACGTC
        131 AAATCGAAGACGATTCAAAACGTC

                       *      *                     *                 *      
        307 ACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTCATAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                           *                                         *       
        372 CTAATCTCACCAAAACGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

               *       *            *
        437 AAACCGAAGACAATTCAAAAC-TGA
        131 AAATCGAAGACGATTCAAAACGT-C

                    *           *                                            
        461 ACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

              *                      *                                       
        526 CTCATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGACATTGAGGTTTAG
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTT-G

                                       
        591 CCAAATACGAAGACGATTCAAAACGTC
        129 CCAAAT-CGAAGACGATTCAAAACGTC

                                                                             
        618 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                *                          *  *  *                           
        683 CTAACCTCACCAAAATGATTATAGTTAGGCCGTACACGATGGAAAGAAAAGCATTGAGGTTTGCC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                             **     
        748 AAATCGAAGACGATTCATTACGTC
        131 AAATCGAAGACGATTCAAAACGTC

                                           *         *                       
        772 ACTAATGGT-CTGCGATAGGCCCAAAATAACGAGTGTTCCATATGAGCTAAAAACTTCACAGTGG
          1 ACTAATGGTCCT-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                                                  *  *        *    *         
        836 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACTATTGAAAGAAAGGCATCGAAGG-TTG
         65 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTG

                                      
        900 CCAAATCGAAGACGATTCAAAACGTC
        129 CCAAATCGAAGACGATTCAAAACGTC

                                                                             
        926 ACTAATGGT-CTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                                             * *  *  * *     
        990 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGTATCGACGATTGCC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                      *             
       1055 AAATCGAAGATGATTCAAAACGTC
        131 AAATCGAAGACGATTCAAAACGTC

                       *      *                                              
       1079 ACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                *                          *  *  *                           
       1144 CTAACCTCACCAAAATGATTATAGTTAGGCCGTACACGATGG-AAGAAAAGCATTGAGGTTTGCC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                                    
       1208 AAATCGAAGACGATTCAAAACGTC
        131 AAATCGAAGACGATTCAAAACGTC

                                           *         *                       
       1232 ACTAATGGT-CTCCGATAGGCCCAAAATAACGAGTGTTCCATATGAGCTAAAAACTTCACAGTGG
          1 ACTAATGGTCCT-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                                                   * *        *    *         
       1296 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTTGAAAGAAAGGCATCGTAGG-TTG
         65 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTG

                                      
       1360 CCAAATCGAAGACGATTCAAAACGTC
        129 CCAAATCGAAGACGATTCAAAACGTC

                    *        *   *                  *                        
       1386 ACTAATGGGCCTCGATAAGCCAAAAATAACAAGTGTTCCATATGAGCT-AAAACTTCACAGTGGA
          1 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                            *       *        *    
       1450 CTAATCTCACCAAAATGATTATAGTTAGGCCACAAACAATTGAAAGAAAGGCAT
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT

       1504 CGAAGGTTG


Statistics
Matches: 1236,  Mismatches: 98, Indels: 32
        0.90            0.07        0.02

Matches are distributed among these distances:
 152   79  0.06
 153  424  0.34
 154  566  0.46
 155   25  0.02
 156   17  0.01
 157  124  0.10
 158    1  0.00

ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22


Consensus pattern (154 bp):   
ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
AAATCGAAGACGATTCAAAACGTC

Found at i:1061 original size:307 final size:307

Alignment explanation


    Indices: 1--1503  Score: 2275
    Period size: 307  Copynumber: 4.9  Consensus size: 307

                                          *    *      *                      
          1 ACTAATGGTCTCCGATAGGCCCAAAATAACGAGTGCTCCAAAGGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCT-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                     *              *                        
         66 CTAATCTCACCAAAATGATTATAGTCAGGCCATAAA-AATAGAAAGAAAAGCATTGAGGTTTGCC
         65 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                 *                                      **                   
        130 AAATCAAAGACGATTCAAAACGTCACTAATGGGCCTCGATA-GCAAAAAATAACAAGTGTTCCAA
        130 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

              *                                              *   *          *
        194 ATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTCAGGACATAAACAATG
        195 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATT

                    * *                                     
        259 GAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
        260 GAAAGAAAGGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                       *      *                     *                 *      
        307 ACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTCATAGTGGA
          1 ACTAATGGT-CTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                           *                                         *       
        372 CTAATCTCACCAAAACGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCC
         65 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

               *       *            *                    *                   
        437 AAACCGAAGACAATTCAAAAC-TGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCA
        130 AAATCGAAGACGATTCAAAACGT-CACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCA

                                       *                      *              
        501 AATGAGCTAAAAACTTCACAGTGGACTCATCTCACCAAAATGATTATAGTCAGGCCATAAACAAT
        194 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

            *          *                                        
        566 GGAAAGAAAAGACATTGAGGTTTAGCCAAATACGAAGACGATTCAAAACGTC
        259 TGAAAG-AAAGGCATTGAGGTTT-GCCAAAT-CGAAGACGATTCAAAACGTC

                                                                             
        618 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGT-CTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                *                          *  *  *                           
        683 CTAACCTCACCAAAATGATTATAGTTAGGCCGTACACGATGGAAAGAAAAGCATTGAGGTTTGCC
         65 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC

                             **              *                     *         
        748 AAATCGAAGACGATTCATTACGTCACTAAT-GGTCTGCGATAGGCCCAAAATAACGAGTGTTCCA
        130 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCT-CGATAGGCCCAAAATAACAAGTGTTCCA

            *                                                             *  
        812 TATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACTAT
        194 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

                          *                                   
        877 TGAAAGAAAGGCATCGAAGG-TTGCCAAATCGAAGACGATTCAAAACGTC
        259 TGAAAGAAAGGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                                                                             
        926 ACTAATGGTCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
          1 ACTAATGGTCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC

                                                            * *  *  * *      
        991 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGTATCGACGATTGCCA
         66 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA

                     *                     *  *      *                       
       1056 AATCGAAGATGATTCAAAACGTCACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCAAA
        131 AATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAA

                                       *                          *  *  *    
       1121 TGAGCTAAAAACTTCACAGTGGACTAACCTCACCAAAATGATTATAGTTAGGCCGTACACGA-TG
        196 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTG

            *      *                                       
       1185 GAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
        261 AAAGAAAGGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                                          *         *                        
       1232 ACTAATGGTCTCCGATAGGCCCAAAATAACGAGTGTTCCATATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGTCT-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                                  * *        *    *          
       1297 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTTGAAAGAAAGGCATCGTAGG-TTGC
         65 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGC

                                                      *   *                  
       1361 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAAGCCAAAAATAACAAGTGTTCCA
        129 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCA

            *                                                        *       
       1426 TATGAGCT-AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCACAAACAAT
        194 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

                          
       1490 TGAAAGAAAGGCAT
        259 TGAAAGAAAGGCAT

       1504 CGAAGGTTG


Statistics
Matches: 1090,  Mismatches: 92, Indels: 29
        0.90            0.08        0.02

Matches are distributed among these distances:
 305    3  0.00
 306  194  0.18
 307  471  0.43
 308  122  0.11
 309   20  0.02
 310   21  0.02
 311  258  0.24
 312    1  0.00

ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22


Consensus pattern (307 bp):   
ACTAATGGTCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTG
AAAGAAAGGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
Done.