Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015406.1 Corchorus olitorius cultivar O-4 contig15439, 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: 3212
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:606 original size:332 final size:331

Alignment explanation


    Indices: 1--2474  Score: 3325
    Period size: 332  Copynumber: 7.5  Consensus size: 331

                             *       *            *           *           *  
          1 AAAAATATGAAAAACGAAATTAAAATCGTGAGAAGTCCACCAATC-TTTTAGCATTAAATTAAAT
          1 AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATAT

                       *       *                                      *      
         65 ATATTTTATGATTATTTTAACCAAAAATTGAGGAAAATTTTTCGCGGTCATTTTTTGGTAAAATT
         66 ATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAATTTTTCGCGGTCATTTTTT-GCAAAATT

               *          *                                            **    
        130 TTATCCAAAATCGTTTACTAACCATCACGG-TTTTGGCTAAAAACGCGTTTC-GGAGTCTTGGCT
        130 TTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGA-TCCCGGCT

                   *       *     *        *                             *    
        193 CAGTTTTACATGATTATTGGCATCAGGATTTCTTGAAATATCTATATTCATCTAATAAAATCTTA
        194 CAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTTA

                                  *       *                    *             
        258 GCCACATTGCATTTAAGGATTTCTTTTC-CCAGGCATTTGAATCTTGTTTCAATTTCATTAGAAA
        259 GCCACATTGCATTTAAGGATTTGTTTTCACGA-GCATTTGAATCTTGTTTCGATTTCATTAGAAA

                      
        322 TTAATTCAAG
        323 TTAATTC-AG

                   *                     *                        *          
        332 AAAAATACGAAAAACGATATTAAAAGCGTCA-ATAGTCCTCCAATCTTTTTGGCGTTAAATTATA
          1 AAAAATATGAAAAACGATATTAAAAGCGTGAGA-AGTCCTCCAATCTTTTTGGCATTAAATTATA

             *    **                                                         
        396 TCTATTCGATGAGTATTTTATCC-AAAATTGAGGAAACATTTTTCGCGGTCATTTTTTGCAAAAT
         65 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAA-ATTTTTCGCGGTCATTTTTTGCAAAAT

                   *           *                            *                
        460 TTTAGCCGAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAACGCTTTTCGGGATCCCGGCT
        129 TTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGATCCCGGCT

                                *       *                            *       
        525 CAGTTTTGCATGATTTTTGGTGTCAGGACTCCTTGAAATATCTATATTCATCTAATAGAAACTTA
        194 CAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTTA

                             **                         *                    
        590 GCCACATTGCATTTAAGCTTTTGTTTT-ATCGAGCATTTGAATCATGTTTCGATTTCATTAGAAA
        259 GCCACATTGCATTTAAGGATTTGTTTTCA-CGAGCATTTGAATCTTGTTTCGATTTCATTAGAAA

                     
        654 TTAATTCAG
        323 TTAATTCAG

                                            *                         *   *  
        663 CAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTACATTGTA
          1 -AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA

                                                      *                      
        728 TATATTTTATGAGTATTTTATCCAAAAATTGAGGATAAATTTATCGCGGTCATTTTTTTGCAAAA
         65 TATATTTTATGAGTATTTTATCCAAAAATTGAGGA-AAATTTTTCGCGGTCA-TTTTTTGCAAAA

                   *                   *           *      *          *     * 
        793 TTTTAGCAAAAATCGTGTACTAACCATAACGG-TTTTGGTTAAAAATGCGTTTCGGGGT-CCGAC
        128 TTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGATCCCGGC

                                  * * **                              *      
        856 TCAGTTTTGCATGATTTTTGGCATTACAATTCCTTGAAATATCTATATTCATCTAATAGAAACTT
        193 TCAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTT

                                        *               *                    
        921 AGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTCATTAGAAA
        258 AGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAA

                     
        986 TTAATTCAG
        323 TTAATTCAG

                                *                                            
        995 CAAAAATATGAAAAACGATAATAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA
          1 -AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA

                                   *                  *                      
       1060 TATATTTTATGAGTATTTTATCCTAAAATTGAGGATAAATTTATCGCGGTCATTTTTTGCAAAAT
         65 TATATTTTATGAGTATTTTATCCAAAAATTGAGGA-AAATTTTTCGCGGTCATTTTTTGCAAAAT

                                           *                                 
       1125 TTTAGCCAAAATCGTGTACTAACCATCACGGATTTTGGCTAAAAACGCGTTTC-GGAGTCCCGGC
        129 TTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGA-TCCCGGC

                                                                             
       1189 TCAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAA-ATCTATATTCATCTAATAAAAACTT
        193 TCAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTT

                             *             *   *                             
       1253 AGCCACATTGCATTTAATGATTTGTTTTC-CTAGGTATTTGAATCTTGTTTCGATTTCATTAGAA
        258 AGCCACATTGCATTTAAGGATTTGTTTTCACGA-GCATTTGAATCTTGTTTCGATTTCATTAGAA

                   *   
       1317 ATTAATTAAGG
        322 ATTAATTCA-G

                          *                                      *        *  
       1328 AAAAATATGAAAAAGGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCGTTACAA-TGTA
          1 AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTA-AATTATA

                                          *              *    *  *         * 
       1392 TATATTTTATGAGTATTTTATCCAAAAATTCAGGGAAAATTTTTCACGGTAATGTTTTGCAAATT
         65 TATATTTTATGAGTATTTTATCCAAAAATTGA-GGAAAATTTTTCGCGGTCATTTTTTGCAAAAT

                  *                                        *      *        * 
       1457 TTTAGCAAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCATGG-TCCCGAC
        129 TTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGATCCCGGC

                               *      *                                      
       1521 TCAGTTTTGCATGATTTTTTGCGTCACGATTCCTTGAAATATCTATA-TCATCTAATAAAAACTT
        193 TCAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTT

                            *      *    *        *                           
       1585 AGCCACATTGCATTTATGGATTTTTTTTTACGAGCATATGAATCTTGTTTCGATTTCATTAGAAA
        258 AGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAA

                      
       1650 TTAATTTC-G
        323 TTAA-TTCAG

                                    *   *                                    
       1659 AAAAAATATGAAAAACGATATTAAGAGCATGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA
          1 -AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA

                                                        *                    
       1724 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAATATTTTTTGCGGTCATTTTTTTGCAAAA
         65 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAA-ATTTTTCGCGGTCA-TTTTTTGCAAAA

                                          *                *         *       
       1789 TTTTAGCCAAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACACGTTTCGGGGTCCCGGC
        128 TTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGATCCCGGC

             * *                         *            *                *     
       1854 TTAATTTT-CATGATTTTTGGCGTCAGGAGTCCTTGAAATATTTATATTCATCTAATAATAACTT
        193 TCAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTT

                          *        *    *                *           *       
       1918 AGCCACATTGCATTGAAGGATTTCTTTTTACGAGCATTTGAATCTCGTTTCGATTTCGTTAGAAA
        258 AGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAA

                     
       1983 TTAATTCAG
        323 TTAATTCAG

                     *     *                                      *       *  
       1992 AAAAAATATTAAAAATGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCGTTAAATTGTA
          1 -AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATA

                                                        * **          *   *  
       2057 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAATATTTTTGGAAGTCATTTTTTACAAGAT
         65 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAA-ATTTTTCGCGGTCATTTTTTGCAAAAT

                                         *      * *       *  *      *       *
       2122 TTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTTGATAAAAACACGATTCGGGGTCCCGGCA
        129 TTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGATCCCGGCT

                    *  *       *   *    *        *                       *   
       2187 C-GTTTTGAATTATTTTTGACGTAAGGACTCCTTGAAGTATCTATATTCATCTAATAAAAATTTA
        194 CAGTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTTA

                                         *              *                    
       2251 GCCACATTGCATTTAAGGATTTGTTTTCCTCGA-CATTTGAATCATGTTTCGATTTCATTAGAAA
        259 GCCACATTGCATTTAAGGATTTGTTTT-CACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAA

                     
       2315 TTAATTCAG
        323 TTAATTCAG

                                           *                         *   *   
       2324 --------G-AAAA--ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTACATTGTAT
          1 AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATAT

               *     *                    *  *       *   *                   
       2378 ATAATTTATAAGTATTTTATCCAAAAATCTAAGAAAAATTTATCGAGGTCATTTTTTTGCAAAAT
         66 ATATTTTATGAGTATTTTATCCAAAAAT-TGAGGAAAATTTTTCGCGGTCA-TTTTTTGCAAAAT

                  *              *          
       2443 TTTAGCAAAAATCGTGTACTACCCATCACGGT
        129 TTTAGCCAAAATCGTGTACTAACCATCACGGT

       2475 AATAAATTAT


Statistics
Matches: 1919,  Mismatches: 188, Indels: 82
        0.88            0.09        0.04

Matches are distributed among these distances:
 320   83  0.04
 321   46  0.02
 322    4  0.00
 330    1  0.00
 331  144  0.08
 332  1225  0.64
 333  372  0.19
 334   44  0.02

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Consensus pattern (331 bp):   
AAAAATATGAAAAACGATATTAAAAGCGTGAGAAGTCCTCCAATCTTTTTGGCATTAAATTATAT
ATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAATTTTTCGCGGTCATTTTTTGCAAAATTT
TAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGATCCCGGCTCA
GTTTTGCATGATTTTTGGCGTCAGGATTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGC
CACATTGCATTTAAGGATTTGTTTTCACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTA
ATTCAG

Found at i:3141 original size:2 final size:2

Alignment explanation


    Indices: 3134--3212  Score: 112
    Period size: 2  Copynumber: 41.5  Consensus size: 2

       3124 CCATCTTGGG

                               *                          *               
       3134 GA GA GA GA GA GA GG GA GA GA GA GA G- GA G- GG GA GA G- GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                                         
       3173 GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G


Statistics
Matches: 70,  Mismatches: 3, Indels: 8
        0.86            0.04        0.10

Matches are distributed among these distances:
   1    4  0.06
   2   66  0.94

ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00


Consensus pattern (2 bp):   
GA

Done.