Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014270.1 Corchorus olitorius cultivar O-4 contig14303, 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: 1697
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1322 original size:331 final size:331

Alignment explanation


    Indices: 2--1694  Score: 2534
    Period size: 331  Copynumber: 5.1  Consensus size: 331

          1 A

                                     *                    *                  
          2 AAAAATAATAGAAAAATTTTTTTCGAGTCAGTTTTGTCAAAAGTTTAAGCAGAAATACGTGTA-T
          1 AAAAATAATAG-AAAA-TTTTTTCGGGTCAGTTTTG-CAAAA-TTTTAGCAGAAAT-CGTGTACT

            *                 *                                    *   *     
         66 TA-CATCACAGTTTTTTGTCGAAAAACGCATTCCGTG-ACCCCGGCTCAGTTTTGTATGGTTTTT
         61 AACCATCACAG-TTTTTGGCGAAAAACGCATTCCG-GAACCCCGGCTCAGTTTTGCATGATTTTT

               *        **                 *             * * *    ***  *     
        129 TGCACCAAGACTTTTTGAAATATCTATATTCTTCTAAACCAAA-CGCGGTCACATTGGAATTAAG
        124 TGCGCCAAGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTCAGCCACAACCGATTTAAG

                                *                                            
        193 GATTTGTTTTTACGAGCATCAGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAATAG
        188 GATTTGTTTTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAATAG

                          *                                   *           *  
        258 CAAAAACGATATTCAAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAGTTATATAATTTGTA
        253 CAAAAACGATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTA

                          
        323 CAAGTATTGTGGCC
        318 CAAGTATTGTGGCC

                *                   *                                        
        337 AAAAGTAATAGAAAATTTTTTCGGATCAGTTTTGCAAAATTTTAGCAGAAATC--G---TAACCA
          1 AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA

                                          *                             *    
        397 TCACAGTTTTTGGCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGTGCCA
         66 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA

                                   *                                         
        462 AGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTT
        131 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTT

                              *                  *      *            *      *
        527 TTTACGAGCATCGGAATCTTGTTTCGATTTTATTATATATTAATACA-AAAAAATAGGAAAAACA
        196 TTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAATAGCAAAAACG

                 **                                                     *    
        591 ATATTTTAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAATTATT
        261 ATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATT

                  
        656 GTGGCC
        326 GTGGCC

                                   *                               *         
        662 AAAAATAATAGAAAATTTTTTCGAGTCAGTTTTGCAAAATTTTAGCAGAAATCGTCTACTAACCA
          1 AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA

                                               * *                           
        727 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCTGCCTCAGTTTTGCATGATTTTTTGCGCCA
         66 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA

                                    *             *   * *  ***              *
        792 AGACTCCTTGAAATATCTATATTCTTCTAAACCAAA-CGCAGTCGCATTGGATTTAAGGATTTGG
        131 AGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTCAGCCACAACCGATTTAAGGATTTGT

                    * *                                                      
        856 TTTTACGATCTTCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAA
        195 TTTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAA-ATAGCAAAAA

                                                                          *  
        921 CGATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAATTA
        259 CGATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTA

                    
        986 TTGTGGCC
        324 TTGTGGCC

                                                                             
        994 AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA
          1 AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA

                                               ***                       *   
       1059 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCTACCTCAGTTTTGCATG-TTTTTTGCACCA
         66 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA

                                   *                                     **  
       1123 AGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTCATT
        131 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTT

                                                                             
       1188 TTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAAC
        196 TTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAA-ATAGCAAAAAC

                                                                             
       1253 GATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTAT
        260 GATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTAT

                   
       1318 TGTGGCC
        325 TGTGGCC

                     *                                                       
       1325 AAAAATAATTGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA
          1 AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA

                        **                *                                  
       1390 TCACAGTTTTTGATGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA
         66 TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA

                                                                 *        *  
       1455 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAACCGATTGAAGGATTTATT
        131 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTT

                    *   *     *                                      *       
       1520 TTTACGAGAATCAGAATCTTGTTTCGATTTTATTATAAATTAATTC-GAAAAAATAGGAAAAACG
        196 TTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAATAGCAAAAACG

                                              *     *  *    *                
       1584 ATATTCGAAGCGTGAAATGCCCTTTAATATTTTTAGCATTAAAATATACAATTTTTACAAGTATT
        261 ATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATT

                  
       1649 GTGGCC
        326 GTGGCC

                            *                         
       1655 AAAAATTAA-AGAAAAATTTTT-GGGTCAGTTTTGCAAAATT
          1 AAAAA-TAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATT

       1695 CTA


Statistics
Matches: 1247,  Mismatches: 97, Indels: 34
        0.90            0.07        0.02

Matches are distributed among these distances:
 325  139  0.11
 326  143  0.11
 327    8  0.01
 328    1  0.00
 329   19  0.02
 330  258  0.21
 331  334  0.27
 332  314  0.25
 333   17  0.01
 334    4  0.00
 335   10  0.01

ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Consensus pattern (331 bp):   
AAAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCA
TCACAGTTTTTGGCGAAAAACGCATTCCGGAACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCA
AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTT
TTTACGAGCATCGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAATAGCAAAAACG
ATATTCGAAGCGTGAAATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATT
GTGGCC
Done.