Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012114.1 Corchorus olitorius cultivar O-4 contig12147, 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, 908

Length: 1514
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Found at i:628 original size:154 final size:154

Alignment explanation


    Indices: 1--1514  Score: 2041
    Period size: 154  Copynumber: 9.9  Consensus size: 154

                                       *       *         *       *           
          1 ATAGTTAAGGCCATAAACAATGG-AA-CAAAGCATCGAGGGTTGCGAAATCGATGACGATTCAAA
          1 ATAGTT-AGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA

            *  **        *  *      *   *                     *               
         64 TCGAAACTAATGGCCCCCGGA-ACGCCTAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCAC
         65 ACGTCACTAATGGGCCTC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC

                                      
        128 AGTGGACTAATCTCACCAAAATGATT
        129 AGTGGACTAATCTCACCAAAATGATT

                                *                  *  *                      
        154 ATAGTTAGGCCATAAACAATCGAAAGAAAA-CATTGAGGTTTCCCAAATCGAAGACGATTCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

               *           *   *      *                                      
        218 CG-AACTAATGGGCCCCGAAAGGCCTTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
         66 CGTCACTAATGGGCCTCGATAGGCC-CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA

                                     
        282 GTGGACTAATCTCACCAAAATGATT
        130 GTGGACTAATCTCACCAAAATGATT

                            *            *                   *               
        307 ATAGTTAGGCCATAAATAATGGAAAGAAAGGCATTGAGGGTTG-CAAATAGAAGTA-GATTCAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAG-ACGATTCAAA

                                  *   * *               *                    
        370 ACGTCACTAATGGGGCCT-GATTGGCTCGAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCAC
         65 ACGTCACTAAT-GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC

                                      
        434 AGTGGACTAATCTCACCAAAATGATT
        129 AGTGGACTAATCTCACCAAAATGATT

                                                   *  *  *                   
        460 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCTAATCGAAGACGATTCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

                            *                                                
        525 CGTCACTAATGGGCCTAGATAGGCCCAAAATAA-AATGTGTTCCAAATGAGCTAAAAACTTCACA
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACA

              *                  *   
        589 GTAGACTAATCTCACCAAAATAATT
        130 GTGGACTAATCTCACCAAAATGATT

                     *              *                        *        *      
        614 ATAGTTAGGTCATAAACAATGGAATGAAAAGCATTGAGGGTTGCCAAATTGAAGACGAATCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

              **                                   *  *       *              
        679 CGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGCTCAAAATGAGTTAAAAACTTCACAG
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG

                      ** *          
        744 TGGACTAATCAAAACAAAATGATT
        131 TGGACTAATCTCACCAAAATGATT

                                         *     *            *      *    *    
        768 ATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTAAGGGTTGCCAAAGCGAAGATGATTTAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

                      *              *                       *           *   
        833 CGTCACTAATTGGCC-CTGATAGGCTCAAAATAACAAGTGTTCCAAATGTGCT-AAAACTTGACA
         66 CGTCACTAATGGGCCTC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA

            *                       *
        896 TTGGACTAATCTCACCAAAATGATA
        130 GTGGACTAATCTCACCAAAATGATT

               *                               *                             
        921 ATAATTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGGTTGCCAAATCGAAGACGATTCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

              **  *        *                                                 
        986 CGGAACCAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA-A-
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG

                         *          
       1049 TGGACTAATCTCAACAAAATGATT
        131 TGGACTAATCTCACCAAAATGATT

             * *            *            *     *      *     *      *         
       1073 ACAATTAGGCCATAAAAAATGGAAAGAAAGGCATTAAGGGTTACCAAAGCGAAGATGATTCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

                           *        *                                        
       1138 CGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG

                                    
       1203 TGGACTAATCTCACCAAAATGATT
        131 TGGACTAATCTCACCAAAATGATT

                                         *         *  *  *              *    
       1227 ATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGTTTACCTAATCGAAGACGATTTAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

                            *    *       *                               *   
       1292 CGTCACTAATGGGCCTAGATATGCCCAAAGTAA-AATGTGTTCCAAATGAGCTAAAAACTTTACA
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACA

                                     
       1356 GTGGACTAATCTCACCAAAATGATT
        130 GTGGACTAATCTCACCAAAATGATT

                     **                         *            *        *      
       1381 ATAGTTAGGTTATAAACAATGGAAAGAAAAGCATTGGGGGTTGCCAAATTGAAGACGAATCAAAA
          1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA

              **           *                       *                         
       1446 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCT-CAAATGAGCTAAAAACTTCACAG
         66 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG

                 
       1510 TGGAC
        131 TGGAC


Statistics
Matches: 1205,  Mismatches: 136, Indels: 40
        0.87            0.10        0.03

Matches are distributed among these distances:
 151    2  0.00
 152  171  0.14
 153  423  0.35
 154  600  0.50
 155    9  0.01

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (154 bp):   
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACCAAAATGATT

Found at i:1475 original size:767 final size:767

Alignment explanation


    Indices: 91--1514  Score: 2426
    Period size: 767  Copynumber: 1.9  Consensus size: 767

         81 CGGAACGCCT

                                                                          *  
         91 AAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
          1 AAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATAAT

             *                              *   *                            
        156 AGTTAGGCCATAAACAATCGAAAGAAAACATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGA
         66 AATTAGGCCATAAACAATCGAAAGAAAACATTAAGGGTTCCCAAATCGAAGACGATTCAAAACGA

              *                   *                                          
        221 ACTAATGGGCCCCGAAAGGCCTTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
        131 ACCAATGGGCCCCGAAAGGCCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                      *           * *            *                  *      * 
        286 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAGGCATTGAGGGTTGC
        196 ACTAATCTCAACAAAATGATTACAATTAGGCCATAAAAAATGGAAAGAAAGGCATTAAGGGTTCC

               *                             *  *   *     *               *  
        351 AAATAGAAGTAGATTCAAAACGTCACTAATGGGGCCTGATTGGCTCGAAATAACAAGTGTTCTAA
        261 AAAGAGAAGTAGATTCAAAACGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAA

                                                                             
        416 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
        326 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                                                                             
        481 GAAAGAAAAGCATTGAGGTTTACCTAATCGAAGACGATTCAAAACGTCACTAATGGGCCTAGATA
        391 GAAAGAAAAGCATTGAGGTTTACCTAATCGAAGACGATTCAAAACGTCACTAATGGGCCTAGATA

                                                                             
        546 GGCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATA
        456 GGCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATA

                                       *                                     
        611 ATTATAGTTAGGTCATAAACAATGGAATGAAAAGCATTGAGGGTTGCCAAATTGAAGACGAATCA
        521 ATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGAATCA

                              *                                  *           
        676 AAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGCTCAAAATGAGTTAAAAACTTCA
        586 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCTC-AAATGAGCTAAAAACTTCA

                                                                             
        741 CAGTGGACTAATCAAAACAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTAAG
        650 CAGTGGACTAATCAAAACAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTAAG

                                                                 
        806 GGTTGCCAAAGCGAAGATGATTTAAAACGTCACTAATTGGCCCTGATAGGCTC
        715 GGTTGCCAAAGCGAAGATGATTTAAAACGTCACTAATTGGCCCTGATAGGCTC

                                 **           *   *                          
        859 AAAATAACAAGTGTTCCAAATGTGCT-AAAACTTGACATTGGACTAATCTCACCAAAATGATAAT
          1 AAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATAAT

                              *                     *                        
        923 AATTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGGTTGCCAAATCGAAGACGATTCAAAACG
         66 AATTAGGCCATAAACAATCGAAAGAAAA-CATTAAGGGTTCCCAAATCGAAGACGATTCAAAAC-

                             *                                               
        988 GAACCAATGGGCCCCGATAGGCC-CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA-A-T
        129 GAACCAATGGGCCCCGAAAGGCCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                                                                             
       1050 GGACTAATCTCAACAAAATGATTACAATTAGGCCATAAAAAATGGAAAGAAAGGCATTAAGGGTT
        194 GGACTAATCTCAACAAAATGATTACAATTAGGCCATAAAAAATGGAAAGAAAGGCATTAAGGGTT

                   *                                                         
       1115 ACCAAAGCGAAG-ATGATTCAAAACGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTT
        259 -CCAAAGAGAAGTA-GATTCAAAACGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTT

                                                                             
       1179 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
        322 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC

                        *                              *                     
       1244 AATGGAAAGAAAGGCATTGAGGTTTACCTAATCGAAGACGATTTAAAACGTCACTAATGGGCCTA
        387 AATGGAAAGAAAAGCATTGAGGTTTACCTAATCGAAGACGATTCAAAACGTCACTAATGGGCCTA

                *       *                              *     *               
       1309 GATATGCCCAAAGTAAAATGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAA
        452 GATAGGCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAA

               *             *                         *                     
       1374 AATGATTATAGTTAGGTTATAAACAATGGAAAGAAAAGCATTGGGGGTTGCCAAATTGAAGACGA
        517 AATAATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGA

                                                                             
       1439 ATCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCAAATGAGCTAAAAACT
        582 ATCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCAAATGAGCTAAAAACT

                       
       1504 TCACAGTGGAC
        647 TCACAGTGGAC


Statistics
Matches: 614,  Mismatches: 38, Indels: 10
        0.93            0.06        0.02

Matches are distributed among these distances:
 766   88  0.14
 767  413  0.67
 768   92  0.15
 769   21  0.03

ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22


Consensus pattern (767 bp):   
AAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATAAT
AATTAGGCCATAAACAATCGAAAGAAAACATTAAGGGTTCCCAAATCGAAGACGATTCAAAACGA
ACCAATGGGCCCCGAAAGGCCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
ACTAATCTCAACAAAATGATTACAATTAGGCCATAAAAAATGGAAAGAAAGGCATTAAGGGTTCC
AAAGAGAAGTAGATTCAAAACGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTACCTAATCGAAGACGATTCAAAACGTCACTAATGGGCCTAGATA
GGCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATA
ATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGAATCA
AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCAAATGAGCTAAAAACTTCAC
AGTGGACTAATCAAAACAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTAAGG
GTTGCCAAAGCGAAGATGATTTAAAACGTCACTAATTGGCCCTGATAGGCTC
Done.