Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013728.1 Corchorus olitorius cultivar O-4 contig13761, 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: 12236
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1084 original size:322 final size:318

Alignment explanation


    Indices: 1--1372  Score: 1640
    Period size: 322  Copynumber: 4.3  Consensus size: 318

                *     *           *                   *                      
          1 ATCTCTTTGGCGTTGAATTATAAATTTTTTATGAGTATTGTGACCAAAAATTGAGGAAAATAAAT
          1 ATCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAA-AAAT

                    * *     *         *                        *             
         66 TT-GTGTCAATTTTTTTCAAAATTCGACGAAATCGTG---T-ACCATCACGATTTTTGGCTAAAA
         65 TTCGTG-CCAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA

                     *    *       *                  * *                     
        126 ACGCGTTCTTGGG-CCCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCT
        129 ACGCGTT-TCGGGATCCCGACTCAGTTTTGCATGATTTTTGACATCAAGACTCATTGAAATATCT

                       *                                                     
        190 ATATTAATCTAGCAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATC
        193 ATATTAATCTAACAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATC

             *      *                           *     **     *              
        255 AGGTTTCGTTTAAAATTC-GAAAAAATAGGAAAAACTTTATTTCAAGCGCGAAAAGCCCTTCAA
        258 ATGTTTCGATT--AATTCGGAAAAAATAGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTC-A

                           *                         *             *         
        318 AT-TTTTTGGTGTTGGATTATACATTTTTTATGAGTATTGTTGCCAAAAATTGAGAAAAAAAATT
          1 ATCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAAATT

             *    *                                                          
        382 TTGTGCTAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAA
         66 TCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAA

                  *           *                                       *      
        447 CGCGTTCCGGGA-CTCCGGCTCAGTTTTGCATGATTTTTGGA-ATCAAGACTCATTGAGATATCT
        130 CGCGTTTCGGGATC-CCGACTCAGTTTTGCATGATTTTT-GACATCAAGACTCATTGAAATATCT

                      * *         *                             *   *  *     
        510 ATATTAATCTTATAAAATCTCAACCACACTGGATTTAAGGATTTATTTTTAGAAGCTTCCGAATC
        193 ATATTAATCTAACAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATC

            *           *          *                  *  **              
        575 CTGTTTCGATTACTTCGGAAAAAGTAGGAAAAACGTTATTAGTAGTATGAAAAGCCCTTCA
        258 ATGTTTCGATTAATTCGGAAAAAATAGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTCA

             *                                                  *            
        636 AACTTTTTGGTGTTGAATTATACA-TTTTTATGAGTATTGTGGCC-AAAATTAAGAGAAAAAAAT
          1 ATCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAG-GAAAAAAAT

             *                                 *      **     *               
        699 TCCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTATACTAAATATCACCGTTTTTGGCTAAAAA
         65 TTCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA

             *                                                               
        764 CACGTTTCGGGATCCCGACTCAGTTTTGCATGATTTTTGACATCAAGACTCATTGAAATATCTAT
        130 CGCGTTTCGGGATCCCGACTCAGTTTTGCATGATTTTTGACATCAAGACTCATTGAAATATCTAT

                                            *                          *     
        829 ATTAATCTAACAAAATCTCAGCCACACTGGATATAA-GATTTATTTTTAGGAGCATCTGGATCAT
        195 ATTAATCTAACAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATCAT

                                        *                                   
        893 GTTTCGATTAATTCGGAAAAAAAAAAATTGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTCA
        260 GTTTCGATTAATTCGG-----AAAAAATAGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTCA

                    *                                        *               
        957 ATCTTTTTTGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAATTTGAGGAAAAAAATT
          1 ATCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAAATT

                                      *                                      
       1022 TCGTGCCAGTTTTTGCAAAATTCGGCAAAATCGTGTACTAACCATCACGGTTTTCT-GCTAAAAA
         66 TCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGGTTTT-TGGCTAAAAA

                        *     ** *                  * *     *                
       1086 CGCGTTTCGAGGCT-CCGGTTTAGTTTTGCATGATTTTTGGCGTCAAGGCTCATTGAAATATCTA
        130 CGCGTTTCG-GGATCCCGACTCAGTTTTGCATGATTTTTGACATCAAGACTCATTGAAATATCTA

                      *        *                                             
       1150 TATTAATCTAGCAAAATCTAAGCCACAC------T--GGATTTATTTTTAGGAGCATCTGAATCA
        194 TATTAATCTAACAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATCA

                  *                   * *                            *    
       1207 TGTTTCAATTAATTCGGAAAAAAAATTGAAAAAACGTTATTAGAAGCGTGAAAAGCCTTTCA
        259 TGTTTCGATTAATTCGG--AAAAAATAGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTCA

                *     **        *                *      ***       *          
       1269 ATTTTTTTTTTATGTTGAATCATACA-TTTTTATGAGCATTGTGATTAAAAATTAAGGAAAAAAA
          1 A--TCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAGG-AAAAAA

                   * *       **        *            
       1333 ATTTCGTTCTAGTTTTTATAAAATTCGACGAAATCGTGTA
         63 ATTTCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTGTA

       1373 TCGATTGAAA


Statistics
Matches: 920,  Mismatches: 108, Indels: 57
        0.85            0.10        0.05

Matches are distributed among these distances:
 312   44  0.05
 313   25  0.03
 314   60  0.07
 315   74  0.08
 316   94  0.10
 317  112  0.12
 318   79  0.09
 319   68  0.07
 320  128  0.14
 321   61  0.07
 322  164  0.18
 323   11  0.01

ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Consensus pattern (318 bp):   
ATCTTTTTGGTGTTGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAAATT
TCGTGCCAGTTTTTGCAAAATTCGGCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
GCGTTTCGGGATCCCGACTCAGTTTTGCATGATTTTTGACATCAAGACTCATTGAAATATCTATA
TTAATCTAACAAAATCTCAGCCACACTGGATTTAAGGATTTATTTTTAGGAGCATCTGAATCATG
TTTCGATTAATTCGGAAAAAATAGGAAAAACGTTATTAGAAGCGTGAAAAGCCCTTCA

Found at i:5583 original size:6 final size:6

Alignment explanation


    Indices: 5572--5597  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       5562 GGAGATAGCG

                                          
       5572 ACGGCC ACGGCC ACGGCC ACGGCC AC
          1 ACGGCC ACGGCC ACGGCC ACGGCC AC

       5598 TCCCCATCGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.19, C:0.50, G:0.31, T:0.00


Consensus pattern (6 bp):   
ACGGCC

Done.