Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010965.1 Corchorus olitorius cultivar O-4 contig10997, 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, 781

Length: 1303
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27


Found at i:282 original size:154 final size:154

Alignment explanation


    Indices: 1--694  Score: 1106
    Period size: 154  Copynumber: 4.5  Consensus size: 154

                 *                    *                               *      
          1 AAAACAGAACTTATGGGCCTCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGTTAATAACTTC
          1 AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC

                                                                             
         66 ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGT
         66 ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-T

             *                       
        131 -CGTTTGCCAAATCGAAGACGATTC
        130 AGGTTTGCCAAATCGAAGACGATTC

                     *                                        *       *      
        155 AAAACGGAAATTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGTTAATAACTTC
          1 AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC

                                                                     *       
        220 ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAATGCATTTA
         66 ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTA

                                    
        285 GGTTTGCCAAATCGAAGACGATTC
        131 GGTTTGCCAAATCGAAGACGATTC

                       *       *                                  **         
        309 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTC
          1 AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC

                             *      **                               *       
        374 ACAGTGGACTAATCTCAGCAAAATTTTTATAGTTAGGCCATAAACAATGGAAAGAAATGCATTTA
         66 ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTA

                                    
        439 GGTTTGCCAAATCGAAGACGATTC
        131 GGTTTGCCAAATCGAAGACGATTC

                       *       *    *               *    *                   
        463 AAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAATGTTTCAAATGAGCTT-AAAACTT
          1 AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-TTAAAAACTT

                  *                  *                                       
        527 CACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
         65 CACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-

                                      
        592 T-GGTTTGCCAAATCGAAGACGATTC
        129 TAGGTTTGCCAAATCGAAGACGATTC

                                          *           *           *          
        617 AAAACGGAACTTATGGGCCTCGATAGGCCCTAAATAACAAGTCTTCCAAATGAGCTAAAAACTTC
          1 AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC

                         
        682 ACAGTGGACTAAT
         66 ACAGTGGACTAAT

        695 TGATGCGCCA


Statistics
Matches: 501,  Mismatches: 35, Indels: 8
        0.92            0.06        0.01

Matches are distributed among these distances:
 153    2  0.00
 154  498  0.99
 155    1  0.00

ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23


Consensus pattern (154 bp):   
AAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC
ACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTA
GGTTTGCCAAATCGAAGACGATTC

Found at i:827 original size:21 final size:21

Alignment explanation


    Indices: 801--913  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        791 TGCTAGAAGT

                                 
        801 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
        822 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
        843 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                     *           *
        864 TCATTGGA-AAAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
        885 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        906 TCATTGGA
          1 TCATTGGA

        914 AATGCCTAAG


Statistics
Matches: 83,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
  20    1  0.01
  21   82  0.99

ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.