Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015183.1 Corchorus olitorius cultivar O-4 contig15216, 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: 8510
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:984 original size:332 final size:333

Alignment explanation


    Indices: 1--1169  Score: 1760
    Period size: 332  Copynumber: 3.5  Consensus size: 333

                *                                                *           
          1 AAAATTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAATACACGATTTC
          1 AAAACTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC

               *    *                   *   **                              *
         66 GGCCAAATTTTTTTGAAAAAACTGACCCGAAAGTTTTTTACTCAATTTTTTGCCACAATACTCAT
         66 GGCTAAA-ATTTTTGAAAAAACTGACCCAAAACATTTTTACTCAATTTTTTGCCACAATACTCAC

                              *                                              
        131 AAAAAATTATATAA-TCAGTGCCAAAATAATTGAAGGG-TTTTCACGCTTCTAATATCGTCTTTC
        130 AAAAAA-TATATAATTCAATGCCAAAATAATTGAAGGGCTTTTCACGCTTCTAATATCGTCTTTC

                       *                          *               *          
        194 AAAATTTTTTCAAAATTAATTTCTAACTAAATCGAAACTTGATTCAGATGCTCGTAAAAACAAAT
        194 AAAA-TTTTTCCAAATTAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAAT

                         *             *                                     
        259 CCTTAAATCCATTACGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACA
        258 CCTTAAATCCATTGCGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACA

                       
        324 AAAAATCATGC
        323 AAAAATCATGC

                        * *   *    *          *                     * *      
        335 AAAACTGAGCCGCGTCCCTATAGTGCATTTTTAGGCAAAAATCATGATGGTTAGTAGAGGATTTC
          1 AAAACTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC

            **    *         *                     *     *    *               
        400 AACTAAGATTTTTGAAGAAACTGACCCAAAACATTTTTCCTCAACTTTTGGCCACAATACTCAC-
         66 GGCTAAAATTTTTGAAAAAACTGACCCAAAACATTTTTACTCAATTTTTTGCCACAATACTCACA

                              *      *          *        *          * *      
        464 AAAAATATATAATTCAATACCAAAAAAATTGAAGGGTTTTTCACGTTTCTAATATCATTTTTCGA
        131 AAAAATATATAATTCAATGCCAAAATAATTGAAGGGCTTTTCACGCTTCTAATATCGTCTTTC-A

             **                     *                      * *               
        529 AGTTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATCCAC-CTAAAAACAAATC
        195 AAATTTTTCCAAATTAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGC-AAAAACAAATC

                                     *                                     * 
        593 CTTAAATCCATTGCGGCTGAGATTTAGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCA
        259 CTTAAATCCATTGCGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACAA

                      
        658 AAAATCATGC
        324 AAAATCATGC

                           *                                                 
        668 AAAACTGAGCCGGGGTCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC
          1 AAAACTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC

                                       *              *                      
        733 GGCTAAAATTTTTGAAAAAACTGACCCGAAA-ATTTTTACTCCATTTTTTGCCACAATACTCACA
         66 GGCTAAAATTTTTGAAAAAACTGACCCAAAACATTTTTACTCAATTTTTTGCCACAATACTCACA

                                                                             
        797 AAAAATTATATAATTCAATGCCAAAATAATTGAAGGG-TTTTCACGCTTCTAATATCGTCTTTCA
        131 AAAAA-TATATAATTCAATGCCAAAATAATTGAAGGGCTTTTCACGCTTCTAATATCGTCTTTCA

                                *                                            
        861 AAATTTTTCCAAATTAATTTTTAACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCC
        195 AAATTTTTCCAAATTAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCC

                 *                                                        *  
        926 TTAAACCCATTGCGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACTAA
        260 TTAAATCCATTGCGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACAAA

                     
        991 AAATCATGC
        325 AAATCATGC

                                           *                                 
       1000 AAAACTGAGCCGGGGCCCCATAGCGCATTTTAAGCCAAAAATCATGATGGTTAGTACACGATTTC
          1 AAAACTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC

              *                                   *   *                      
       1065 GGATAAAATTTTTGAAAAAACTGACCCAAAA-ATTTTTCCTCCATTTTTTGCCACAATACTCACA
         66 GGCTAAAATTTTTGAAAAAACTGACCCAAAACATTTTTACTCAATTTTTTGCCACAATACTCACA

                                                      
       1129 AAAAATATATAATTCAATGCCAAAA-ATATTGAAGGGCTTTT
        131 AAAAATATATAATTCAATGCCAAAATA-ATTGAAGGGCTTTT

       1170 TACACTTCAA


Statistics
Matches: 750,  Mismatches: 76, Indels: 20
        0.89            0.09        0.02

Matches are distributed among these distances:
 330    1  0.00
 331   36  0.05
 332  315  0.42
 333  308  0.41
 334   90  0.12

ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31


Consensus pattern (333 bp):   
AAAACTGAGCCGGGGCCCCATAGCGCATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTC
GGCTAAAATTTTTGAAAAAACTGACCCAAAACATTTTTACTCAATTTTTTGCCACAATACTCACA
AAAAATATATAATTCAATGCCAAAATAATTGAAGGGCTTTTCACGCTTCTAATATCGTCTTTCAA
AATTTTTCCAAATTAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCT
TAAATCCATTGCGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACAAAA
AATCATGC

Found at i:1436 original size:15 final size:15

Alignment explanation


    Indices: 1416--1445  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1406 GTGATTTATA

                           
       1416 TATTTATTTTAAAGG
          1 TATTTATTTTAAAGG

                           
       1431 TATTTATTTTAAAGG
          1 TATTTATTTTAAAGG

       1446 CCTTATAAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53


Consensus pattern (15 bp):   
TATTTATTTTAAAGG
Done.