Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011294.1 Corchorus olitorius cultivar O-4 contig11327, 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, 809

Length: 1349
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35


Found at i:1291 original size:321 final size:323

Alignment explanation


    Indices: 4--1326  Score: 1139
    Period size: 321  Copynumber: 4.0  Consensus size: 323

          1 TTT

                        *                *                       *           
          4 GATTTAATTAGACATTAATTCT-G--AAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCC
          1 GATTTAATTAGAAATTAATTCTGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAGCCC

                  *        *     *                       ***         *     **
         66 GTCAATCTTTTTGGCATTGAACTATATA-TTTTTCTAAATATTTTATTAAAAAATTGGGTTTAGG
         65 GTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAATA-TTTGGCAAAAAATTGAG---AAA

             *       ** ** **                        *                       
        130 ATAAGTTT-TTGCAAAATTTTAGCCGAAATCCTGTACGGCTGTACTAACTATCACGATTTTTGGC
        126 AGAA-TTTCGGGTTAGTTTTTAGCCGAAAT-C-GT---G-TATA--AACTATCACGATTTTTGGC

             *                *   *           *              *               
        194 AAAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTGAAA
        182 -TAAAAACGCGTTCCGGACTCCAGGCTCAATTTTACATGATTTTTGGCAGAAAGACTCCTTGAAA

                           *        *                    *           ** *  * 
        259 TATCTATATTCATC-GATCCAAATGTCAACCACATTGGATATAAGGATTTGTTTTTATTACCACC
        246 TATCTATATTCATCTAAT-CAAATCTCAACCACATTGGATATAAGAATTTGTTTTTACGAGCATC

                   *     *
        323 TCG-ATCATGTTTT
        310 TCGAATCTTGTTTC

                                     *   *                       *           
        336 GATTTAATTAGAAATTAATTCT---TAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCC
          1 GATTTAATTAGAAATTAATTCTGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAGCCC

              * * *        *       *                      **                *
        398 GTTAGTCTTTTTGGCATTGAATTTTATA-TTTTTCTAAATATTTCGTTAAAAAATTGAGAAAAAA
         65 GTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAATATTT-GGCAAAAAATTGAG-AAAAG

                   *  *                             *                        
        462 AATTTCGTGTCAGTTTTTAGCCGAAATCGTGTA-ATAACTGTCACGATTTTTGGCTAAAAACGCG
        128 AATTTCGGGTTAGTTTTTAGCCGAAATCGTGTATA-AACTATCACGATTTTTGGCTAAAAACGCG

              * *     *   **   *     *              *                        
        526 TTTCAGA-TCGACGATTCAGTTTTAAATGATTTTTGGGCAAAAAGACTGCCTTGAAATATCTAGT
        192 TTCCGGACTCCA-GGCTCAATTTTACATGATTTTT-GGCAGAAAGACT-CCTTGAAATATCTA-T

                       **      * *         *                   *             
        590 ATTCAGTCTAAAAAAATCTTAGCCACAATTGAAT-TAAGAATTT-TTTTTATGAGCATCTC-AAT
        253 ATTCA-TCTAATCAAATCTCAACCAC-ATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAAT

                     
        652 CTTTGTTTC
        316 C-TTGTTTC

                           *      *           *  *                *       *  
        661 GATTTAATTAGAAATAAATTCGGGGAAAAAAAAACGAAAAAAACGATATTAGAAACGTGAAAACC
          1 GATTTAATTAGAAATTAATTC-TGGAAAAAAAAATG-GAAAAACGATATTAGAAGCGTGAAAGCC

             *             *  **                   *                         
        726 CTTCAATATTTTTGGTGTCAAATTATATATTTTTTCTAACTATTATGGCAAAAAATTGAGGAAAA
         64 CGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAATATT-TGGCAAAAAATTGA-GAAAA

                                   **                                        
        791 GAATTTCGAGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AACTATCACGATTTTTGG
        127 GAATTTCG-G---G---TT---AGTTTTTAGCCGAAATCGTGTA-TAAACTATCACGATTTTTGG

                                  *           *         *        *        *  
        855 C-AAAAACGCGTTCCGGACTCCCGGCTCAATTTTGCATGATTTTAGGC-GTAATGACTCCTTCAA
        181 CTAAAAACGCGTTCCGGACTCCAGGCTCAATTTTACATGATTTTTGGCAG-AAAGACTCCTTGAA

                           *  *         *        *       *                   
        918 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACGAGCATC
        245 ATATCTATATTCATCTAATCAAATCTCAACCACATTGGATATAAGAATTTGTTTTTACGAGCATC

                          
        983 -CGAATCTTGTTTC
        310 TCGAATCTTGTTTC

                                                *                  *         
        996 GATTTAATTAGAAATTAATT-TGGAAAAAAAAATGGTAAAACGATATTAGAAGCGCGTAAAGCCC
          1 GATTTAATTAGAAATTAATTCTGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAGCCC

                    *           *               * *             *            
       1060 GTCAATATATTTGGCGTTGAGTTATATATTTTTTCTGAGTATTTGGCAAAAATTTGAG-AAAGAC
         65 GTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAATATTTGGCAAAAAATTGAGAAAAGA-

            *                                                                
       1124 TTTTCGGGTTAGTTTTTAGCCGAAATCGTGTATAAAGC-ATCACGATTTTTGGCTAAAAACGCGT
        129 ATTTCGGGTTAGTTTTTAGCCGAAATCGTGTATAAA-CTATCACGATTTTTGGCTAAAAACGCGT

             *         *     *     *                                         
       1188 TTCGGA-TCCAAGCTCAGTTTTATATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCA
        193 TCCGGACTCCAGGCTCAATTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCA

                  *                    *             *                *    * 
       1252 TCTAATTAAATCTCAACCACATTGGATTTAAGAATTTGTTTGTACGAGCATCT-GAATATTGTAT
        258 TCTAATCAAATCTCAACCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATCTTGTTT

             
       1316 C
        323 C

                      
       1317 GATTTAATTA
          1 GATTTAATTA

       1327 CGAATAAATT


Statistics
Matches: 819,  Mismatches: 128, Indels: 99
        0.78            0.12        0.09

Matches are distributed among these distances:
 320    3  0.00
 321  180  0.22
 322   47  0.06
 323   15  0.02
 324   25  0.03
 325   46  0.06
 326    7  0.01
 327    1  0.00
 328    2  0.00
 329   36  0.04
 330   80  0.10
 331   11  0.01
 332  139  0.17
 333   53  0.06
 334    7  0.01
 335   51  0.06
 336   23  0.03
 337   14  0.02
 338    9  0.01
 339   30  0.04
 340   40  0.05

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


Consensus pattern (323 bp):   
GATTTAATTAGAAATTAATTCTGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAGCCCG
TCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAATATTTGGCAAAAAATTGAGAAAAGAAT
TTCGGGTTAGTTTTTAGCCGAAATCGTGTATAAACTATCACGATTTTTGGCTAAAAACGCGTTCC
GGACTCCAGGCTCAATTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCT
AATCAAATCTCAACCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATCTTGTTTC
Done.