Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017555.1 Corchorus olitorius cultivar O-4 contig17588, 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, 864

Length: 1441
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37


Found at i:895 original size:335 final size:333

Alignment explanation


    Indices: 1--1138  Score: 1770
    Period size: 335  Copynumber: 3.4  Consensus size: 333

                                                                             
          1 TCAATATTTTTGGCGTTGATTTTTATAT-TTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT
          1 TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT

                      *                               *                      
         65 TTTTCGGATCTTTTTTTGCAAAATTTTAGCCGAAATCGTGTATTATCCATCACGG-TTTTGGACT
         66 TTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGG-CT

                       **   *   *       *                                    
        129 AAAAACGCATTTGAGGACCCTGGCTCAAATTTGCTTGATTTTTGGC-CTCTAGAACCCTTGAAAT
        130 AAAAACGCATTCCAGGCCCCCGGCTCAATTTTGCTTGATTTTTGGCGC-CTAGAACCCTTGAAAT

              *      *    *                   *                              
        193 TTCAATATTGATCTTACCAAATCTCAACCACATTGAATTTAAAAATTTGATTTTACGAGCATCTG
        194 TTTAATATTCATCTAACCAAATCTCAACCACATTAAATTTAAAAATTTGATTTTACGAGCATCTG

                 *                                                           
        258 AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGT
        259 AATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGT

                      
        323 GAAAAACCCT
        324 GAAAAACCCT

                                              **         *                 * 
        333 TCAATATTTTTGGCGTTGATTTTTATATATTTTCAAAGTATTGTGCCCAAAATTTGAGGAAAACT
          1 TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT

                                                           *                 
        398 TTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTG---TA-CGATCACGGTTTTTGGCTA
         66 TTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTA

                 * *   *       *         **                                  
        459 AAAACACGTTCTAGGCCCCGGGCTCAATTCAGCTTGATTTTTGGCGCCTAGAACCCTTGAAATTT
        131 AAAACGCATTCCAGGCCCCCGGCTCAATTTTGCTTGATTTTTGGCGCCTAGAACCCTTGAAATTT

                                    *                 *                      
        524 TAATATTCATCTAACCAAATCTCAGCCACATTAAATTTAAAACTTTGATTTTACGAGCATCTGAA
        196 TAATATTCATCTAACCAAATCTCAACCACATTAAATTTAAAAATTTGATTTTACGAGCATCTGAA

                                                             *               
        589 TCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATTGGAAAAATGATATTAGAAGCGTG
        261 TCTAGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATTGGAAAAACGATATTAGAAGCGTG

                     
        654 AAAAACCCT
        325 AAAAACCCT

                          *  *    **    *               *             *      
        663 TCAATATTTTTGGCATTCATTTACATATTTTTTCTGAGTATTGTTGCCAAAATTTGAGAAAAAAT
          1 TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT

            *                                                                
        728 ATTTCGGATCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCT
         66 TTTTCGGATCA-TTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCT

                    *     *                             *                    
        793 AAAAACGCGTTCCAAGCCCCCGGCTCAATTTTGCTTGATTTTTGACGCCTAGAACCCTTGAAATT
        130 AAAAACGCATTCCAGGCCCCCGGCTCAATTTTGCTTGATTTTTGGCGCCTAGAACCCTTGAAATT

              *             *    *                     *                     
        858 TTGATATTCATCTAACTAAATTTCAACCACATTAAATTTAAAATTTTGATTTTACGAGCATCTGA
        195 TTAATATTCATCTAACCAAATCTCAACCACATTAAATTTAAAAATTTGATTTTACGAGCATCTGA

                                            *                                
        923 ATCTTA-TTTCGATTTAATTAGAAATTAATTCTGAAAAAAATTGGAAAAACGATATTAGAAGCGT
        260 ATC-TAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGT

                      
        987 GAAAAACCCT
        324 GAAAAACCCT

                                                                  *          
        997 TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTAGAGGAAAAAT
          1 TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT

                 *                                                     *     
       1062 TTTTCTGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTGGGCTA
         66 TTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTA

                        
       1127 AAAACGCATTCC
        131 AAAACGCATTCC

       1139 CGGGTCCCGA


Statistics
Matches: 734,  Mismatches: 62, Indels: 19
        0.90            0.08        0.02

Matches are distributed among these distances:
 329  155  0.21
 330  113  0.15
 331   29  0.04
 332   28  0.04
 333  135  0.18
 334  108  0.15
 335  164  0.22
 336    2  0.00

ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37


Consensus pattern (333 bp):   
TCAATATTTTTGGCGTTGATTTTTATATATTTTCTGAGTATTGTGGCCAAAATTTGAGGAAAAAT
TTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTA
AAAACGCATTCCAGGCCCCCGGCTCAATTTTGCTTGATTTTTGGCGCCTAGAACCCTTGAAATTT
TAATATTCATCTAACCAAATCTCAACCACATTAAATTTAAAAATTTGATTTTACGAGCATCTGAA
TCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGA
AAAACCCT

Found at i:1371 original size:182 final size:182

Alignment explanation


    Indices: 1040--1393  Score: 419
    Period size: 182  Copynumber: 1.9  Consensus size: 182

       1030 CTGAGTATTG

                                 *     *     *              *          *     
       1040 TGGCCAAAATTAGAGGAAAAATTTTTCTGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
          1 TGGCCAAAATTAGAGGAAAAAATTTTCGGATCAATTTTTGCAAAATTTGAGCCGAAATCATGTAC

                                               *  *         *                
       1105 TATCCATCACGGTTTTGGGCTAAAAACGCATTCCCGGGTCCCGACACAGTTTTGCATGATTTTTT
         66 TATCCATCACGGTTTTGGGCTAAAAACGCATTCCCAGGCCCCGACACAATTTTGCATGATTTTTT

                    *   *          *     *                      
       1170 GGGAAAAGGCTCTTTGAAATATCTATATTGATCTTACCAAATTGGAAAACTT
        131 GGGAAAAGACTCCTTGAAATATCAATATTCATCTTACCAAATTGGAAAACTT

                                            *                                
       1222 TGGCCAAATATT-GAGGAAAAAATTTTCGGATTAATTTTTGCAAAATTTGAGCCGAAATCATGTA
          1 TGGCCAAA-ATTAGAGGAAAAAATTTTCGGATCAATTTTTGCAAAATTTGAGCCGAAATCATGTA

            *                            **   **         * *         *       
       1286 TTATCCATCACGGTTTTGGGCTAAAAACGGGTT-TTAGGCCCCTGGCTCAATTTTGCTTGA-TTT
         65 CTATCCATCACGGTTTTGGGCTAAAAACGCATTCCCAGGCCCC-GACACAATTTTGCATGATTTT

                  ***               *                     
       1349 TTGGCGCTTAGAAC-CCTTGAAATTTCAATATTCATCTTACCAAAT
        129 TTGG-GAAAAG-ACTCCTTGAAATATCAATATTCATCTTACCAAAT

       1394 CACAACCACA


Statistics
Matches: 143,  Mismatches: 25, Indels: 8
        0.81            0.14        0.05

Matches are distributed among these distances:
 181   12  0.08
 182  127  0.89
 183    4  0.03

ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35


Consensus pattern (182 bp):   
TGGCCAAAATTAGAGGAAAAAATTTTCGGATCAATTTTTGCAAAATTTGAGCCGAAATCATGTAC
TATCCATCACGGTTTTGGGCTAAAAACGCATTCCCAGGCCCCGACACAATTTTGCATGATTTTTT
GGGAAAAGACTCCTTGAAATATCAATATTCATCTTACCAAATTGGAAAACTT
Done.