Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011658.1 Corchorus olitorius cultivar O-4 contig11691, 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, 603

Length: 1006
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--1006  Score: 1541
    Period size: 154  Copynumber: 6.5  Consensus size: 154

                                        *          *         *     *         
          1 AACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTATTTAGCTCAATTGGATCACTTG-TA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                                       **                 *                * 
         65 CTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAG
         66 -TTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG

              *       *      *     *  
        130 CTATTCTTT-AAGTTGTGTATGGCCT
        130 CTTTTCTTTCCA-TTGTTTATGGACT

                            *                       *                        
        155 AACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                *                     **                                     
        220 TTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
         66 TTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC

                                    
        285 TTTTCTTTCCATTGTTTATGGACT
        131 TTTTCTTTCCATTGTTTATGGACT

                                *                       *                    
        309 AACTATAATCATTTTGGTGAAATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                *                                                            
        374 TTTTCGGCCTATCGCGGG-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
         66 TTTTGGGCCTATCG-GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG

                       *          *  
        438 CTTTTCTTTCCGTTGTTTATGGCCT
        130 CTTTTCTTTCCATTGTTTATGGACT

                       *                            *     **                 
        463 AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCAGATTTGGAACACTTGTTA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                   *                     *                       *           
        528 TTTTGGGTCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCGAACCTCAATGC
         66 TTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC

                                    
        593 TTTTCTTTCCATTGTTTATGGACT
        131 TTTTCTTTCCATTGTTTATGGACT

                           *    *           *                                
        617 AACTATAATCATTTTCGTGAAATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                     *          *      **      *       *          *          
        682 TTTTGGGTCATATCGGGGCCAATTAGTTCCGTTTTCAATCGTCCTCGATTTGGCTAACCTCAATG
         66 TTTTGGG-CCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG

                                     
        747 CTTTTCTTTCCATTGTTTATGGACT
        130 CTTTTCTTTCCATTGTTTATGGACT

                                               *            *                
        772 AACTATAATCAGTTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTGATTTGGAACACTTGTT
          1 AACTATAATCA-TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT

                                    *                                        
        837 ATTTTGGGCCTATCGGGGCCCATTCGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
         65 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG

             *                       
        902 CCTTTCTTTCCATTGTTTATGGACT
        130 CTTTTCTTTCCATTGTTTATGGACT

                       *                   *                                 
        927 AACTATAATCACTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
          1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA

                           
        992 TTTTGGGCCTATCGG
         66 TTTTGGGCCTATCGG


Statistics
Matches: 778,  Mismatches: 68, Indels: 12
        0.91            0.08        0.01

Matches are distributed among these distances:
 153    3  0.00
 154  545  0.70
 155  174  0.22
 156   56  0.07

ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Consensus pattern (154 bp):   
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
TTTTCTTTCCATTGTTTATGGACT

Found at i:952 original size:464 final size:461

Alignment explanation


    Indices: 1--1006  Score: 1570
    Period size: 464  Copynumber: 2.2  Consensus size: 461

                       *                *                    *     *         
          1 AACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTATTTAGCTCAATTGGATCACTTG-TA
          1 AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGT-TTTAGCTCATTTGGAACACTTGTTA

                                       ** *                                  
         65 CTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAG
         65 -TTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCAATTTGGCAAACCTCAAAG

                                  *                      *           *       
        130 CTATTCTTTAAGTTGTGTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTT
        129 CTATTCTTTAAGTTGTGTATGGACTAACTATAATCATTTTGATGAAATTAGTCCACTATGAAGTT

                                             *          *              *     
        195 CTTAGCTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCG
        194 CTTAGCTCATTTGGAACACTTGTTATTTTAGGCATATCGGGGCCAATTAGTTCCGTTTTCAATCG

              *                                                              
        260 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG
        259 TCCTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG

                              *                                              
        325 GTGAAATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTCGGCCTATCGCG
        324 GTGAAATTAGTCCACTGTAAAGTTTTTAACTCATTTGGAACACTTGTTATTTTCGGCCTATCGCG

                                                             *         *     
        390 GGCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCGTTGTT
        389 GGCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTT

                 *  
        455 TATGGCCT
        454 TATGGACT

                                                          **                 
        463 AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCAGATTTGGAACACTTGTTA
          1 AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTT-TTAGCTCATTTGGAACACTTGTTA

                   *                                     *       *        *  
        528 TTTTGGGTCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCGAACCTCAATGC
         65 TTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGC

             *       *      *                                                
        593 TTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTCG-TGAAATTAGTCCACTATGAAGT
        130 TATTCTTT-AAGTTGTGTATGGACTAACTATAATCATTTT-GATGAAATTAGTCCACTATGAAGT

             *                            *                                  
        656 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGTCATATCGGGGCCAATTAGTTCCGTTTTCAAT
        193 TCTTAGCTCATTTGGAACACTTGTTATTTTAGG-CATATCGGGGCCAATTAGTTCCGTTTTCAAT

                           *                                                 
        721 CGTCCTCGATTTGGCTAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCAGTT
        257 CGTCCTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCA-TT

                   *                       *  *                     *        
        786 TTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTGATTTGGAACACTTGTTATTTTGGGCCTATC
        321 TTGGTGAAATTAGTCCACTGTAAAGTTTTTAACTCATTTGGAACACTTGTTATTTTCGGCCTATC

                       *                                                     
        851 G-GGGCCCATTCGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCAT
        386 GCGGG-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCAT

                        
        915 TGTTTATGGACT
        450 TGTTTATGGACT

                       *                   *                                 
        927 AACTATAATCACTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
          1 AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTA

                           
        992 TTTTGGGCCTATCGG
         65 TTTTGGGCCTATCGG


Statistics
Matches: 496,  Mismatches: 40, Indels: 14
        0.90            0.07        0.03

Matches are distributed among these distances:
 461    1  0.00
 462  196  0.40
 463   95  0.19
 464  202  0.41
 465    2  0.00

ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Consensus pattern (461 bp):   
AACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTAT
TTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCT
ATTCTTTAAGTTGTGTATGGACTAACTATAATCATTTTGATGAAATTAGTCCACTATGAAGTTCT
TAGCTCATTTGGAACACTTGTTATTTTAGGCATATCGGGGCCAATTAGTTCCGTTTTCAATCGTC
CTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGT
GAAATTAGTCCACTGTAAAGTTTTTAACTCATTTGGAACACTTGTTATTTTCGGCCTATCGCGGG
CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTTTA
TGGACT
Done.