Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011598.1 Corchorus olitorius cultivar O-4 contig11631, 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: 2520
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38


Found at i:695 original size:156 final size:155

Alignment explanation


    Indices: 1--1123  Score: 1557
    Period size: 154  Copynumber: 7.3  Consensus size: 155

                   **         *                   *                          
          1 TTAGTTCCATTTT-GAATAGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
          1 TTAGTTCGGTTTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATG

             *                         *       *             *       *   *   
         65 GACTAACTATAATC-TTATTGGTGAGATTAGTCCACTGTGAAGTTTTTATCTCATTTGGAATACT
         66 GCCTAACTATAATCATT-TTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                               *       
        129 TGTTATTTTGGGCC-TATCAGGGCCCA
        130 TGTTATTTTGGGCCAT-TCGGGGCCCA

                  *                                *                         
        155 TTAGTGAC-GTTTT-GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
          1 TTAGT-TCGGTTTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT

              **            *          *       **                    *  *    
        218 GGTGTAACTATAATCAATTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTGGATCACT
         65 GGCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                                       
        283 TGTTATTTTGGGCC-TATCGGGGCCCA
        130 TGTTATTTTGGGCCAT-TCGGGGCCCA

                  *  *                             *   *                     
        309 TTAGTGAC-ATTTT-GAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCATTGTTTAT
          1 TTAGT-TCGGTTTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT

                  *                  * *       *                     *       
        372 GGCCTATCTATAATCATTTTGGTGACATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
         65 GGCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                              *   *   
        437 TGTTATTTTGGG-CATTCAGGGTCCA
        130 TGTTATTTTGGGCCATTCGGGGCCCA

                                *                            *               
        462 TTAGTTCGGTTTTAGAATCGCCTTCGATTTGGCCAAACCACAATGCTTTACTTTCCATTGTTTAT
          1 TTAGTTCGGTTTTAGAATCGTCTTCGATTTGG-CAAACCACAATGCTTTTCTTTCCATTGTTTAT

                                   *   *                                     
        527 GGCCTAACTATAATCATTTTGGTTAGAGTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT
         65 GGCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                       *              
        592 TGTTATTTTGGACCATTCGGGGCCCA
        130 TGTTATTTTGGGCCATTCGGGGCCCA

                           *                      *                          
        618 TTAGTTCGGTTTTAAAAATCGTCTTCGATTTGGCAAACAACAATGCTTTTCTTTCCATTGTTTAT
          1 TTAGTTCGGTTTT-AGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTA-

                                    *                 *                      
        683 TGG-CTAACTATAATCATTTTGGTAAGACTAGTCCATTGTGATGTTTTTAGCTCATTTTGAACAC
         64 TGGCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACAC

              *         *              
        747 TTATTATTTTGGACCATTCGGGGCCCA
        129 TTGTTATTTTGGGCCATTCGGGGCCCA

                    *    * *  *                               *              
        774 TTAGTTCGATATTAAAAACCGTCTTCGATTTGGCAAACCACAATGCTTTTATTTCCATTGTTTAT
          1 TTAGTTCGGT-TTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT

                 *              *  *                                         
        839 GGCCTTACTATAATCATTTTTGTTAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT
         65 GGCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT

                                  * * 
        904 TGTTATTTTGGGCCATTCGGGGTCTA
        130 TGTTATTTTGGGCCATTCGGGGCCCA

                                           *                                 
        930 TTAGTTCGGTTTT-GAATCGTCTTCGATTTGACAAACCACAATGCTTTTCTTTCCATTGTTTATG
          1 TTAGTTCGGTTTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATG

                                  *                                   *      
        994 GCCTAACTATAATCATTTTGGTAAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGGACACTT
         66 GCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTT

                                     
       1059 GTTATTTTGGGCCATTCGGGGCCCA
        131 GTTATTTTGGGCCATTCGGGGCCCA

                          *     *                   
       1084 TTAGTTCGGTTTTAAAATTCATCTTCGATTTGGCAAACCA
          1 TTAGTTCGGTTTTAGAA-TCGTCTTCGATTTGGCAAACCA

       1124 TAATTGATGC


Statistics
Matches: 883,  Mismatches: 73, Indels: 24
        0.90            0.07        0.02

Matches are distributed among these distances:
 152    1  0.00
 153   18  0.02
 154  432  0.49
 155  108  0.12
 156  302  0.34
 157   22  0.02

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41


Consensus pattern (155 bp):   
TTAGTTCGGTTTTAGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATG
GCCTAACTATAATCATTTTGGTGAGACTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTT
GTTATTTTGGGCCATTCGGGGCCCA

Found at i:2261 original size:156 final size:156

Alignment explanation


    Indices: 2075--2520  Score: 775
    Period size: 156  Copynumber: 2.9  Consensus size: 156

       2065 TCGTATCAAT

                                                                  *          
       2075 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAATCCATTGTGA
          1 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAGTCCATTGTGA

                                                                             
       2140 AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA
         66 AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA

                             *        
       2205 AAATCGTCTTCGATTTGGCAAACAAC
        131 AAATCGTCTTCGATTTGACAAACAAC

                      *                        *    *          *             
       2231 AATGCTTTTCCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGACTAGTCCATTGTGA
          1 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAGTCCATTGTGA

                                                                             
       2296 AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA
         66 AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA

                                   * *
       2361 AAATCGTCTTCGATTTGACAAACCAT
        131 AAATCGTCTTCGATTTGACAAACAAC

                *                                                          * 
       2387 AATGTTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAGTCCATTGTAA
          1 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAGTCCATTGTGA

                *                              *                    *        
       2452 AGTTCTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCATTAGTTAGGTTTTAA
         66 AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA

                
       2517 AAAT
        131 AAAT


Statistics
Matches: 273,  Mismatches: 17, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 156  273  1.00

ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41


Consensus pattern (156 bp):   
AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATGATCACTTTGGTAAGATTAGTCCATTGTGA
AGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGACCATTCGGGGCCCATTAGTTCGGTTTTAA
AAATCGTCTTCGATTTGACAAACAAC
Done.