Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011079.1 Corchorus olitorius cultivar O-4 contig11112, 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: 1959
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41


Found at i:424 original size:154 final size:154

Alignment explanation


    Indices: 7--1695  Score: 2460
    Period size: 154  Copynumber: 11.0  Consensus size: 154

          1 CATTTC

                                                                             
          7 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTT

                                                * *       *   **             
         72 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATAGAGGCCCATCAGTGACGTTTTGAATCGT
         65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT

                                * *  
        137 CTTCGATTTGGCAAACCTCATTTC-
        130 CTTCGATTTGGCAAACCTCAATGCT

                                                                             
        161 TTTCTTTCCATTG-TTATGGCCTAACATATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TT
          1 TTTCTTTCCATTGTTTATGGCCTAAC-TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT

                                         *        *                       *  
        224 TTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTGT
         65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT

                                     
        289 CTTCGATTTGGCAAACCTCAATGCT
        130 CTTCGATTTGGCAAACCTCAATGCT

                               *                           *                 
        314 TTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

             *      *                            *             *     *       
        379 TCGCTCATATGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCTGTTTTAAATCGTC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

                            *     * 
        444 TTCGATTTGGCAAACCCCAATGTT
        131 TTCGATTTGGCAAACCTCAATGCT

                        *                    *                        *      
        468 TTTCTTTCCATTTTTTATGGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGTAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

            *                                *      **            *         *
        533 AAGCTCATTTGGAACACTTGTTATGTTTTTGGGACTATCGACGCCCATTAGTTCTGTTTTGAATT
         66 TAGCTCATTTGGAACACTTGTTA---TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC

                                       
        598 GTCTTCGATTTGGCAAACCTCAATGC-
        128 GTCTTCGATTTGGCAAACCTCAATGCT

                *                        *                 *                 
        624 TTTCATTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                           *                         *        **             
        689 TAGCTCATTTGGAACGCTTGTTATTTTGGGTCCTATCGGGGACCATTAGTGACGTTTTGAATCGT
         66 TAGCTCATTTGGAACACTTGTTATTTTGGG-CCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT

                                *    *
        754 CTTCGATTTGGC-AACCTTCGATGCC
        130 CTTCGATTTGGCAAACC-TCAATGCT

                                                   *       *                 
        779 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTTGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

               *   *                   *     *        *         *            
        844 TAGATCAATTGGAACACTTGTTATTTTTGGCCTTTCGGGGCCAATTAGTTCCATTTTGAATCGTC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

                          *          
        909 TTCGATTTGGCAATTCC-CAATGCT
        131 TTCGATTTGGCAA-ACCTCAATGCT

                    *   *                                                    
        933 TTTCTTTCTATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                               * *      *        *              *        *   
        998 TAGCTCATTTGGAACACTTATAATTTTGTGCCTATCGAGGCCCATTAGTTCCATTTTGAATTGTC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

                                     
       1063 TTCGATTTGG-AGAACCTCAATGCT
        131 TTCGATTTGGCA-AACCTCAATGCT

                                        *         *    *                     
       1087 TTTCTTTCCATTGTTTATGGCCTAACTACAATCATTTTCGTGAAATTAGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                    *                * *            *        **              
       1152 TAGCTCATATGGAACACTTGTTATTCTCGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

               *                    
       1217 TTCAATTTGGCAAACCTCAATGCT
        131 TTCGATTTGGCAAACCTCAATGCT

                             *  *                                            
       1241 TTTCTTTCCATTGTTTACGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                                                                             
       1306 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

                                    
       1371 TTCGATTTGGCAAACCTCAATGCT
        131 TTCGATTTGGCAAACCTCAATGCT

                                                                             
       1395 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                      *     *                       *        ** *         *  
       1460 TAGCTCATTTAGAACAATTGTTATTTTGGGCCTATCGGGGACCATTAGTGACATTTTGAATCATC
         66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC

                           *       *
       1525 TTCGATTTGGCAAACTTCAATGCC
        131 TTCGATTTGGCAAACCTCAATGCT

                    **                                                       
       1549 TTTCTTTCTTTTGTTTATGGCCTAACTATAATCATTATT-GTGAGATTAGTCCACTGTGAAGTTT
          1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATT-TTGGTGAGATTAGTCCACTGTGAAGTTT

              *   *    *                             *     *                *
       1613 TTTGCTAATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGT-CGTTTTGAATCT
         65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCCGTTTTGAATCG

                        *      
       1677 TCTTCGATTTGGAAAACCT
        129 TCTTCGATTTGGCAAACCT

       1696 GGAACACTTG


Statistics
Matches: 1385,  Mismatches: 133, Indels: 34
        0.89            0.09        0.02

Matches are distributed among these distances:
 152   83  0.06
 153   73  0.05
 154  996  0.72
 155   92  0.07
 156   82  0.06
 157   59  0.04

ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42


Consensus pattern (154 bp):   
TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAAACCTCAATGCT

Found at i:1705 original size:72 final size:72

Alignment explanation


    Indices: 1625--1767  Score: 241
    Period size: 72  Copynumber: 2.0  Consensus size: 72

       1615 TGCTAATTTA

                            *   *                  *           *             
       1625 GAACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGTCGTTTTGAATCTTCTTCGATTTGGA
          1 GAACACTTGTTATTTTAGGCATATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGA

                   
       1690 AAACCTG
         66 AAACCTG

                                                                            *
       1697 GAACACTTGTTATTTTAGGCATATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGC
          1 GAACACTTGTTATTTTAGGCATATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGA

                  
       1762 AAACCT
         66 AAACCT

       1768 CAATGCTTTT


Statistics
Matches: 66,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  72   66  1.00

ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39


Consensus pattern (72 bp):   
GAACACTTGTTATTTTAGGCATATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGA
AAACCTG

Found at i:1871 original size:226 final size:225

Alignment explanation


    Indices: 1471--1920  Score: 679
    Period size: 226  Copynumber: 2.0  Consensus size: 225

       1461 AGCTCATTTA

                            *   *                                            
       1471 GAACAATTGTTATTTTGGGCCTATCGGGGACCATTAGTGACATTTTGAATCATCTTCGATTTGGC
          1 GAACAATTGTTATTTTAGGCATATCGGGGACCATTAGTGACATTTTGAATCATCTTCGATTTGGC

                *                **                                          
       1536 AAACTTCAATGCCTTTCTTTCTTTTGTTTATGGCCTAACTATAATCATTATTGTGAGATTAGTCC
         66 AAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATTGTGAGATTAGTCC

                       *  *      *        *                            *     
       1601 ACTGTGAAGTTTTTTGCTAATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGT-
        131 ACTGTGAAGTTCTTAGCTAATCTAGAACACATGTTATTTTGGGCCTATCGGGGTCCATTAGT-TC

                                            
       1665 CGTTTTGAATCTTCTTCGATTTGGAAAACCTG
        195 CG-TTTGAATCTTCTTCGATTTGGAAAACCTG

                 *                       *     *     *         *             
       1697 GAACACTTGTTATTTTAGGCATATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGC
          1 GAACAATTGTTATTTTAGGCATATCGGGGACCATTAGTGACATTTTGAATCATCTTCGATTTGGC

                        *                                          *         
       1762 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT-TTGGTTAGATTAGTC
         66 AAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATT-GTGAGATTAGTC

                               *                                             
       1826 CACTGTGAAGTTCTTAGCTCATCTAGAACACATGTTATTTTGGGCCTATCGGGGTCCATTAGTTC
        130 CACTGTGAAGTTCTTAGCTAATCTAGAACACATGTTATTTTGGGCCTATCGGGGTCCATTAGTTC

                           *       *      
       1891 CGTTTGAATCTTCTTGGATTTGGCAAACCT
        195 CGTTTGAATCTTCTTCGATTTGGAAAACCT

       1921 CAGTGCTTTT


Statistics
Matches: 202,  Mismatches: 20, Indels: 5
        0.89            0.09        0.02

Matches are distributed among these distances:
 225   29  0.14
 226  173  0.86

ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41


Consensus pattern (225 bp):   
GAACAATTGTTATTTTAGGCATATCGGGGACCATTAGTGACATTTTGAATCATCTTCGATTTGGC
AAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATTGTGAGATTAGTCC
ACTGTGAAGTTCTTAGCTAATCTAGAACACATGTTATTTTGGGCCTATCGGGGTCCATTAGTTCC
GTTTGAATCTTCTTCGATTTGGAAAACCTG
Done.