Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011504.1 Corchorus olitorius cultivar O-4 contig11537, 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: 3110
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35


Found at i:566 original size:154 final size:153

Alignment explanation


    Indices: 1--1424  Score: 2075
    Period size: 154  Copynumber: 9.2  Consensus size: 153

                                      *                                      
          1 AACACTTGTTATTTTGGGCCTATCGCAGCCCATTAGTGATCGTTTTGAATCGTCTTCGATTTGGC
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGA-CGTTTTGAATCGTCTTCGATTTGGC

                                         *      *                            
         66 AAACCTCAATGCTTTTCTTTCCATTGTTTGTGGCCTTACTATAATCAATTTGGTGAGATTAGTCC
         65 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC-ATTTGGTGAGATTAGTCC

                                     
        131 ACTGTGAAGTTCTTAGCTCATTTGG
        129 ACTGTGAAGTTCTTAGCTCATTTGG

                                     *                                       
        156 AACACTTGTTATTTTGGGCCTATCGAGG-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

             *    *   *     *           *                      *             
        220 ACCCTCTATGTTTTTCCTTCCATTGTTTGTGGCCTAACTATAATCATTTTGATGAGATTAGTCCA
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCA

                                    
        285 CTGTGAAGTTCTTAGCTCATTTGG
        130 CTGTGAAGTTCTTAGCTCATTTGG

                                      *           **                         
        309 AACACTTGTTATTTTAGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
          1 AACACTTGTTATTTT-GGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC

                  *                  * *     *                 *             
        374 AAACCTTAATGCTTTTCTTTCCATTATATATGGACTAACTATAATCATTTTTGTGAGATTAGTCC
         65 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCC

                       *             
        439 ACTGTGAAGTTTTTAGCTCATTTGG
        129 ACTGTGAAGTTCTTAGCTCATTTGG

                         *                               *                 * 
        464 AACACTTGTTATTCTGGGCCTATCGCGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGGA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                    *                      *                   *           * 
        529 AACCTCAAGGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGATGAGATTAGTCTA
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCA

                           *       * 
        594 CTGTGAAGTAT-TTACCTCATTTAG
        130 CTGTGAAGT-TCTTAGCTCATTTGG

                                      *           **                 *       
        618 AACACTTG-TACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGGC
          1 AACACTTGTTA-TTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC

                     *   *       *                               *           
        682 AAACCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTC
         65 AAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTC

                                      
        746 CACTGTGAAGTTCTTAGCTCATTTGG
        128 CACTGTGAAGTTCTTAGCTCATTTGG

                   *      *          * *         **                          
        772 AACACTTATTATTTCGGGCCTATCGAGTCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

              *                         *   *                                
        837 AATCTCAATGCTTTTCTTTCCATTGTTTGTGGACTAACTATAATCATTTTGGTGA-AGTTAGTCC
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGA-TTAGTCC

                       *             
        901 ACTGTGAAGTTTTTAGCTCATTTGG
        129 ACTGTGAAGTTCTTAGCTCATTTGG

                                      **                                     
        926 AACACTTGTTATTTTGGGCCTATCGCAACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                               *                             
        991 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTTACTATAATCAATTTGGTGAGATTAGTCCA
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC-ATTTGGTGAGATTAGTCCA

                 *                  
       1056 CTGTGTAGTTCTTAGCTCATTTGG
        130 CTGTGAAGTTCTTAGCTCATTTGG

                              *      *              *                        
       1080 AACACTTGTTATTTTGGGTCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                 *                          *    *            *    *         
       1145 AACCTTAATGCTTTTCTTTCCATTGTTTATGGACTAATTATAATCATTTTCGTGAAATTAGTCCA
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCA

                      *             
       1210 CTGTGAAGTTTTTAGCTCATTTGG
        130 CTGTGAAGTTCTTAGCTCATTTGG

                         *                              *                    
       1234 AACACTTGTTATTATGGGCCTATCGCGGCCCATTAGTGACGTTTGGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                      *                                                      
       1299 AACCTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCA
         66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC-ATTTGGTGAGATTAGTCCA

             *            **        
       1364 CAGTGAAGTTCTTAATTCATTTGG
        130 CTGTGAAGTTCTTAGCTCATTTGG

                                   * *           
       1388 AACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGT
          1 AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGT

       1425 TCTGATGCGC


Statistics
Matches: 1144,  Mismatches: 111, Indels: 29
        0.89            0.09        0.02

Matches are distributed among these distances:
 152    1  0.00
 153  128  0.11
 154  857  0.75
 155  158  0.14

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


Consensus pattern (153 bp):   
AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTGGTGAGATTAGTCCAC
TGTGAAGTTCTTAGCTCATTTGG

Found at i:1973 original size:11 final size:11

Alignment explanation


    Indices: 1922--1966  Score: 90
    Period size: 11  Copynumber: 4.1  Consensus size: 11

       1912 AGGAGTAGGG

                       
       1922 TCCTTCCTAGC
          1 TCCTTCCTAGC

                       
       1933 TCCTTCCTAGC
          1 TCCTTCCTAGC

                       
       1944 TCCTTCCTAGC
          1 TCCTTCCTAGC

                       
       1955 TCCTTCCTAGC
          1 TCCTTCCTAGC

             
       1966 T
          1 T

       1967 TTTTCCTTTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   34  1.00

ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38


Consensus pattern (11 bp):   
TCCTTCCTAGC

Done.