Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011522.1 Corchorus olitorius cultivar O-4 contig11555, 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: 1873
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37


Found at i:778 original size:154 final size:154

Alignment explanation


    Indices: 564--1335  Score: 1181
    Period size: 154  Copynumber: 5.0  Consensus size: 154

        554 CCATATCACT

                                                        *                    
        564 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAA
          1 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA

                      **            *                         *              
        629 GTTTTTAGCTTGTTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATAAGTGACATATTGAA
         66 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAA

                             *       
        694 TTC-TCTTCGATTTGGCTAACCTCA
        131 -TCGTCTTCGATTTGGCAAACCTCA

                                                                *            
        718 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAA
          1 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA

                      *                    *                       *  * *    
        783 GTTTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATC-GGGCCCATTAGT-TCTGTTTTGA
         66 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGAC-ATATTGA

                                     
        846 ATCGTCTTCGATTTGGCAAACCTCA
        130 ATCGTCTTCGATTTGGCAAACCTCA

             *                    *                                          
        871 AAGCTTTTCTTTCCATTGTTTAGGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
          1 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA

                                                      **          *  * *     
        936 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGCCCATTAGTAACGTTTTGAA
         66 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAA

                 *                  
       1001 TCGTCATCGATTTGGCAAACCTCA
        131 TCGTCTTCGATTTGGCAAACCTCA

                                                                      * **  *
       1025 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCAATACGAT
          1 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA

                                                     *  *                    
       1090 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGTCCCATTAGTGACATATTGAA
         66 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAA

              *           *         
       1155 TCCTCTTCGATTTGACAAACCTCA
        131 TCGTCTTCGATTTGGCAAACCTCA

                                                                             
       1179 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
          1 ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA

              *                                        *              * *    
       1244 GAATTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGA
         66 G-TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGA

            *        *           *   
       1309 GTCGTCTTCTATTTGGCAAACGTCA
        130 ATCGTCTTCGATTTGGCAAACCTCA

              
       1334 AT
          1 AT

       1336 AGTAGTTTTG


Statistics
Matches: 562,  Mismatches: 51, Indels: 9
        0.90            0.08        0.01

Matches are distributed among these distances:
 152    3  0.01
 153  138  0.25
 154  341  0.61
 155   80  0.14

ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40


Consensus pattern (154 bp):   
ATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAA
TCGTCTTCGATTTGGCAAACCTCA

Found at i:1120 original size:307 final size:308

Alignment explanation


    Indices: 566--1335  Score: 1213
    Period size: 307  Copynumber: 2.5  Consensus size: 308

        556 ATATCACTAT

                                                      *                      
        566 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGT
          1 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT

                    **            *                 *       *      * *       
        631 TTTTAGCTTGTTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATAAGTGACATATTGAATT
         66 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAA-T

                           *                                                 
        696 C-TCTTCGATTTGGCTAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTT
        130 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTT

                      *     * **                                             
        760 TGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATC-
        195 TGGTGAGATTAGTCCAATACGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATCA

                         *  * *       *           *           
        824 GGGCCCATTAGT-TCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAA
        260 GGGCCCATTAGTGAC-ATATTGAATCCTCTTCGATTTGACAAACCTCAAA

                                *                                            
        873 GCTTTTCTTTCCATTGTTTAGGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
          1 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT

                                                     *          *            
        938 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGACGCCCATTAGTAACGTTTTGAATC
         66 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATC

               *                                                             
       1003 GTCATCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTT
        131 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTT

                                 *          *                    *           
       1068 GGTGAGATTAGTCCAATACGATGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAG
        196 GGTGAGATTAGTCCAATACGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATCAG

             *                                             *
       1133 GTCCCATTAGTGACATATTGAATCCTCTTCGATTTGACAAACCTCAAT
        261 GGCCCATTAGTGACATATTGAATCCTCTTCGATTTGACAAACCTCAAA

                                                                             
       1181 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGA
          1 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-

            *                                                              * 
       1246 ATTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAGT
         65 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAAT

                   *           *     
       1311 CGTCTTCTATTTGGCAAACGTCAAT
        130 CGTCTTCGATTTGGCAAACCTCAAT

       1336 AGTAGTTTTG


Statistics
Matches: 424,  Mismatches: 35, Indels: 6
        0.91            0.08        0.01

Matches are distributed among these distances:
 306    2  0.00
 307  235  0.55
 308  103  0.24
 309   84  0.20

ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40


Consensus pattern (308 bp):   
GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATC
GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTT
GGTGAGATTAGTCCAATACGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATCAG
GGCCCATTAGTGACATATTGAATCCTCTTCGATTTGACAAACCTCAAA
Done.