Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011756.1 Corchorus olitorius cultivar O-4 contig11789, 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, 892

Length: 1487
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35


Found at i:941 original size:154 final size:154

Alignment explanation


    Indices: 659--1487  Score: 1376
    Period size: 154  Copynumber: 5.4  Consensus size: 154

        649 AATATTGGAG

                        *     *          *                                   
        659 GACCATTAGTGATGTTTTAAATCGTCTTCCATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
          1 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT

                                                                      *      
        724 TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAAC
         66 TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC

                                 *  
        789 ACTCGTTATTTTGGGCCTATCAGA
        131 ACTCGTTATTTTGGGCCTATCGGA

                        *                                                    
        813 GACCATTAGTGAGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
          1 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT

                   *          *                                              
        878 TATGGCCCGACTATAATCGTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
         66 TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC

               *         **         
        943 ACTTGTTATTTTGTTCCTATC-GA
        131 ACTCGTTATTTTGGGCCTATCGGA

              *                                                              
        966 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTCAATGCTTTTCTTTCCATTGT
          1 -GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT

                                                                       *     
       1030 TTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAA
         65 TTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA

                                     
       1095 CACTCGTTATTTTGGGCCTATCGGA
        130 CACTCGTTATTTTGGGCCTATCGGA

                                                                             
       1120 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
          1 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT

                 *           *     *                                         
       1185 TATGGTCTGACTATAATAATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
         66 TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC

                                    
       1250 ACTCGTTATTTTGGGCCTATCGGA
        131 ACTCGTTATTTTGGGCCTATCGGA

                                                     *       *           *  *
       1274 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTTCAATG-ATTTCTTTCCATCGTG
          1 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT

              *     * *    *             *                                   
       1338 TACGGCCTAATTATATTCATTTTGGTGAGGTTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
         66 TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC

               *            *      *
       1403 ACTTGTTATTTTGGGCTTATCGGG
        131 ACTCGTTATTTTGGGCCTATCGGA

                                                                         
       1427 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
          1 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT


Statistics
Matches: 632,  Mismatches: 39, Indels: 8
        0.93            0.06        0.01

Matches are distributed among these distances:
 153  283  0.45
 154  349  0.55

ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40


Consensus pattern (154 bp):   
GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
TATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
ACTCGTTATTTTGGGCCTATCGGA

Found at i:1251 original size:307 final size:308

Alignment explanation


    Indices: 656--1487  Score: 1391
    Period size: 307  Copynumber: 2.7  Consensus size: 308

        646 CTGAATATTG

                           *     *          *                                
        656 GAGGACCATTAGTGATGTTTTAAATCGTCTTCCATTTGGCAAACCTCAATGCTTTTCTTTCCATT
          1 GAGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT

                                                                             
        721 GTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGG
         66 GTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGG

                                    *              *                         
        786 AACACTCGTTATTTTGGGCCTATCAGAGACCATTAGTGAGGTTTTGAATCGTCTTCGATTTGGCA
        131 AACACTCGTTATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                                        **    *              
        851 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCCGACTATAATCGTTTTGGTGAGATTAGTCCA
        196 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCCGACTATAATAATTTTAGTGAGATTAGTCCA

                                          *         **      
        916 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTTCCTATC
        261 CTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATC

                *                                                            
        964 GAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTCAATGCTTTTCTTTCCATT
          1 GAGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT

                                                                             
       1028 GTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGG
         66 GTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGG

                                                                             
       1093 AACACTCGTTATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
        131 AACACTCGTTATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                            * *                              
       1158 AACCTCAATGCTTTTCTTTCCATTGTTTATGGTCTGACTATAATAATTTTAGTGAGATTAGTCCA
        196 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCCGACTATAATAATTTTAGTGAGATTAGTCCA

                                                            
       1223 CTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATC
        261 CTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATC

                                                         *       *           
       1271 G-GAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTTCAATG-ATTTCTTTCCAT
          1 GAG-GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT

            *  *  *     * *    *             *                            *  
       1334 CGTGTACGGCCTAATTATATTCATTTTGGTGAGGTTAGTCCACTGTGAAGTTTTTAGCTCATTTG
         65 TGTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATG

                   *            *      *                                     
       1399 GAACACTTGTTATTTTGGGCTTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC
        130 GAACACTCGTTATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC

                                    
       1464 AAACCTCAATGCTTTTCTTTCCAT
        195 AAACCTCAATGCTTTTCTTTCCAT


Statistics
Matches: 494,  Mismatches: 28, Indels: 5
        0.94            0.05        0.01

Matches are distributed among these distances:
 306    1  0.00
 307  448  0.91
 308   45  0.09

ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40


Consensus pattern (308 bp):   
GAGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
GTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGG
AACACTCGTTATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCCGACTATAATAATTTTAGTGAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATC
Done.