Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010746.1 Corchorus olitorius cultivar O-4 contig10778, 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: 1784
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36


Found at i:331 original size:20 final size:21

Alignment explanation


    Indices: 293--334  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        283 TCCTTTGTTG

                                 
        293 ATGATCTCCAATGGGCTTTAA
          1 ATGATCTCCAATGGGCTTTAA

                     *           
        314 ATGATCTCCGAT-GGCTTTAA
          1 ATGATCTCCAATGGGCTTTAA

             
        334 A
          1 A

        335 CTCTTCAAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTTAA

Found at i:470 original size:21 final size:21

Alignment explanation


    Indices: 446--487  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        436 GCATCTTAGG

                                 
        446 CAACTCCAATGAGCTTGAAAC
          1 CAACTCCAATGAGCTTGAAAC

                  **             
        467 CAACTCTGATGAGCTTGAAAC
          1 CAACTCCAATGAGCTTGAAAC

        488 TTCTTCCTTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21


Consensus pattern (21 bp):   
CAACTCCAATGAGCTTGAAAC

Found at i:1134 original size:154 final size:154

Alignment explanation


    Indices: 596--1782  Score: 1792
    Period size: 154  Copynumber: 7.7  Consensus size: 154

        586 TTGGCGCATC

                 *          *     *  *    *         *           *     *  *   
        596 ATTAGACCACTGTGAATTTTTTGGCCCATTAGGAACACTTTTTATTTTGGGCCTATCGGGGCCCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                     *         *                                             
        661 TTAGTGT-CATTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATG
         66 TTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATG

                                     
        725 GCCTAACTATAATCATTTTGGTGAG
        130 GCCTAACTATAATCATTTTGGTGAG

                                       *                        *        *   
        750 ATTAGTCCACTGTGAAGTTTTTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTATCG-GGGCCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                                                             *   *           
        814 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCTATTGTTTATGG
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                               *    
        879 CCTAACTATAATCA-TTTGTTGAG
        131 CCTAACTATAATCATTTTGGTGAG

                               *        *                                    
        902 ATTAGTCCACTGTGAAGTTCTTAGCTCAATTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                                                *                  *         
        967 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCTTCAATGCTTTTCTTTCCAATGTTTATGG
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                                    
       1032 CCTAACTATAATCATTTTGGTGAG
        131 CCTAACTATAATCATTTTGGTGAG

                                           *                             *   
       1056 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTCGAACACTTGTTATTTTGGGCATATCGAGGTCCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                                *         *                                  
       1121 TTAGTTCCGTTTTGAATCGTGTTCGATTTGACAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                     *              
       1186 CCTAACTATGATCATTTTGGTGAG
        131 CCTAACTATAATCATTTTGGTGAG

                               *        *                                    
       1210 ATTAGTCCACTGTGAAGTTCTTAGCTCAATTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                                                                   *         
       1275 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGG
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                                    
       1340 CCTAACTATAATCATTTTGGTGAG
        131 CCTAACTATAATCATTTTGGTGAG

                                                                             
       1364 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                 *                                           *               
       1429 TTAGTCCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGG
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG

                                    
       1494 CCTAACTATAATCATTTTGGTGAG
        131 CCTAACTATAATCATTTTGGTGAG

                            *     * *     *   *      *         * *     *  *  
       1518 ATTAGTCCACTGTGAATTTTTTGGTTCATTAGGAGCGA-TTTTTATTTTGGTCCTATCGGGGCCC
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTTGGGCATATCGAGGACC

                  **           *                              *   *          
       1582 ATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGC-TTTCGTTCTATTGTTTATG
         65 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATG

                                    *
       1646 GCCTAACTATAATCATTTTGGTGAA
        130 GCCTAACTATAATCATTTTGGTGAG

                                  * *     *                     * *   *  *   
       1671 ATTAGTCCACTGTGAA-TTTTTGGTTCATTAGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCA
          1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA

                 **           *       *                     
       1735 TTAGTGACGTTTTGAATCATCTTCGAATTGGCAACCCTCAATGCTTTT
         66 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT

       1783 TT


Statistics
Matches: 962,  Mismatches: 65, Indels: 13
        0.93            0.06        0.01

Matches are distributed among these distances:
 151    1  0.00
 152  148  0.15
 153  219  0.23
 154  593  0.62
 155    1  0.00

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40


Consensus pattern (154 bp):   
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTGAG

Done.