Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014094.1 Corchorus capsularis cultivar CVL-1 contig14115, 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: 14620
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:114 original size:23 final size:23

Alignment explanation


    Indices: 88--150  Score: 65
    Period size: 26  Copynumber: 2.6  Consensus size: 23

         78 ATGTTTTACT

                                   
         88 AATAAATAATATATATACTAATA
          1 AATAAATAATATATATACTAATA

                     *       *        
        111 AATAAATATTTACTAATTTACTAATA
          1 AATAAATA-ATA-T-ATATACTAATA

                           
        137 ATATAAAT-ATATAT
          1 A-ATAAATAATATAT

        151 TAAAAATATA


Statistics
Matches: 33,  Mismatches: 3, Indels: 8
        0.75            0.07        0.18

Matches are distributed among these distances:
  23   10  0.30
  24    3  0.09
  25    3  0.09
  26   11  0.33
  27    6  0.18

ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40


Consensus pattern (23 bp):   
AATAAATAATATATATACTAATA

Found at i:119 original size:16 final size:19

Alignment explanation


    Indices: 84--127  Score: 72
    Period size: 19  Copynumber: 2.4  Consensus size: 19

         74 AGATATGTTT

                               
         84 TACTAATAAATAATATATA
          1 TACTAATAAATAATATATA

                              *
        103 TACTAATAAATAA-ATATT
          1 TACTAATAAATAATATATA

                   
        121 TACTAAT
          1 TACTAAT

        128 TTACTAATAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  18   11  0.46
  19   13  0.54

ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39


Consensus pattern (19 bp):   
TACTAATAAATAATATATA

Found at i:1695 original size:59 final size:59

Alignment explanation


    Indices: 1603--1874  Score: 336
    Period size: 59  Copynumber: 4.6  Consensus size: 59

       1593 CTCCATACTC

                                     *                         *        
       1603 AGCATCCCTCGGTCGCAC-AACTCAGTGGGCATCCCCCACTAGTGCCAAAACAACGATCG
          1 AGCATCCCTCGGTCGCACGAAC-CAATGGGCATCCCCCACTAGTGCCAAAAGAACGATCG

                               *                                         
       1662 AGCATCCCTCGGGT-GCACTAACCAATGGGCATCCCCCACTCA-TGCCAAAAGAACGATCG
          1 AGCATCCCTC-GGTCGCACGAACCAATGGGCATCCCCCACT-AGTGCCAAAAGAACGATCG

                                *                   *      *     *   * 
       1721 AGCATCCCTCGGTCGCACGACCCAATGGGCATCCCCCACTCGTGCCATAAGAATGATTG
          1 AGCATCCCTCGGTCGCACGAACCAATGGGCATCCCCCACTAGTGCCAAAAGAACGATCG

                                *          *        *      *      *    
       1780 AGCATCCCTCGGTCGCACGATCCAATGGGCACCCCCCACTCGTGCCATAAGAACAATCG
          1 AGCATCCCTCGGTCGCACGAACCAATGGGCATCCCCCACTAGTGCCAAAAGAACGATCG

                  *        *         *           
       1839 AGCATCTCTCGGTCGTACG-ACCTATTGGGCATCCCC
          1 AGCATCCCTCGGTCGCACGAACC-AATGGGCATCCCC

       1875 TACGAGCAAT


Statistics
Matches: 189,  Mismatches: 18, Indels: 12
        0.86            0.08        0.05

Matches are distributed among these distances:
  58    5  0.03
  59  177  0.94
  60    7  0.04

ACGTcount: A:0.25, C:0.37, G:0.21, T:0.17


Consensus pattern (59 bp):   
AGCATCCCTCGGTCGCACGAACCAATGGGCATCCCCCACTAGTGCCAAAAGAACGATCG

Found at i:2609 original size:27 final size:27

Alignment explanation


    Indices: 2570--2698  Score: 98
    Period size: 27  Copynumber: 4.8  Consensus size: 27

       2560 ATCAAAAGCG

                  *                 *  
       2570 GCCGTGTGCCCACCATCGGAAGAGTGC
          1 GCCGTGCGCCCACCATCGGAAGAGAGC

                    *                  
       2597 GCCGTGCGACCACCATCGGAAGAGAGC
          1 GCCGTGCGCCCACCATCGGAAGAGAGC

            *   *    *    *   *    *   
       2624 ACCGCGCG-GCACCGTCGAAAGAAAGC
          1 GCCGTGCGCCCACCATCGGAAGAGAGC

             *      *        *    * * *
       2650 GTCGTGCGTCCACCATCAGAAGTGTGT
          1 GCCGTGCGCCCACCATCGGAAGAGAGC

              *   *               
       2677 GCTGTGTGCCCACCATCGGAAG
          1 GCCGTGCGCCCACCATCGGAAG

       2699 TGGAAGAGCG


Statistics
Matches: 76,  Mismatches: 25, Indels: 2
        0.74            0.24        0.02

Matches are distributed among these distances:
  26   19  0.25
  27   57  0.75

ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14


Consensus pattern (27 bp):   
GCCGTGCGCCCACCATCGGAAGAGAGC

Found at i:2736 original size:24 final size:24

Alignment explanation


    Indices: 2685--2737  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       2675 GTGCTGTGTG

                                 * *
       2685 CCCACCATCGGAAGTGGAAGAGCG
          1 CCCACCATCGGAAGTGGAAGAACA

                              *      
       2709 CCCACCATC-GAATGTGGGAGAACA
          1 CCCACCATCGGAA-GTGGAAGAACA

                 
       2733 CCCAC
          1 CCCAC

       2738 AGGGGGCAAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  23    3  0.12
  24   22  0.88

ACGTcount: A:0.30, C:0.34, G:0.26, T:0.09


Consensus pattern (24 bp):   
CCCACCATCGGAAGTGGAAGAACA

Found at i:12293 original size:21 final size:22

Alignment explanation


    Indices: 12254--12303  Score: 66
    Period size: 21  Copynumber: 2.3  Consensus size: 22

      12244 GGAGATGAAA

                                   
      12254 TTTTTTTAAAAAACTTAAAACAC
          1 TTTTTTTAAAAAAC-TAAAACAC

                   *            * 
      12277 TTTTTTTTAAAAA-TAAAACCC
          1 TTTTTTTAAAAAACTAAAACAC

                  
      12298 TTTTTT
          1 TTTTTT

      12304 ATTTTAATAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  21   13  0.52
  23   12  0.48

ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48


Consensus pattern (22 bp):   
TTTTTTTAAAAAACTAAAACAC
Done.