Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015731.1 Corchorus capsularis cultivar CVL-1 contig15752, 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: 36637
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:1729 original size:21 final size:22

Alignment explanation


    Indices: 1703--1749  Score: 69
    Period size: 21  Copynumber: 2.2  Consensus size: 22

       1693 AAATGTTTAG

                            *     
       1703 AAAAGAATATAAAAAATATA-A
          1 AAAAGAATATAAAAAAAATACA

                  *               
       1724 AAAAGACTATAAAAAAAATACA
          1 AAAAGAATATAAAAAAAATACA

                
       1746 AAAA
          1 AAAA

       1750 CGAAAAAAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   18  0.78
  22    5  0.22

ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15


Consensus pattern (22 bp):   
AAAAGAATATAAAAAAAATACA

Found at i:3969 original size:23 final size:23

Alignment explanation


    Indices: 3918--3969  Score: 95
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       3908 TGATGGAGTG

                 *                 
       3918 GTGAAATTTGAAAATTAAAATGA
          1 GTGAATTTTGAAAATTAAAATGA

                                   
       3941 GTGAATTTTGAAAATTAAAATGA
          1 GTGAATTTTGAAAATTAAAATGA

                  
       3964 GTGAAT
          1 GTGAAT

       3970 ATGTGAATGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33


Consensus pattern (23 bp):   
GTGAATTTTGAAAATTAAAATGA

Found at i:4196 original size:21 final size:21

Alignment explanation


    Indices: 4152--4203  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       4142 CCAGGGCACA

                   *     *     * 
       4152 TGGGTGCCCAAGCCAACCGGC
          1 TGGGTGCACAAGCAAACCGCC

                            *    
       4173 TGGGTGCACAAGCAAAGCGCC
          1 TGGGTGCACAAGCAAACCGCC

                *     
       4194 TGGGCGCACA
          1 TGGGTGCACA

       4204 GCCAACGTCG


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.23, C:0.33, G:0.35, T:0.10


Consensus pattern (21 bp):   
TGGGTGCACAAGCAAACCGCC

Found at i:7697 original size:28 final size:27

Alignment explanation


    Indices: 7632--7697  Score: 69
    Period size: 28  Copynumber: 2.4  Consensus size: 27

       7622 CAAGTAACTT

                             *     *    
       7632 GAAAAATAAAAATTAAAGGAAAATTAAC
          1 GAAAAA-AAAAATTAAAAGAAAAATAAC

            *   **                      
       7660 TAAACTAAAAATTGAAAAGAAAAATAAC
          1 GAAAAAAAAAATT-AAAAGAAAAATAAC

                      
       7688 GAAAAAAAAA
          1 GAAAAAAAAA

       7698 TAAAGGTAAG


Statistics
Matches: 29,  Mismatches: 8, Indels: 2
        0.74            0.21        0.05

Matches are distributed among these distances:
  27    7  0.24
  28   22  0.76

ACGTcount: A:0.71, C:0.05, G:0.09, T:0.15


Consensus pattern (27 bp):   
GAAAAAAAAAATTAAAAGAAAAATAAC

Found at i:22851 original size:28 final size:29

Alignment explanation


    Indices: 22777--22851  Score: 68
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      22767 CAATAAACTT

                         *   *           
      22777 GAAAAAT-AAAAAGTAAGGAAAAATTAAC
          1 GAAAAATAAAAAAATAAAGAAAAATTAAC

             *   *                         
      22805 -TAAACTAAAAATTAA-AAAGAAAAA-TAAC
          1 GAAAAATAAAAA--AATAAAGAAAAATTAAC

                               
      22833 GAAAAATAAAAAAATAAAG
          1 GAAAAATAAAAAAATAAAG

      22852 GTAAGAAATT


Statistics
Matches: 36,  Mismatches: 6, Indels: 10
        0.69            0.12        0.19

Matches are distributed among these distances:
  27    6  0.17
  28   12  0.33
  29   17  0.47
  30    1  0.03

ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15


Consensus pattern (29 bp):   
GAAAAATAAAAAAATAAAGAAAAATTAAC

Found at i:29857 original size:21 final size:21

Alignment explanation


    Indices: 29824--29872  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      29814 AAGAATTGTA

                          **     
      29824 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
      29844 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
      29865 GCATTCCT
          1 GC-TTCCT

      29873 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT
Done.