Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023518.1 Corchorus olitorius cultivar O-4 contig23551, 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: 21112
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:2012 original size:30 final size:31

Alignment explanation


    Indices: 1976--2070  Score: 83
    Period size: 30  Copynumber: 3.1  Consensus size: 31

       1966 TTAATGTCCC

                                 *          
       1976 TTTTGCCCC-TGAACTTGTATGATTTT-GACA
          1 TTTTGCCCCATGAACTTGT-TAATTTTAGACA

                           *                
       2006 TTTTGCCCCCAT-AAATT-TTAATTTTAGACA
          1 TTTTG-CCCCATGAACTTGTTAATTTTAGACA

                     *         *         *  
       2036 TTTTGCCCCTTGAACTTG-CAATTTTAAGTCA
          1 TTTTGCCCCATGAACTTGTTAATTTT-AGACA

                
       2067 TTTT
          1 TTTT

       2071 AGTCCATCTC


Statistics
Matches: 53,  Mismatches: 6, Indels: 11
        0.76            0.09        0.16

Matches are distributed among these distances:
  29   11  0.21
  30   25  0.47
  31   16  0.30
  32    1  0.02

ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45


Consensus pattern (31 bp):   
TTTTGCCCCATGAACTTGTTAATTTTAGACA

Found at i:2139 original size:32 final size:32

Alignment explanation


    Indices: 2094--2175  Score: 94
    Period size: 32  Copynumber: 2.6  Consensus size: 32

       2084 CAATATTACT

                 *  *                       
       2094 AACGTAGCCTTGCCACATGACA-TTTTGGTCC
          1 AACGTGGCATTGCCACATGACATTTTTGGTCC

                             *  *            
       2125 AAACGTGGCATTGCCACCTGGCATTTTTGGTCC
          1 -AACGTGGCATTGCCACATGACATTTTTGGTCC

            *           *     
       2158 GACGTGGCATTGTCACAT
          1 AACGTGGCATTGCCACAT

       2176 CAATAATACC


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  32   33  0.79
  33    9  0.21

ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29


Consensus pattern (32 bp):   
AACGTGGCATTGCCACATGACATTTTTGGTCC

Found at i:9199 original size:40 final size:40

Alignment explanation


    Indices: 9155--9233  Score: 158
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       9145 CAAAGTTTAA

                                                    
       9155 ACCAAGTACTCTAGATTTTTCCAAACCTATATCTCACCGC
          1 ACCAAGTACTCTAGATTTTTCCAAACCTATATCTCACCGC

                                                   
       9195 ACCAAGTACTCTAGATTTTTCCAAACCTATATCTCACCG
          1 ACCAAGTACTCTAGATTTTTCCAAACCTATATCTCACCG

       9234 AATTGGCTTG


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   39  1.00

ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30


Consensus pattern (40 bp):   
ACCAAGTACTCTAGATTTTTCCAAACCTATATCTCACCGC

Found at i:9577 original size:21 final size:21

Alignment explanation


    Indices: 9553--9626  Score: 73
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       9543 ATCGTGTTCA

                                 
       9553 GAGCAATTGTGGAGTGGAGTT
          1 GAGCAATTGTGGAGTGGAGTT

                                  
       9574 GAGCAATTGT-GAG-GGAAG-T
          1 GAGCAATTGTGGAGTGG-AGTT

               ***                 
       9593 GAGTGGTGCTGTGGAGTGGAGTT
          1 GAGCAAT--TGTGGAGTGGAGTT

                       
       9616 GAGCAATTGTG
          1 GAGCAATTGTG

       9627 AGGGAAGTGA


Statistics
Matches: 41,  Mismatches: 6, Indels: 12
        0.69            0.10        0.20

Matches are distributed among these distances:
  19    7  0.17
  20    5  0.12
  21   17  0.41
  22    5  0.12
  23    7  0.17

ACGTcount: A:0.23, C:0.05, G:0.45, T:0.27


Consensus pattern (21 bp):   
GAGCAATTGTGGAGTGGAGTT

Found at i:9606 original size:42 final size:42

Alignment explanation


    Indices: 9560--9641  Score: 164
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       9550 TCAGAGCAAT

                                                      
       9560 TGTGGAGTGGAGTTGAGCAATTGTGAGGGAAGTGAGTGGTGC
          1 TGTGGAGTGGAGTTGAGCAATTGTGAGGGAAGTGAGTGGTGC

                                                    
       9602 TGTGGAGTGGAGTTGAGCAATTGTGAGGGAAGTGAGTGGT
          1 TGTGGAGTGGAGTTGAGCAATTGTGAGGGAAGTGAGTGGT

       9642 CCGTGAGCCG


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.22, C:0.04, G:0.48, T:0.27


Consensus pattern (42 bp):   
TGTGGAGTGGAGTTGAGCAATTGTGAGGGAAGTGAGTGGTGC
Done.