Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013082.1 Corchorus capsularis cultivar CVL-1 contig13103, 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: 10023
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:2165 original size:53 final size:53

Alignment explanation


    Indices: 2102--2250  Score: 183
    Period size: 53  Copynumber: 2.8  Consensus size: 53

       2092 ATATTATTCT

                                    *       *                     
       2102 TGGTGAATGGAACAATGTTTCAACTAAGTCTTCTGTTTATAATTTATAGTAT-A
          1 TGGTGAATGGAACAATGTTTCAACAAAGTCTTTTGTTTATAATTTATAGT-TCA

                                  *             * *  *          *
       2155 TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTATCTAGTTTATAGTTCT
          1 TGGTGAATGGAACAATGTTTCAACAAAGTCTTTTGTTTATAATTTATAGTTCA

                    *  *          *   *                
       2208 TGGTGAATTGATCAATGTTTCACCAACGTCTTTTGTTTATAAT
          1 TGGTGAATGGAACAATGTTTCAACAAAGTCTTTTGTTTATAAT

       2251 ACTTGCAATT


Statistics
Matches: 82,  Mismatches: 13, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  52    1  0.01
  53   81  0.99

ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42


Consensus pattern (53 bp):   
TGGTGAATGGAACAATGTTTCAACAAAGTCTTTTGTTTATAATTTATAGTTCA

Found at i:7234 original size:7 final size:7

Alignment explanation


    Indices: 7222--7263  Score: 66
    Period size: 7  Copynumber: 5.9  Consensus size: 7

       7212 AAGGGTTTCG

                   
       7222 AAAAATA
          1 AAAAATA

                   
       7229 AAAAATA
          1 AAAAATA

                   
       7236 AAAAATA
          1 AAAAATA

                    
       7243 AAAAATTA
          1 AAAAA-TA

                 * 
       7251 AAAAAAA
          1 AAAAATA

                  
       7258 AAAAAT
          1 AAAAAT

       7264 TTCATTCCAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   7   25  0.78
   8    7  0.22

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (7 bp):   
AAAAATA

Found at i:7264 original size:15 final size:15

Alignment explanation


    Indices: 7222--7264  Score: 70
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       7212 AAGGGTTTCG

                           
       7222 AAAAATAAAAAA-TA
          1 AAAAATAAAAAATTA

                           
       7236 AAAAATAAAAAATTA
          1 AAAAATAAAAAATTA

                 *        
       7251 AAAAAAAAAAAATT
          1 AAAAATAAAAAATT

       7265 TCATTCCAAG


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  14   12  0.44
  15   15  0.56

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (15 bp):   
AAAAATAAAAAATTA
Done.