Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005516.1 Corchorus capsularis cultivar CVL-1 contig05534, 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: 14826
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1334 original size:17 final size:18

Alignment explanation


    Indices: 1289--1338  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1279 GCGCTGTTAT

                *    *      * 
       1289 AATATGCTTCACTTCAGG
          1 AATACGCTTTACTTCAAG

            *                 
       1307 TATACGCTTTACTTCAAG
          1 AATACGCTTTACTTCAAG

                           
       1325 AATA-GCTTTACTTC
          1 AATACGCTTTACTTC

       1339 CAAAATGAAA


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  17   10  0.37
  18   17  0.63

ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38


Consensus pattern (18 bp):   
AATACGCTTTACTTCAAG

Found at i:9482 original size:19 final size:20

Alignment explanation


    Indices: 9436--9483  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 20

       9426 TGTGGCACGC

                                 *
       9436 CACATGTACCAAAAAGTCGTGC
          1 CACATGTACCAAAAA--CGTGA

                                
       9458 CACATGTACCAAAAA-GTGA
          1 CACATGTACCAAAAACGTGA

                   
       9477 CACATGT
          1 CACATGT

       9484 CACACCACCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19   10  0.40
  22   15  0.60

ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19


Consensus pattern (20 bp):   
CACATGTACCAAAAACGTGA

Found at i:9497 original size:53 final size:53

Alignment explanation


    Indices: 9403--9503  Score: 148
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       9393 GACGTGGCAC

                 *                 **      *                     
       9403 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT

                                       *        *           
       9456 GCCACATGTACCAAAAAGTGACACATGTCACACCACCTGTACCAAAAA
          1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAA

       9504 ATGACACGTG


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   42  1.00

ACGTcount: A:0.38, C:0.29, G:0.18, T:0.16


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT

Found at i:13412 original size:2 final size:2

Alignment explanation


    Indices: 13405--13434  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      13395 AAAACCCTTC

                                                        
      13405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13435 TTTCTCAAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14146 original size:106 final size:106

Alignment explanation


    Indices: 13960--14380  Score: 745
    Period size: 106  Copynumber: 4.0  Consensus size: 106

      13950 TCATGTTCGT

                                                                             
      13960 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAATGTTAATATGTCTCAACTTTAGATTAGT
          1 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAA-GTTAATATGTCTCAACTTTAGATTAGT

                                                      
      14025 CGGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG
         65 CGGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG

                            *                   *                            
      14067 TTGGATTGAGTGAATAGATAAAATAAGATTTGAAAAGGTTAATATGTCTCAACTTTAGATTAGTC
          1 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAAGTTAATATGTCTCAACTTTAGATTAGTC

                                                    *
      14132 GGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGA
         66 GGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG

                            *                                                
      14173 TTGGATTGAGTGAATAGATAAAATAAGATTTGAAAAAGTTAATATGTCTCAACTTTAGATTAGTC
          1 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAAGTTAATATGTCTCAACTTTAGATTAGTC

                                                     
      14238 GGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG
         66 GGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG

                                                        *            *       
      14279 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAAGTTAATACGTCTCAACTTTAAATTAGTC
          1 TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAAGTTAATATGTCTCAACTTTAGATTAGTC

                       *         *                
      14344 GGAACTTAATACGACTCTGATCAGATACTT-GGTATGG
         66 GGAACTTAATATGACTCTGATTAGATA-TTGGGTATGG

      14381 GTTTGATGGA


Statistics
Matches: 303,  Mismatches: 10, Indels: 3
        0.96            0.03        0.01

Matches are distributed among these distances:
 106  266  0.88
 107   37  0.12

ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34


Consensus pattern (106 bp):   
TTGGATTGAGTGAATAAATAAAATAAGATTTGAAAAAGTTAATATGTCTCAACTTTAGATTAGTC
GGAACTTAATATGACTCTGATTAGATATTGGGTATGGTCGG

Done.