Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006454.1 Corchorus capsularis cultivar CVL-1 contig06475, 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: 2567
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28


Found at i:1002 original size:529 final size:529

Alignment explanation


    Indices: 1--1211  Score: 2034
    Period size: 529  Copynumber: 2.3  Consensus size: 529

                                        *  *      *                          
          1 GAATCTTTACACAATGTCATAATATACAGATGTGTTAGAAGTGTGTTCATAGATAGTATTACAAA
          1 GAATCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCATAGATAGTATTACAAA

                                                *          *   *    *        
         66 TACATTTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTCCACTCCCCGAACTATTTTACAT
         66 TACATTTAGCCAATTAAGTCTAGTTACAATTTTGATATTTTTCCACTGCCCAAACTCTTTTACAT

                                                                            *
        131 TAAATTCTAACATCAAATACTAGAGCTAAACACAATAGGGTACCATAAAAACCTATAATTTTATG
        131 TAAATTCT-ACATCAAATACTAGAGCTAAACACAATAGGGTACCATAAAAACCTATAATTTTATA

                     *                          *                            
        196 GGAACTTCACATTATCTTTATTTAGGGTAAAATTTTTAGACATGAATTCTATATTTGCCACGGTT
        195 GGAACTTCAAATTATCTTTATTTAGGGTAAAATTTTAAGACATGAATTCTATATTTGCCACGGTT

                                                                 *           
        261 TTTGAAACGGTTATCTAAAAACCGTGGGAAAATCCGTGGCTATTTGGCACGGCTTTTGCCACAAC
        260 TTTGAAACGGTTATCTAAAAACCGTGGGAAAATCCGTGGCTATTTGGCACGGCCTTTGCCACAAC

                          *            * *                         *         
        326 TTTTCAATTTGCCATGGGTTTTGCAGCGGGTTTACAAAATCCCGTGGAAAAAGATGTGGCAAATT
        325 TTTTCAATTTGCCAAGGGTTTTGCAGCAGATTTACAAAATCCCGTGGAAAAAGATATGGCAAATT

                   *   *                                                     
        391 GAGAAAATATTTACCTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATT
        390 GAGAAAAGATTGACCTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATT

                                                                             
        456 GCATTTATATAATCTCAAAATTCTATATTGTCCCCAAAAATTGTGTAATTTCTAATTACTTACAA
        455 GCATTTATATAATCTCAAAATTCTATATTGTCCCCAAAAATTGTGTAATTTCTAATTACTTA-AA

                       
        521 AAA-CTTAATT
        519 AAAGCTTAATT

                                                                             
        531 GAATCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCATAGATAGTATTACAAA
          1 GAATCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCATAGATAGTATTACAAA

                                      *                *                     
        596 TACATTTAGCCAATTAAGTCTAGTTAAAATTTTGATATTTTTCGACTGCCCAAACTCTTTTACAT
         66 TACATTTAGCCAATTAAGTCTAGTTACAATTTTGATATTTTTCCACTGCCCAAACTCTTTTACAT

                     *                     *          *          *          *
        661 TAAATTCTATATCAAATACTAGAGCTAAACAGAATAGGGTACTAT-AAAACCTTTAATTTTATAT
        131 TAAATTCTACATCAAATACTAGAGCTAAACACAATAGGGTACCATAAAAACCTATAATTTTATAG

                                                                             
        725 GAACTTCAAATTATC-TTAGTTTAGGGTAAAATTTTAAGACATGAATTCTATATTTGCCACGGTT
        196 GAACTTCAAATTATCTTTA-TTTAGGGTAAAATTTTAAGACATGAATTCTATATTTGCCACGGTT

                                                              *             *
        789 TTTGAAACGGTTATCTTAAAAACCGTGGGAAAATTCC-TGGCTATTTGGCCCGGCCTTTGCCACG
        260 TTTGAAACGGTTATC-TAAAAACCGTGGGAAAA-TCCGTGGCTATTTGGCACGGCCTTTGCCACA

                                                  *                *         
        853 ACTTTTCAATTTGCCAAGGGTTTTGCAGCAGATTTACAGAATCCCGTGGAAAAAGCTATGGCAAA
        323 ACTTTTCAATTTGCCAAGGGTTTTGCAGCAGATTTACAAAATCCCGTGGAAAAAGATATGGCAAA

                                                                             
        918 TTGAGAAAAGATTGACCTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAA
        388 TTGAGAAAAGATTGACCTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAA

                        *                                                    
        983 TTGCATTTATATCATCTCAAAATTCTATATTGTCCCCAAAAATTGTGTAATTTCTAATTACTTAA
        453 TTGCATTTATATAATCTCAAAATTCTATATTGTCCCCAAAAATTGTGTAATTTCTAATTACTTAA

                 *      
       1048 AAAAGTTTAATT
        518 AAAAGCTTAATT

            * *                                             *                
       1060 TAGTCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCTTAGATAGTATTACAAA
          1 GAATCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCATAGATAGTATTACAAA

                                               **                            
       1125 TACATTTAGCCAATTAAGTCTAGTTACAATTTTGAGCTTTTTCCACTGCCCAAACTCTTTTACAT
         66 TACATTTAGCCAATTAAGTCTAGTTACAATTTTGATATTTTTCCACTGCCCAAACTCTTTTACAT

                                  
       1190 TAAATTCTACATCAAATACTAG
        131 TAAATTCTACATCAAATACTAG

       1212 TGTCACGCCC


Statistics
Matches: 639,  Mismatches: 38, Indels: 9
        0.93            0.06        0.01

Matches are distributed among these distances:
 527    3  0.00
 528   94  0.15
 529  410  0.64
 530  132  0.21

ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Consensus pattern (529 bp):   
GAATCTTTACACAATGTCATAATATACAAATCTGTTAGTAGTGTGTTCATAGATAGTATTACAAA
TACATTTAGCCAATTAAGTCTAGTTACAATTTTGATATTTTTCCACTGCCCAAACTCTTTTACAT
TAAATTCTACATCAAATACTAGAGCTAAACACAATAGGGTACCATAAAAACCTATAATTTTATAG
GAACTTCAAATTATCTTTATTTAGGGTAAAATTTTAAGACATGAATTCTATATTTGCCACGGTTT
TTGAAACGGTTATCTAAAAACCGTGGGAAAATCCGTGGCTATTTGGCACGGCCTTTGCCACAACT
TTTCAATTTGCCAAGGGTTTTGCAGCAGATTTACAAAATCCCGTGGAAAAAGATATGGCAAATTG
AGAAAAGATTGACCTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTG
CATTTATATAATCTCAAAATTCTATATTGTCCCCAAAAATTGTGTAATTTCTAATTACTTAAAAA
AGCTTAATT

Found at i:2190 original size:14 final size:13

Alignment explanation


    Indices: 2173--2213  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       2163 ACCCAAAATA

                          
       2173 ATTTAATAAAAACC
          1 ATTTAAT-AAAACC

                         
       2187 ATTT-ATAAAA-C
          1 ATTTAATAAAACC

                          
       2198 ATGTTAATAAAACC
          1 AT-TTAATAAAACC

              
       2212 AT
          1 AT

       2214 AATTAAAATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  11    3  0.12
  12    6  0.25
  13    8  0.33
  14    7  0.29

ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32


Consensus pattern (13 bp):   
ATTTAATAAAACC
Done.