Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009821.1 Corchorus capsularis cultivar CVL-1 contig09842, 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: 10900
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31


Found at i:77 original size:49 final size:49

Alignment explanation


    Indices: 2--286  Score: 384
    Period size: 49  Copynumber: 5.9  Consensus size: 49

          1 T

                     *                                       
          2 GGAAGGCACTTG-TTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC
          1 GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

                                                   *         
         50 GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCATTCCCGGAC
          1 GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

                                   *   *                       
         99 GGAAGGCA-CTGGTTTTTTATCTACTACTTCCCAAAATGCCCTTCCCGGAC
          1 GGAAGGCACCT-G-TTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

                     *               *    *                  
        149 GGAAGGCACTTGTTTTTATCTGCTACTTCCTAAAATGCCCTTCCCGGAC
          1 GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

                     *                                   *   
        198 GGAAGGCACTTGTTTTTATCTGCTATTT-CCAAAATGCCCTTCCCAGAC
          1 GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

                 **                               *     
        246 GGAAGATA-CT-TATTTTA-CTTGCTATTTCCCAAAATACCCTT
          1 GGAAGGCACCTGT-TTTTATC-TGCTATTTCCCAAAATGCCCTT

        287 TCGGACCAAG


Statistics
Matches: 215,  Mismatches: 15, Indels: 14
        0.88            0.06        0.06

Matches are distributed among these distances:
  46    2  0.01
  47   14  0.07
  48   49  0.23
  49  106  0.49
  50   43  0.20
  51    1  0.00

ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33


Consensus pattern (49 bp):   
GGAAGGCACCTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGAC

Found at i:171 original size:99 final size:97

Alignment explanation


    Indices: 2--280  Score: 386
    Period size: 99  Copynumber: 2.9  Consensus size: 97

          1 T

                        *                                             *      
          2 GGAAGGCACT-TGTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTGTTTT
          1 GGAAGGCACTGTTTTTTATCTGCTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTT

                                             
         66 TATCTGCTATTTCCCAAAATGCCATTCCCGGAC
         65 TATCTGCTATTTCCCAAAATGCCATTCCCGGAC

                                  *                                          
         99 GGAAGGCACTGGTTTTTTATCTACTACTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTT
          1 GGAAGGCACT-GTTTTTTATCTGCTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTT

                      *    *        *         
        164 TTATCTGCTACTTCCTAAAATGCCCTTCCCGGAC
         64 TTATCTGCTATTTCCCAAAATGCCATTCCCGGAC

                                        *                *        **     *   
        198 GGAAGGCACT-TGTTTTTATCTGCTATTTCCAAAATGCCCTTCCCAGACGGAAGATACTT-ATTT
          1 GGAAGGCACTGT-TTTTTATCTGCTATTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTT

                                 
        261 TA-CTTGCTATTTCCCAAAAT
         65 TATC-TGCTATTTCCCAAAAT

        281 ACCCTTTCGG


Statistics
Matches: 163,  Mismatches: 15, Indels: 9
        0.87            0.08        0.05

Matches are distributed among these distances:
  95    1  0.01
  96   19  0.12
  97   41  0.25
  98   12  0.07
  99   90  0.55

ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33


Consensus pattern (97 bp):   
GGAAGGCACTGTTTTTTATCTGCTATTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTT
ATCTGCTATTTCCCAAAATGCCATTCCCGGAC

Found at i:413 original size:63 final size:64

Alignment explanation


    Indices: 270--432  Score: 157
    Period size: 64  Copynumber: 2.6  Consensus size: 64

        260 TTACTTGCTA

                                *  *  *  * *    *    *    *        *        
        270 TTTCCCAAAATACCCTTTCGGACCAAGGGTTGGTTTTGTCATATTCTTGCATTCAGGTTCTAGT
          1 TTTCCCAAAATACCCTTTCGAACAAAAGGCTAGTTTCGTCACATTCCTGCATTCAAGTTCTAGT

                 *    **      *        *                         *          
        334 TTTCCTAAAACGCCCTTTTGAACAAAATGCTAGTTTCGTCACATTCCTGCATTTAAGTT-TAGT
          1 TTTCCCAAAATACCCTTTCGAACAAAAGGCTAGTTTCGTCACATTCCTGCATTCAAGTTCTAGT

                                *     *  *      
        397 TTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTT
          1 TTTCCCAAAATACCCTTTCGAACAAAAGGCTAGTTT

        433 TATCATGTTT


Statistics
Matches: 76,  Mismatches: 23, Indels: 1
        0.76            0.23        0.01

Matches are distributed among these distances:
  63   32  0.42
  64   44  0.58

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37


Consensus pattern (64 bp):   
TTTCCCAAAATACCCTTTCGAACAAAAGGCTAGTTTCGTCACATTCCTGCATTCAAGTTCTAGT

Found at i:6326 original size:32 final size:32

Alignment explanation


    Indices: 6290--6352  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       6280 GGCGGCATAT

                    *   *      *            
       6290 CTCCTAGCTTGGTGCGGACTTGGCATGGTAGA
          1 CTCCTAGCATGGCGCGGACATGGCATGGTAGA

                          *                
       6322 CTCCTAGCATGGCGGGGACATGGCATGGTAG
          1 CTCCTAGCATGGCGCGGACATGGCATGGTAG

       6353 GGACCTAACT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24


Consensus pattern (32 bp):   
CTCCTAGCATGGCGCGGACATGGCATGGTAGA
Done.