Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015715.1 Corchorus olitorius cultivar O-4 contig15748, 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: 3399
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30


Found at i:2555 original size:49 final size:47

Alignment explanation


    Indices: 2500--2656  Score: 111
    Period size: 49  Copynumber: 3.2  Consensus size: 47

       2490 GAACGTTGCC

                                                             
       2500 GTTCTCACAAAGAGTCTGGGGCTTTACGTTCGGCCAACTTAGATTCGAT
          1 GTTCTCACAAAGAGTC--GGGCTTTACGTTCGGCCAACTTAGATTCGAT

                    ***     *  *  *  *        *              * **
       2549 GTTCTCACGGGGAGTCCGGATTGA-ATTCTAAGGTCAA-TTACGAATGTTGCC
          1 GTTCTCACAAAGAGTCGGGCTTTACGTTC---GGCCAACTTA-G-AT-TCGAT

                                                             
       2600 GTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGAT
          1 GTTCTCACAAAGAGT-C-GGGCTTTACGTTCGGCCAACTTAGATTCGAT

                    
       2649 GTTCTCAC
          1 GTTCTCAC

       2657 GGGGAGTCCG


Statistics
Matches: 76,  Mismatches: 22, Indels: 20
        0.64            0.19        0.17

Matches are distributed among these distances:
  46    3  0.04
  47    5  0.07
  48    3  0.04
  49   29  0.38
  50    4  0.05
  51   20  0.26
  52    4  0.05
  53    5  0.07
  54    3  0.04

ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30


Consensus pattern (47 bp):   
GTTCTCACAAAGAGTCGGGCTTTACGTTCGGCCAACTTAGATTCGAT

Found at i:2563 original size:100 final size:100

Alignment explanation


    Indices: 2383--2983  Score: 985
    Period size: 100  Copynumber: 6.0  Consensus size: 100

       2373 TTGTTTGTTA

                       *   *       *                   *   *                 
       2383 CAATTACGAACATTGTCGTTCTCTCAAAGAGTCCA-GGCTTTATGTTTGGCCACAACTTAG-TCT
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGG-C-CAACTTAGAT-T

                                  *      **        
       2446 CGATGTTCTCATC--GGAGTCCAGATCGAGGTCTAAGGT
         63 CGATGTTCTCA-CGGGGAGTCCGGATCGAATTCTAAGGT

                                             **                              
       2483 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCTGGGGCTTTACGTTCGGCCAACTTAGATTCGA
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA

                                  *            
       2548 TGTTCTCACGGGGAGTCCGGATTGAATTCTAAGGT
         66 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

                      *                                                      
       2583 CAATTACGAATGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA

                                               
       2648 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT
         66 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

                                                                             
       2683 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA

                           *   *      *        
       2748 TGTTCTCACGGGGAGGCCGAATCGAAGTCTAAGGT
         66 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

                                                                             
       2783 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA

                                               
       2848 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT
         66 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

                           *                  *                              
       2883 CAATTACGAACGTTGTCGTTCTCACAAAGAGTCCGGGGCTTTACGTTCGGCCAACTTAGATTCGA
          1 CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA

                                               
       2948 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT
         66 TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

             
       2983 C
          1 C

       2984 GAAGATAAAA


Statistics
Matches: 473,  Mismatches: 24, Indels: 8
        0.94            0.05        0.02

Matches are distributed among these distances:
  98    1  0.00
  99   20  0.04
 100  440  0.93
 101   12  0.03

ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28


Consensus pattern (100 bp):   
CAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGA
TGTTCTCACGGGGAGTCCGGATCGAATTCTAAGGT

Done.