Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010273.1 Corchorus olitorius cultivar O-4 contig10305, 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: 1777
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34


Found at i:428 original size:37 final size:36

Alignment explanation


    Indices: 304--511  Score: 214
    Period size: 37  Copynumber: 5.8  Consensus size: 36

        294 AAAAATGTTT

                              *              *     *
        304 TGGATGGGAACTTTCCCATTTTGAAAACTAAAACTAAAAA
          1 TGGATGGGAACTTTCCCAATTTGAAAACT----TTAAAAC

                *               *          *    * 
        344 T-GACGGGAACTTTCCCTAAATTGAAAA--TGATAACC
          1 TGGATGGGAACTTTCCC-AATTTGAAAACTTTA-AAAC

                                                 
        379 T-GATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC
          1 TGGATGGGAACTTTCCCAATTTGAAAACTTT-AAAAC

                                           *     
        415 TGGATGGGAACTTTCCCAATTTGAAAACTTAAAAAAC
          1 TGGATGGGAACTTTCCCAATTTGAAAACTT-TAAAAC

                             *                  
        452 TGG-TGGGAACTTTCCCCATTTGAAAAC-TTAAAA-
          1 TGGATGGGAACTTTCCCAATTTGAAAACTTTAAAAC

                                       
        485 TGGATGGGAACTTTCCCAATTTGAAAA
          1 TGGATGGGAACTTTCCCAATTTGAAAA

        512 AAACTTGAAT


Statistics
Matches: 145,  Mismatches: 15, Indels: 22
        0.80            0.08        0.12

Matches are distributed among these distances:
  33    3  0.02
  34   36  0.25
  35   18  0.12
  36   28  0.19
  37   37  0.26
  39   14  0.10
  40    9  0.06

ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28


Consensus pattern (36 bp):   
TGGATGGGAACTTTCCCAATTTGAAAACTTTAAAAC

Found at i:466 original size:36 final size:36

Alignment explanation


    Indices: 308--511  Score: 202
    Period size: 34  Copynumber: 5.6  Consensus size: 36

        298 ATGTTTTGGA

                          *           *        *  *
        308 TGGGAACTTTCCCATTTTGAAAACTAAAACTAAAAATGA
          1 TGGGAACTTTCCCAATTTGAAAACT-TAA--AAAACTGG

            *               *          * *  *   *
        347 CGGGAACTTTCCCTAAATTGAAAA--TGATAACCTGA
          1 TGGGAACTTTCCC-AATTTGAAAACTTAAAAAACTGG

                                      **        
        382 TGGGAACTTTCCCAATTTGAAAACTTTGAAAACTGG
          1 TGGGAACTTTCCCAATTTGAAAACTTAAAAAACTGG

                                                 
        418 ATGGGAACTTTCCCAATTTGAAAACTTAAAAAACTGG
          1 -TGGGAACTTTCCCAATTTGAAAACTTAAAAAACTGG

                         *                      
        455 TGGGAACTTTCCCCATTTGAAAACTT--AAAA-TGG
          1 TGGGAACTTTCCCAATTTGAAAACTTAAAAAACTGG

                                    
        488 ATGGGAACTTTCCCAATTTGAAAA
          1 -TGGGAACTTTCCCAATTTGAAAA

        512 AAACTTGAAT


Statistics
Matches: 141,  Mismatches: 19, Indels: 15
        0.81            0.11        0.09

Matches are distributed among these distances:
  33    3  0.02
  34   35  0.25
  35   17  0.12
  36   31  0.22
  37   35  0.25
  39   12  0.09
  40    8  0.06

ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28


Consensus pattern (36 bp):   
TGGGAACTTTCCCAATTTGAAAACTTAAAAAACTGG

Found at i:502 original size:107 final size:109

Alignment explanation


    Indices: 304--511  Score: 271
    Period size: 107  Copynumber: 1.9  Consensus size: 109

        294 AAAAATGTTT

                              *                                              
        304 TGGATGGGAACTTTCCCATTTTGAAAACTAAAACTAAAAATGACGGGAACTTTCCCTAAATTGAA
          1 TGGATGGGAACTTTCCCAATTTGAAAACTAAAAC-AAAAATGACGGGAACTTTCCCTAAATTGAA

                    **                                    
        369 AATGATAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC
         65 AAT-ATAAAATGATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC

                                          *       *  **             * *      
        415 TGGATGGGAACTTTCCCAATTTGAAAACT-TAA-AAAACTGGTGGGAACTTTCCC-CATTTGAAA
          1 TGGATGGGAACTTTCCCAATTTGAAAACTAAAACAAAAATGACGGGAACTTTCCCTAAATTGAAA

                                                
        477 ACT-TAAAATGGATGGGAACTTTCCCAATTTGAAAA
         66 A-TATAAAAT-GATGGGAACTTTCCCAATTTGAAAA

        512 AAACTTGAAT


Statistics
Matches: 86,  Mismatches: 9, Indels: 8
        0.83            0.09        0.08

Matches are distributed among these distances:
 106    4  0.05
 107   33  0.38
 108   19  0.22
 110    2  0.02
 111   28  0.33

ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28


Consensus pattern (109 bp):   
TGGATGGGAACTTTCCCAATTTGAAAACTAAAACAAAAATGACGGGAACTTTCCCTAAATTGAAA
ATATAAAATGATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC

Found at i:517 original size:73 final size:73

Alignment explanation


    Indices: 348--511  Score: 230
    Period size: 73  Copynumber: 2.3  Consensus size: 73

        338 TAAAAATGAC

                           *          * *  *   *                             
        348 GGGAACTTTCCCTAAATTGAAAA--TGATAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGA
          1 GGGAACTTTCCC-AATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCAATTTGAAAACTTTGA

                     
        411 AAACTGGAT
         65 AAACTGGAT

                                                            *                
        420 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCCATTTGAAAAC-TT-AA
          1 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCAATTTGAAAACTTTGAA

                    
        483 AA-TGGAT
         66 AACTGGAT

                                  
        490 GGGAACTTTCCCAATTTGAAAA
          1 GGGAACTTTCCCAATTTGAAAA

        512 AAACTTGAAT


Statistics
Matches: 84,  Mismatches: 6, Indels: 6
        0.88            0.06        0.06

Matches are distributed among these distances:
  70   27  0.32
  71   13  0.15
  72   14  0.17
  73   30  0.36

ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29


Consensus pattern (73 bp):   
GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCAATTTGAAAACTTTGAA
AACTGGAT
Done.