Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008479.1 Corchorus capsularis cultivar CVL-1 contig08500, 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: 27973
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:2729 original size:238 final size:238

Alignment explanation


    Indices: 2311--2788  Score: 929
    Period size: 238  Copynumber: 2.0  Consensus size: 238

       2301 AATCTTTTAG

                                                                             
       2311 GAACTAAAGAAGATAACAACAAGGCTCTAGTAGTTTCCATGATATGGCGATGTTTTCTTTCAGCA
          1 GAACTAAAGAAGATAACAACAAGGCTCTAGTAGTTTCCATGATATGGCGATGTTTTCTTTCAGCA

                                  *                                          
       2376 ACACCATTCTGTTGTGGTGTATCAGTACAAGATAATTCAAGAAGGGTACCTTGAGAAGCGAGAAA
         66 ACACCATTCTGTTGTGGTGTATAAGTACAAGATAATTCAAGAAGGGTACCTTGAGAAGCGAGAAA

                                                    *                        
       2441 CTCTTTTAAACCACCTGATTTATACTCTCCAGCAGAATCAGCACGAAGACGCTTTATAGGTTTGG
        131 CTCTTTTAAACCACCTGATTTATACTCTCCAGCAGAATCAACACGAAGACGCTTTATAGGTTTGG

                                                       
       2506 AAAATTGTGTTCTAACCATGGTAGAAAAGTCTTGATAAATTTT
        196 AAAATTGTGTTCTAACCATGGTAGAAAAGTCTTGATAAATTTT

                                                 *                           
       2549 GAACTAAAGAAGATAACAACAAGGCTCTAGTAGTTTCGATGATATGGCGATGTTTTCTTTCAGCA
          1 GAACTAAAGAAGATAACAACAAGGCTCTAGTAGTTTCCATGATATGGCGATGTTTTCTTTCAGCA

                                                                             
       2614 ACACCATTCTGTTGTGGTGTATAAGTACAAGATAATTCAAGAAGGGTACCTTGAGAAGCGAGAAA
         66 ACACCATTCTGTTGTGGTGTATAAGTACAAGATAATTCAAGAAGGGTACCTTGAGAAGCGAGAAA

                                                                             
       2679 CTCTTTTAAACCACCTGATTTATACTCTCCAGCAGAATCAACACGAAGACGCTTTATAGGTTTGG
        131 CTCTTTTAAACCACCTGATTTATACTCTCCAGCAGAATCAACACGAAGACGCTTTATAGGTTTGG

                                                       
       2744 AAAATTGTGTTCTAACCATGGTAGAAAAGTCTTGATAAATTTT
        196 AAAATTGTGTTCTAACCATGGTAGAAAAGTCTTGATAAATTTT

              
       2787 GA
          1 GA

       2789 GTAAGTCTGA


Statistics
Matches: 237,  Mismatches: 3, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 238  237  1.00

ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30


Consensus pattern (238 bp):   
GAACTAAAGAAGATAACAACAAGGCTCTAGTAGTTTCCATGATATGGCGATGTTTTCTTTCAGCA
ACACCATTCTGTTGTGGTGTATAAGTACAAGATAATTCAAGAAGGGTACCTTGAGAAGCGAGAAA
CTCTTTTAAACCACCTGATTTATACTCTCCAGCAGAATCAACACGAAGACGCTTTATAGGTTTGG
AAAATTGTGTTCTAACCATGGTAGAAAAGTCTTGATAAATTTT

Found at i:19105 original size:34 final size:34

Alignment explanation


    Indices: 19067--19134  Score: 102
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      19057 ATTAACACAT

                                       *       
      19067 TACTGAAACA-TAAATCTATAAGCCAATAAATAAA
          1 TACTGAAACACT-AATCTATAAGCCAACAAATAAA

                               *              
      19101 TACTGAAACACTAATCTATGAGCCAACAAATAAA
          1 TACTGAAACACTAATCTATAAGCCAACAAATAAA

      19135 CCCAGTATAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  34   30  0.97
  35    1  0.03

ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22


Consensus pattern (34 bp):   
TACTGAAACACTAATCTATAAGCCAACAAATAAA

Found at i:27455 original size:33 final size:33

Alignment explanation


    Indices: 27418--27504  Score: 131
    Period size: 33  Copynumber: 2.6  Consensus size: 33

      27408 CCACGGCGAA

                       *  *                   
      27418 GCCGCCCCACTAGGACGGCTTCACC-ATAAACAG
          1 GCCGCCCCACTGGGGCGGCTTCACCTATAAA-AG

                                        *    
      27451 GCCGCCCCACTGGGGCGGCTTCACCTATGAAAG
          1 GCCGCCCCACTGGGGCGGCTTCACCTATAAAAG

                                 
      27484 GCCGCCCCACTGGGGCGGCTT
          1 GCCGCCCCACTGGGGCGGCTT

      27505 AGCCAGGGCA


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  33   46  0.92
  34    4  0.08

ACGTcount: A:0.18, C:0.39, G:0.29, T:0.14


Consensus pattern (33 bp):   
GCCGCCCCACTGGGGCGGCTTCACCTATAAAAG

Found at i:27564 original size:32 final size:32

Alignment explanation


    Indices: 27496--27567  Score: 81
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      27486 CGCCCCACTG

                          *      * *       *
      27496 GGGCGGCTTAGCCAGGGCAGGTCGCCCCGGTG
          1 GGGCGGCTTAGCCACGGCAGGCCACCCCGGTA

                     *       *        *     
      27528 GGGCGGCTTCGCCACGGTAGGCCACCTCGGTA
          1 GGGCGGCTTAGCCACGGCAGGCCACCCCGGTA

                    
      27560 GGGCGGCT
          1 GGGCGGCT

      27568 CGGCTATTTT


Statistics
Matches: 33,  Mismatches: 7, Indels: 0
        0.82            0.17        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.10, C:0.32, G:0.44, T:0.14


Consensus pattern (32 bp):   
GGGCGGCTTAGCCACGGCAGGCCACCCCGGTA
Done.