Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006305.1 Corchorus olitorius cultivar O-4 contig06330, 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: 6182
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35


Found at i:847 original size:16 final size:16

Alignment explanation


    Indices: 783--838  Score: 59
    Period size: 16  Copynumber: 3.8  Consensus size: 16

        773 TTTAATTTAA

                           *
        783 ATATATTATTAATAAC
          1 ATATATTATTAATAAT

                      *     
        799 AT-TATT-TTTATAAT
          1 ATATATTATTAATAAT

                            
        813 -T-T-TTATTAATAAT
          1 ATATATTATTAATAAT

                         
        826 ATATATTATTAAT
          1 ATATATTATTAAT

        839 TATTAATATA


Statistics
Matches: 33,  Mismatches: 3, Indels: 8
        0.75            0.07        0.18

Matches are distributed among these distances:
  12    2  0.06
  13    9  0.27
  14    7  0.21
  15    5  0.15
  16   10  0.30

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (16 bp):   
ATATATTATTAATAAT

Found at i:2567 original size:34 final size:37

Alignment explanation


    Indices: 2524--2606  Score: 109
    Period size: 39  Copynumber: 2.3  Consensus size: 37

       2514 CTACATATGA

                                                *
       2524 AATTTTCCCTGTT-A-A-TTTCTTCTCATTAATTATT
          1 AATTTTCCCTGTTAATATTTTCTTCTCATTAATTATC

                                            *      
       2558 AATTTTCCCTGTTAAATATTTTTCTTCTCATTGATTATC
          1 AATTTTCCCTGTT-AATA-TTTTCTTCTCATTAATTATC

                      
       2597 AATTTTCCCT
          1 AATTTTCCCT

       2607 CCGTGAGAAT


Statistics
Matches: 42,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
  34   13  0.31
  36    1  0.02
  37    1  0.02
  39   27  0.64

ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54


Consensus pattern (37 bp):   
AATTTTCCCTGTTAATATTTTCTTCTCATTAATTATC

Found at i:4415 original size:141 final size:142

Alignment explanation


    Indices: 4214--4635  Score: 774
    Period size: 142  Copynumber: 3.0  Consensus size: 142

       4204 ACACACCCTC

                                                                             
       4214 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC
          1 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC

                                                                             
       4279 GAAACCCTTTCCCCGTTCTACGGATGAA-TCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG
         66 GAAACCCTTTCCCCGTTCTACGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG

                        
       4343 GGTTGTTCAGAG
        131 GGTTGTTCAGAG

                                                                             
       4355 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC
          1 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC

                  *     *                                                   *
       4420 GAAACCTTTTCCTCGTTCTACGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGA
         66 GAAACCCTTTCCCCGTTCTACGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG

                   *    
       4485 GGTTGTTAAGAG
        131 GGTTGTTCAGAG

                                                                         *   
       4497 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTATCTC
          1 GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC

                *               *                                            
       4562 GAAATCCTTTCCCCGTTCTATGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG
         66 GAAACCCTTTCCCCGTTCTACGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG

                     
       4627 GGTTGTTCA
        131 GGTTGTTCA

       4636 AATACACTTT


Statistics
Matches: 269,  Mismatches: 11, Indels: 1
        0.96            0.04        0.00

Matches are distributed among these distances:
 141   91  0.34
 142  178  0.66

ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34


Consensus pattern (142 bp):   
GGAAAATTATTTGGGTTGAACGTTAAATATTTCACTTCTAGTGGTGGAAGCTTTAGTAGTACCTC
GAAACCCTTTCCCCGTTCTACGGATGAATTCTAGAATTTAAAATTGTGGCGGGGTAAGAAGCTGG
GGTTGTTCAGAG

Found at i:5606 original size:14 final size:14

Alignment explanation


    Indices: 5589--5616  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       5579 TATCTATACT

                          
       5589 ATATATAAAAGTAC
          1 ATATATAAAAGTAC

                          
       5603 ATATATAAAAGTAC
          1 ATATATAAAAGTAC

       5617 GAATAAGAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29


Consensus pattern (14 bp):   
ATATATAAAAGTAC

Found at i:5841 original size:24 final size:24

Alignment explanation


    Indices: 5809--5857  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5799 TTTTCGTCCA

                                    
       5809 AAACATTCTCCAAGTCGGTTTAGG
          1 AAACATTCTCCAAGTCGGTTTAGG

                                    
       5833 AAACATTCTCCAAGTCGGTTTAGG
          1 AAACATTCTCCAAGTCGGTTTAGG

             
       5857 A
          1 A

       5858 GAAGATCAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Consensus pattern (24 bp):   
AAACATTCTCCAAGTCGGTTTAGG
Done.