Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_195 ID=scaffold_195-JGI_221_v2.0

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: 10478
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.29

Warning! 969 characters in sequence are not A, C, G, or T


Found at i:4136 original size:33 final size:34

Alignment explanation


    Indices: 4094--4158  Score: 96
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       4084 AGTAAAATGG

                             *         *      
       4094 TTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
          1 TTTCCGTAAAATGACTTACTGGAAAATATTTTAC

                *                           
       4127 TTTCTGTAAAATGACTTACTGGAAAATATTTT
          1 TTTCCGTAAAATGACTTACTGGAAAATATTTT

       4159 CTAGTGTTTG


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  33   13  0.46
  34   15  0.54

ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43


Consensus pattern (34 bp):   
TTTCCGTAAAATGACTTACTGGAAAATATTTTAC

Found at i:4145 original size:19 final size:19

Alignment explanation


    Indices: 4108--4146  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4098 CGTAAAATGA

                         **    
       4108 TTTCTGGAAAATGTTTTAC
          1 TTTCTGGAAAATGACTTAC

                  *            
       4127 TTTCTGTAAAATGACTTAC
          1 TTTCTGGAAAATGACTTAC

             
       4146 T
          1 T

       4147 GGAAAATATT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46


Consensus pattern (19 bp):   
TTTCTGGAAAATGACTTAC

Found at i:5694 original size:27 final size:27

Alignment explanation


    Indices: 5664--5733  Score: 79
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       5654 AATAATCAAT

                             *          
       5664 TCAATATCCAACAATGTTAAAACATA-A
          1 TCAATATCCAACAAT-TCAAAACATATA

                    *           *       
       5691 TCAATATCTAACAAATTCAAGACATATA
          1 TCAATATCCAAC-AATTCAAAACATATA

                *          
       5719 TCAAAATCCAACAAT
          1 TCAATATCCAACAAT

       5734 CTAAAATTTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  27   22  0.61
  28   14  0.39

ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26


Consensus pattern (27 bp):   
TCAATATCCAACAATTCAAAACATATA

Found at i:9332 original size:13 final size:13

Alignment explanation


    Indices: 9314--9339  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9304 CCAGAAACTG

                         
       9314 ATTTGCAGAAAAC
          1 ATTTGCAGAAAAC

                         
       9327 ATTTGCAGAAAAC
          1 ATTTGCAGAAAAC

       9340 TACCCATTTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23


Consensus pattern (13 bp):   
ATTTGCAGAAAAC

Found at i:9956 original size:2 final size:2

Alignment explanation


    Indices: 9949--9990  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       9939 TTATTAATTA

                                              *                           
       9949 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9991 CTATTGTATT


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:10258 original size:2 final size:2

Alignment explanation


    Indices: 10195--10238  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      10185 ATGTATAGTG

                                                                          
      10195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
      10237 TA
          1 TA

      10239 AGGTTCTAAT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA
Done.