Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_730 ID=scaffold_730-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: 4211
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:931 original size:38 final size:39

Alignment explanation


    Indices: 889--1009  Score: 110
    Period size: 38  Copynumber: 3.1  Consensus size: 39

        879 ACTAACACAA

                            *        *              
        889 TAACAATAATAATT-GTTTTATACTGAAATAAT-ACTAAC
          1 TAACAATAATAATTAGGTTT-TACTAAAATAATAACTAAC

                                                     
        927 TAACAATAATAATTAGGGTTTTACTAAAATAATAACTAACC
          1 TAACAATAATAATTA-GGTTTTACTAAAATAATAACTAA-C

                *                  *                *
        968 ATAATAATAAT-ATTA-GTTTT-TTAACAATAAT-ACTAAG
          1 -TAACAATAATAATTAGGTTTTACTAA-AATAATAACTAAC

                 
       1005 TAACA
          1 TAACA

       1010 TCTAAACCCT


Statistics
Matches: 71,  Mismatches: 6, Indels: 14
        0.78            0.07        0.15

Matches are distributed among these distances:
  36    4  0.06
  38   22  0.31
  39   22  0.31
  40    9  0.13
  41    5  0.07
  42    9  0.13

ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36


Consensus pattern (39 bp):   
TAACAATAATAATTAGGTTTTACTAAAATAATAACTAAC

Found at i:1829 original size:52 final size:52

Alignment explanation


    Indices: 1751--1852  Score: 204
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       1741 TTTGTCAAAG

                                                                
       1751 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
          1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT

                                                              
       1803 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACT
          1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACT

       1853 AGTTGTGGCA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  52   50  1.00

ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30


Consensus pattern (52 bp):   
GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT

Found at i:2987 original size:28 final size:28

Alignment explanation


    Indices: 2926--2988  Score: 67
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       2916 TTTAAATTAA

                            *       *   
       2926 TAAAAATAAAATTATACTTTAATTTTTT
          1 TAAAAATAAAATTATAATTTAATTCTTT

                                           
       2954 TAAAAATATAAAAATT-TAATTTAA-TCTTT
          1 T-AAAA-AT-AAAATTATAATTTAATTCTTT

                  
       2983 TAAAAA
          1 TAAAAA

       2989 CCATAAAGAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 7
        0.77            0.05        0.18

Matches are distributed among these distances:
  27    1  0.03
  28    5  0.17
  29    9  0.30
  30    9  0.30
  31    6  0.20

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44


Consensus pattern (28 bp):   
TAAAAATAAAATTATAATTTAATTCTTT

Found at i:2995 original size:30 final size:31

Alignment explanation


    Indices: 2933--2995  Score: 76
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       2923 TAATAAAAAT

                     *       *         *   
       2933 AAAATTATACTTTAATTTTTTTAAAAATATA
          1 AAAATTATAATTTAATTCTTTTAAAAACATA

                                            
       2964 AAAATT-TAATTTAA-TCTTTTAAAAACCATA
          1 AAAATTATAATTTAATTCTTTTAAAAA-CATA

              
       2994 AA
          1 AA

       2996 GATATAAATT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  29   10  0.36
  30   12  0.43
  31    6  0.21

ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43


Consensus pattern (31 bp):   
AAAATTATAATTTAATTCTTTTAAAAACATA
Done.