Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_335 ID=scaffold_335-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: 8087
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:5610 original size:22 final size:22

Alignment explanation


    Indices: 5585--5629  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5575 TGAGCAAATG

                                  
       5585 TTCTTTCATTCTTTACGATTTT
          1 TTCTTTCATTCTTTACGATTTT

                          **      
       5607 TTCTTTCATTCTTTTGGATTTT
          1 TTCTTTCATTCTTTACGATTTT

             
       5629 T
          1 T

       5630 CTGCCAAACC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.11, C:0.16, G:0.07, T:0.67


Consensus pattern (22 bp):   
TTCTTTCATTCTTTACGATTTT

Found at i:6559 original size:6 final size:7

Alignment explanation


    Indices: 6535--6590  Score: 62
    Period size: 7  Copynumber: 7.7  Consensus size: 7

       6525 AAAAATGGCG

                   
       6535 AAATGAA
          1 AAATGAA

                     
       6542 AAATGAAAA
          1 AAATG--AA

                   
       6551 AAATGAA
          1 AAATGAA

                    
       6558 AAGATG-A
          1 AA-ATGAA

                   
       6565 AAATGAA
          1 AAATGAA

                   
       6572 AAATGAA
          1 AAATGAA

                    
       6579 AAA-GTAA
          1 AAATG-AA

                 
       6586 AAATG
          1 AAATG

       6591 GAGAGGCTAA


Statistics
Matches: 43,  Mismatches: 0, Indels: 11
        0.80            0.00        0.20

Matches are distributed among these distances:
   6    4  0.09
   7   28  0.65
   8    4  0.09
   9    7  0.16

ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14


Consensus pattern (7 bp):   
AAATGAA

Found at i:7989 original size:50 final size:50

Alignment explanation


    Indices: 7836--8084  Score: 151
    Period size: 50  Copynumber: 5.0  Consensus size: 50

       7826 CGAAACCATA

                                      *                  *  **
       7836 GATCTTACTTCCTTAGCAGTGCAGTGAAACAGATTGAAGCTACGATGGCA
          1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTG

                 ***    *    * *    * **  *     *    *  *   ** 
       7886 GATCTGGTTTCCCT-GATATTGCAATTAAAAAGATTAAAGCCACAACGACG
          1 GATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGTG

                                                      *       
       7936 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTATGACGGTG
          1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTG

                 ***    *    * *    * **  *          *  *       
       7986 GATCTGGTTTCCCT-GATATTGCAATTAAAAAGATTGAAGCCACAACGGGTG
          1 GATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGAC-GGTG

            *                             *                 
       8037 AATCTTACTTCCTTAGCAGTGCAGTGGAACCGATTGAAGCTACGACGG
          1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGG

       8085 GCA


Statistics
Matches: 136,  Mismatches: 58, Indels: 10
        0.67            0.28        0.05

Matches are distributed among these distances:
  49    2  0.01
  50   98  0.72
  51   35  0.26
  52    1  0.01

ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27


Consensus pattern (50 bp):   
GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTG

Found at i:8009 original size:100 final size:100

Alignment explanation


    Indices: 7836--8084  Score: 401
    Period size: 100  Copynumber: 2.5  Consensus size: 100

       7826 CGAAACCATA

                                      *                  *                   
       7836 GATCTTACTTCCTTAGCAGTGCAGTGAAACAGATTGAAGCTACGATGGCAGATCTGGTTTCCCTG
          1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTG

                                                
       7901 ATATTGCAATTAAAAAGATTAAAGCCACAACGACG-
         66 ATATTGCAATTAAAAAGATTAAAGCCACAACG-CGT

                                                      *     **               
       7936 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTATGACGGTGGATCTGGTTTCCCTG
          1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTG

                                *           *  
       8001 ATATTGCAATTAAAAAGATTGAAGCCACAACGGGT
         66 ATATTGCAATTAAAAAGATTAAAGCCACAACGCGT

                                           *                 
       8036 GAATCTTACTTCCTTAGCAGTGCAGTGGAACCGATTGAAGCTACGACGG
          1 G-ATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGG

       8085 GCA


Statistics
Matches: 138,  Mismatches: 9, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
  99    1  0.01
 100   92  0.67
 101   45  0.33

ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27


Consensus pattern (100 bp):   
GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTG
ATATTGCAATTAAAAAGATTAAAGCCACAACGCGT
Done.