Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_392 ID=scaffold_392-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: 7550
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32


Found at i:7014 original size:38 final size:38

Alignment explanation


    Indices: 6942--7017  Score: 100
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       6932 ATGCCAAAAG

                   *                 **           
       6942 CATATATTTATACTTATCAACCACATGTGCCGAATGCA
          1 CATATATATATACTTATCAACCACACATGCCGAATGCA

                                          *        
       6980 CATATATATATACTTAT-AATCCACACATGTCGAATGCA
          1 CATATATATATACTTATCAA-CCACACATGCCGAATGCA

       7018 TACACATATG


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  37    2  0.06
  38   31  0.94

ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32


Consensus pattern (38 bp):   
CATATATATATACTTATCAACCACACATGCCGAATGCA

Found at i:7245 original size:41 final size:41

Alignment explanation


    Indices: 7195--7316  Score: 163
    Period size: 41  Copynumber: 3.0  Consensus size: 41

       7185 TTAATTTAAA

                                                      
       7195 CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
          1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT

                                          **         
       7237 CAGATCACCGGCACTTAGCCTGCTAGGCTTCTAGCCTGATT
          1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT

               *    * *        *          * *      
       7278 CAGTTCACTGCCACTTAGCTTGCTAGGCTTTACGCCTGA
          1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGA

       7317 ATTGATTCAC


Statistics
Matches: 71,  Mismatches: 9, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  41   67  0.94
  42    4  0.06

ACGTcount: A:0.20, C:0.30, G:0.21, T:0.28


Consensus pattern (41 bp):   
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT

Found at i:7326 original size:41 final size:39

Alignment explanation


    Indices: 7197--7346  Score: 151
    Period size: 41  Copynumber: 3.7  Consensus size: 39

       7187 AATTTAAACA

                                          *         
       7197 GATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
          1 GATTCACCGGCACTTAGCCTGCTAGGCTT-TAGCCTGATT

                                                      
       7237 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTCTAGCCTGATT
          1 --GATTCACCGGCACTTAGCCTGCTAGGCTT-TAGCCTGATT

            *       * *        *                      
       7278 CAGTTCACTGCCACTTAGCTTGCTAGGCTTTACGCCTGAATT
          1 GA-TTCACCGGCACTTAGCCTGCTAGGCTTTA-GCCTG-ATT

                   *    *               
       7320 GATTCACTGGCAATATA-CCTGCTAGGC
          1 GATTCACCGGCACT-TAGCCTGCTAGGC

       7347 GCTGAGCCTG


Statistics
Matches: 93,  Mismatches: 10, Indels: 11
        0.82            0.09        0.10

Matches are distributed among these distances:
  39    1  0.01
  40    2  0.02
  41   82  0.88
  42    8  0.09

ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29


Consensus pattern (39 bp):   
GATTCACCGGCACTTAGCCTGCTAGGCTTTAGCCTGATT

Found at i:7355 original size:82 final size:81

Alignment explanation


    Indices: 7207--7357  Score: 182
    Period size: 82  Copynumber: 1.8  Consensus size: 81

       7197 GATTCACCGG

                                                       *               *     
       7207 CACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTCTAGC
          1 CACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACCGGCAATTAGCCTGCTAGGCTGCTAGC

                             
       7272 CTGATTCAGTTCACTGC
         65 CTGATTCAGTTCACTGC

                    *          * *                 *                         
       7289 CACTTAGCTTGCTAGGCTTTACGCCTGAATT-GATTCACTGGCAATATA-CCTGCTAGGC-GCTG
          1 CACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCACCGGCAAT-TAGCCTGCTAGGCTGCT-

                   
       7351 AGCCTGA
         62 AGCCTGA

       7358 ATACTCAATT


Statistics
Matches: 59,  Mismatches: 6, Indels: 8
        0.81            0.08        0.11

Matches are distributed among these distances:
  81    4  0.07
  82   50  0.85
  83    5  0.08

ACGTcount: A:0.21, C:0.28, G:0.22, T:0.28


Consensus pattern (81 bp):   
CACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCACCGGCAATTAGCCTGCTAGGCTGCTAGCC
TGATTCAGTTCACTGC
Done.