Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_94 ID=scaffold_94-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: 14618
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29


Found at i:11673 original size:22 final size:22

Alignment explanation


    Indices: 11645--11689  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      11635 GGGGTGTTAG

                                  
      11645 TGACAAAGCTTCATTGAACAAA
          1 TGACAAAGCTTCATTGAACAAA

                                  
      11667 TGACAAAGCTTCATTGAACAAA
          1 TGACAAAGCTTCATTGAACAAA

             
      11689 T
          1 T

      11690 AAGCAGTGAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24


Consensus pattern (22 bp):   
TGACAAAGCTTCATTGAACAAA

Found at i:12527 original size:50 final size:50

Alignment explanation


    Indices: 12471--12653  Score: 145
    Period size: 50  Copynumber: 3.7  Consensus size: 50

      12461 TTGGCATTAC

                                     *                        
      12471 AGTGGAAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGT
          1 AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT

                   *          *  *     *     ***     * *    * 
      12521 AGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACA-TAT
          1 AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT

              * **                                 *   * **    
      12570 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTTCCTAGTGGTGT
          1 -AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT

                               *  *     *     
      12621 AGT-GAAACAGATTGAAGCTACGACGGCAGATCT
          1 AGTGGAAA-AGATTGAAGCCACAACGGCGGATCT

      12654 GGTTTCCCCG


Statistics
Matches: 97,  Mismatches: 33, Indels: 6
        0.71            0.24        0.04

Matches are distributed among these distances:
  49    5  0.05
  50   90  0.93
  51    2  0.02

ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23


Consensus pattern (50 bp):   
AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT

Found at i:12683 original size:50 final size:50

Alignment explanation


    Indices: 12529--12676  Score: 138
    Period size: 50  Copynumber: 3.0  Consensus size: 50

      12519 GTAGTGGAAC

                                                        *      
      12529 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATAT-CAATTAAAA
          1 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACAT-TGCAGTTAAAA

                      *  *     *      **     **  ***  *   *   *
      12579 AGATTGAAGCCACAACGGCGGATCTTACTTTCCTAG-TGGTGTAGTGAAAC
          1 AGATTGAAGCTACGACGGCAGATC-TGGTTTCCCCGACATTGCAGTTAAAA

                                                            
      12629 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAA
          1 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAA

      12677 GTAGATTAAA


Statistics
Matches: 69,  Mismatches: 26, Indels: 6
        0.68            0.26        0.06

Matches are distributed among these distances:
  49    8  0.12
  50   54  0.78
  51    7  0.10

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25


Consensus pattern (50 bp):   
AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAAAA

Found at i:12683 original size:100 final size:100

Alignment explanation


    Indices: 12476--12667  Score: 330
    Period size: 100  Copynumber: 1.9  Consensus size: 100

      12466 ATTACAGTGG

                                                 *           *               
      12476 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTA
          1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA

                                               
      12541 CGACGGCAGATCTGGTTTCCCCGACATATCAATTA
         66 CGACGGCAGATCTGGTTTCCCCGACATATCAATTA

                                *            *     **                        
      12576 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCCTAGTGGTGTAGTGAAACAGATTGAAGCTA
          1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA

                                       
      12641 CGACGGCAGATCTGGTTTCCCCGACAT
         66 CGACGGCAGATCTGGTTTCCCCGACAT

      12668 TGCAGTTAAG


Statistics
Matches: 86,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 100   86  1.00

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23


Consensus pattern (100 bp):   
AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA
CGACGGCAGATCTGGTTTCCCCGACATATCAATTA

Found at i:14319 original size:3 final size:3

Alignment explanation


    Indices: 14294--14334  Score: 50
    Period size: 3  Copynumber: 14.3  Consensus size: 3

      14284 TTTTTTAAAT

                            *     *                                  
      14294 TTA TT- TTA TTA ATA TTG TTA TTA TTA TTA TTA TTA -TA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      14335 ATGTCATTAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
   2    4  0.12
   3   28  0.88

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (3 bp):   
TTA

Done.