Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_157 ID=scaffold_157-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: 10863
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.31

Warning! 280 characters in sequence are not A, C, G, or T


Found at i:1088 original size:41 final size:41

Alignment explanation


    Indices: 1043--1130  Score: 124
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       1033 ACTGGCAATG

                        *      *                      
       1043 AGCCTGCTAGACTTAAAGTTTGAATTAT-TTCACCGGCATTA
          1 AGCCTGCTAGACATAAAGTCTGAATTATATT-ACCGGCATTA

                    *                            *   
       1084 AGCCTGCTGGACATAAAGTCTGAATTATATTACCGGCCTTA
          1 AGCCTGCTAGACATAAAGTCTGAATTATATTACCGGCATTA

                  
       1125 AGCCTG
          1 AGCCTG

       1131 AAAATTTCCA


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  41   40  0.95
  42    2  0.05

ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Consensus pattern (41 bp):   
AGCCTGCTAGACATAAAGTCTGAATTATATTACCGGCATTA

Found at i:8450 original size:37 final size:37

Alignment explanation


    Indices: 8397--8470  Score: 130
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       8387 AGGCATATCT

                                                 
       8397 GCGGAGTCTAAAAAATTCCCGCTCATATTCAGTGACA
          1 GCGGAGTCTAAAAAATTCCCGCTCATATTCAGTGACA

                     * *                         
       8434 GCGGAGTCTCACAAATTCCCGCTCATATTCAGTGACA
          1 GCGGAGTCTAAAAAATTCCCGCTCATATTCAGTGACA

       8471 TTCATACGAC


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  37   35  1.00

ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24


Consensus pattern (37 bp):   
GCGGAGTCTAAAAAATTCCCGCTCATATTCAGTGACA

Found at i:9361 original size:17 final size:17

Alignment explanation


    Indices: 9328--9360  Score: 59
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       9318 AATATTAAAC

                             
       9328 ATATAATTTTAATTTTT
          1 ATATAATTTTAATTTTT

                             
       9345 ATAT-ATTTTAATTTTT
          1 ATATAATTTTAATTTTT

       9361 TTTCTAACCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   12  0.75
  17    4  0.25

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (17 bp):   
ATATAATTTTAATTTTT

Found at i:10543 original size:41 final size:42

Alignment explanation


    Indices: 10484--10599  Score: 130
    Period size: 41  Copynumber: 2.8  Consensus size: 42

      10474 ACCTGATTCA

                   *                                   
      10484 ATTCACCAGCAATT-AGCCTGCTAGACTTAAAGTTCGAATTA-
          1 ATTCACCGGC-ATTAAGCCTGCTAGACTTAAAGTTCGAATTAC

            *                     *   *      *   *    
      10525 TTTCACCGGCATTAAGCCTGCTGGACATAAAGTCCGACTTAC
          1 ATTCACCGGCATTAAGCCTGCTAGACTTAAAGTTCGAATTAC

                      *                 *     
      10567 ATT-ACCGGCCTTAAGCCTGCTAGACTTTAAGTT
          1 ATTCACCGGCATTAAGCCTGCTAGACTTAAAGTT

      10600 TGAAAATTTC


Statistics
Matches: 61,  Mismatches: 12, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  40    3  0.05
  41   56  0.92
  42    2  0.03

ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29


Consensus pattern (42 bp):   
ATTCACCGGCATTAAGCCTGCTAGACTTAAAGTTCGAATTAC
Done.