Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_78 ID=scaffold_78-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: 16405
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:5299 original size:91 final size:90

Alignment explanation


    Indices: 5150--5318  Score: 230
    Period size: 91  Copynumber: 1.9  Consensus size: 90

       5140 TACCCACAAA

                 *                    *            *      * *                
       5150 TTACTTGCAACTTTTATCTGCAAACTTGTTGTGTATTCACAACCACTGGCAGCGTATTAACCTAC
          1 TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC

                                      
       5215 AAACACTAGTGGTTTATCCATAATTT
         66 -AACACTAGTGGTTTATCCATAATTT

                             *                         *     *   *         * 
       5241 TTACTGGCAACTTTTATTTGCAAACTCGTTGTGTATTCAAAACTACCGATAGCTTATTAACCTGC
          1 TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC

              *          
       5306 AATACTAGTGGTT
         66 AACACTAGTGGTT

       5319 CATCAATGAC


Statistics
Matches: 67,  Mismatches: 11, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  90   12  0.18
  91   55  0.82

ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37


Consensus pattern (90 bp):   
TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC
AACACTAGTGGTTTATCCATAATTT

Found at i:8496 original size:45 final size:45

Alignment explanation


    Indices: 8436--8605  Score: 214
    Period size: 45  Copynumber: 3.8  Consensus size: 45

       8426 TAGGCACTTA

                *   *                        *  *        
       8436 TGTGCCGACTACTGTTACTGTTACTGTTACCGACTCGGCACTTTG
          1 TGTGTCGAATACTGTTACTGTTACTGTTACCGATTCAGCACTTTG

                               *         *        *      
       8481 TGTGTCGAATACTGTTACTATTACTGTTATCGATTCAGTACTTTG
          1 TGTGTCGAATACTGTTACTGTTACTGTTACCGATTCAGCACTTTG

                  *           *           *              
       8526 TGTGTCAAATACTGTTACCGTTACTGTTACAGATTCAGCACTTTG
          1 TGTGTCGAATACTGTTACTGTTACTGTTACCGATTCAGCACTTTG

                 *              *   *     *    
       8571 TGTGTTGAATACTGTTACTGCTACCGTTACTGATT
          1 TGTGTCGAATACTGTTACTGTTACTGTTACCGATT

       8606 ACTGTATACT


Statistics
Matches: 106,  Mismatches: 19, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  45  106  1.00

ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40


Consensus pattern (45 bp):   
TGTGTCGAATACTGTTACTGTTACTGTTACCGATTCAGCACTTTG

Found at i:13569 original size:20 final size:20

Alignment explanation


    Indices: 13552--13594  Score: 68
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      13542 TATGACAATG

                                
      13552 TTTAAAAATTTTATACAAAA
          1 TTTAAAAATTTTATACAAAA

               **               
      13572 TTTTTAAATTTTATACAAAA
          1 TTTAAAAATTTTATACAAAA

               
      13592 TTT
          1 TTT

      13595 TGAAAACAAA


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

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49


Consensus pattern (20 bp):   
TTTAAAAATTTTATACAAAA

Found at i:13573 original size:12 final size:12

Alignment explanation


    Indices: 13556--13595  Score: 52
    Period size: 12  Copynumber: 3.7  Consensus size: 12

      13546 ACAATGTTTA

                        
      13556 AAAATTTTATAC
          1 AAAATTTTATAC

                        
      13568 AAAATTTT-T--
          1 AAAATTTTATAC

                        
      13577 -AAATTTTATAC
          1 AAAATTTTATAC

                    
      13588 AAAATTTT
          1 AAAATTTT

      13596 GAAAACAAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 8
        0.75            0.00        0.25

Matches are distributed among these distances:
   8    7  0.29
   9    1  0.04
  11    1  0.04
  12   15  0.62

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (12 bp):   
AAAATTTTATAC

Found at i:13595 original size:20 final size:20

Alignment explanation


    Indices: 13557--13595  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      13547 CAATGTTTAA

                                
      13557 AAATTTTATACAAAATTTTT
          1 AAATTTTATACAAAATTTTT

                               
      13577 AAATTTTATACAAAATTTT
          1 AAATTTTATACAAAATTTT

      13596 GAAAACAAAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49


Consensus pattern (20 bp):   
AAATTTTATACAAAATTTTT

Found at i:13769 original size:47 final size:49

Alignment explanation


    Indices: 13718--13820  Score: 129
    Period size: 47  Copynumber: 2.1  Consensus size: 49

      13708 GAATACTATT

                                            *           *    
      13718 TAAAAATATTATTAAAAATAAAAAACTATAT-GAA-ATTTAAAATTGTC
          1 TAAAAATATTATTAAAAATAAAAAACTATATAAAATATTTAAAACTGTC

                      *        *   *   *                    *
      13765 TAAAAATATTTTTAAAAATTAAATACTTTATAAAATATTTAAAACTGTT
          1 TAAAAATATTATTAAAAATAAAAAACTATATAAAATATTTAAAACTGTC

                   
      13814 TAAAAAT
          1 TAAAAAT

      13821 CCTAAACCCT


Statistics
Matches: 47,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  47   27  0.57
  48    2  0.04
  49   18  0.38

ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38


Consensus pattern (49 bp):   
TAAAAATATTATTAAAAATAAAAAACTATATAAAATATTTAAAACTGTC
Done.