Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_125 ID=scaffold_125-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: 11884
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33


Found at i:4707 original size:4 final size:4

Alignment explanation


    Indices: 4698--4776  Score: 52
    Period size: 4  Copynumber: 18.2  Consensus size: 4

       4688 ACAAATAAAA

                                                           *             
       4698 AAAG AAAG AAAG AAAAG AAAG CCAAAG CCAAACG AAA- ATAG AAAGG AAAG
          1 AAAG AAAG AAAG -AAAG AAAG --AAAG --AAA-G AAAG AAAG AAA-G AAAG

                    *            **             
       4748 AAAG AAAA AAAG AAAG AGTG AAAG AAAG A
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG A

       4777 CGCAAGGCTA


Statistics
Matches: 61,  Mismatches: 8, Indels: 12
        0.75            0.10        0.15

Matches are distributed among these distances:
   3    2  0.03
   4   38  0.62
   5   11  0.18
   6    9  0.15
   7    1  0.02

ACGTcount: A:0.68, C:0.06, G:0.23, T:0.03


Consensus pattern (4 bp):   
AAAG

Found at i:8180 original size:41 final size:41

Alignment explanation


    Indices: 8135--8318  Score: 191
    Period size: 41  Copynumber: 4.6  Consensus size: 41

       8125 CTTCGAGTCT

                                                     
       8135 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG
          1 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG

                           *                   * **  
       8176 ATGAGACACTGGGTGCCAA-TT--TACTTCGG-TTTAGCCG
          1 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG

                               *   *   *   *          
       8213 ATGAGACACTGGGTGTCAAATTATTACCTCGAATT-A-TCTG
          1 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC-G

                                   *               * 
       8253 ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTTG
          1 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG

                 **   *    *         
       8294 ATGAGGTACTAGGTGCCAATTTACT
          1 ATGAGACACTGGGTGTCAATTTACT

       8319 TCAGTTTAGC


Statistics
Matches: 118,  Mismatches: 18, Indels: 14
        0.79            0.12        0.09

Matches are distributed among these distances:
  37   23  0.19
  38   10  0.08
  39    1  0.01
  40   41  0.35
  41   42  0.36
  42    1  0.01

ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33


Consensus pattern (41 bp):   
ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG

Found at i:8267 original size:40 final size:40

Alignment explanation


    Indices: 8135--8390  Score: 195
    Period size: 40  Copynumber: 6.5  Consensus size: 40

       8125 CTTCGAGTCT

                               *   *       *          
       8135 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAAT-TCG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATCT-G

                             *             **   * * 
       8176 ATGAGACACTGGGTG-CCAA-T-TTACTTCGGTTTAGCCG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG

                                       *            
       8213 ATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCTG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG

                               *   *       *      *  
       8253 ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTTG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATCTG

                 **   *      *               *   *   
       8294 ATGAGGTACTAGGTG-CCAA-T-TTACTTC-AGTTTAGCTG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGA-ATTATCTG

               *       *                          * 
       8331 ATGGGACACTGTGTGTCAAATTATTACTTCGAATTATCCG
          1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG

                 *    *    *    
       8371 ATGAGGCACTAGGTGCCAAA
          1 ATGAGACACTGGGTGTCAAA

       8391 CTGGTGTGTT


Statistics
Matches: 164,  Mismatches: 41, Indels: 21
        0.73            0.18        0.09

Matches are distributed among these distances:
  37   30  0.18
  38   24  0.15
  39    4  0.02
  40   74  0.45
  41   32  0.20

ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32


Consensus pattern (40 bp):   
ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG

Found at i:8347 original size:118 final size:118

Alignment explanation


    Indices: 8135--8385  Score: 385
    Period size: 118  Copynumber: 2.1  Consensus size: 118

       8125 CTTCGAGTCT

                                   *                           *             
       8135 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCGATGAGACACTGGGTGCCAATTTAC
          1 ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTCGATGAGACACTAGGTGCCAATTTAC

               *                                               * 
       8200 TTCGGTTTAGCCGATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCTG
         66 TTCAGTTTAGCCGATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCCG

                                                   *      **                 
       8253 ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTTGATGAGGTACTAGGTGCCAATTTAC
          1 ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTCGATGAGACACTAGGTGCCAATTTAC

                       *    *       *               *            
       8318 TTCAGTTTAGCTGATGGGACACTGTGTGTCAAATTATTACTTCGAATTATCCG
         66 TTCAGTTTAGCCGATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCCG

                 *    *    
       8371 ATGAGGCACTAGGTG
          1 ATGAGACACTGGGTG

       8386 CCAAACTGGT


Statistics
Matches: 120,  Mismatches: 13, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 118  120  1.00

ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33


Consensus pattern (118 bp):   
ATGAGACACTGGGTGTCAATTTAATACTTCGGATTAATTCGATGAGACACTAGGTGCCAATTTAC
TTCAGTTTAGCCGATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCCG

Found at i:11437 original size:12 final size:12

Alignment explanation


    Indices: 11420--11449  Score: 60
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      11410 TCGGTGTTCT

                        
      11420 TGGTGGCAGCAG
          1 TGGTGGCAGCAG

                        
      11432 TGGTGGCAGCAG
          1 TGGTGGCAGCAG

                  
      11444 TGGTGG
          1 TGGTGG

      11450 GTGTTACGCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.13, C:0.13, G:0.53, T:0.20


Consensus pattern (12 bp):   
TGGTGGCAGCAG
Done.