Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_200 ID=scaffold_200-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: 10239
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.30

Warning! 835 characters in sequence are not A, C, G, or T


Found at i:1957 original size:25 final size:25

Alignment explanation


    Indices: 1861--1986  Score: 64
    Period size: 25  Copynumber: 5.1  Consensus size: 25

       1851 CATTAGGGAT

                                      
       1861 TACCGATT-ACAGCTCGT-ATGAGCA
          1 TACCGATTCACAGCTCGTGA-GAGCA

               *     *          * ***
       1885 TACTGATT-GCAGCTCGTGAAATTT
          1 TACCGATTCACAGCTCGTGAGAGCA

               *     *  *   *        *
       1909 TACAGATTCTCAACTCAT-ATGAGCT
          1 TACCGATTCACAGCTCGTGA-GAGCA

                    *                
       1934 TACCGATTTACAGCTCGTGAGAGCA
          1 TACCGATTCACAGCTCGTGAGAGCA

              *       *               
       1959 TATCGATTCATAGCTCGT-ATGAGCA
          1 TACCGATTCACAGCTCGTGA-GAGCA

               
       1984 TAC
          1 TAC

       1987 ATGTACAGGC


Statistics
Matches: 74,  Mismatches: 23, Indels: 9
        0.70            0.22        0.08

Matches are distributed among these distances:
  24   25  0.34
  25   48  0.65
  26    1  0.01

ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30


Consensus pattern (25 bp):   
TACCGATTCACAGCTCGTGAGAGCA

Found at i:9289 original size:22 final size:22

Alignment explanation


    Indices: 9245--9289  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9235 GGTAATTTTT

                           *      
       9245 CCAAAAATATGTTTTTGACTAA
          1 CCAAAAATATGTTTTCGACTAA

                              *   
       9267 CCAAAAATATGTTTTCGATTAA
          1 CCAAAAATATGTTTTCGACTAA

             
       9289 C
          1 C

       9290 TTGAATGAAA


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

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36


Consensus pattern (22 bp):   
CCAAAAATATGTTTTCGACTAA

Found at i:9641 original size:25 final size:25

Alignment explanation


    Indices: 9613--9740  Score: 104
    Period size: 25  Copynumber: 5.2  Consensus size: 25

       9603 TAGCTGGTGA

                   *                 
       9613 GAGCTTACCGATTCTCAGCTCGTAT
          1 GAGCTTATCGATTCTCAGCTCGTAT

                *         *           
       9638 GAGCATATCGATT-GCAGCTCGTGA-
          1 GAGCTTATCGATTCTCAGCTCGT-AT

             *       *  *            
       9662 GCGCTTATCAATACTCAGCTCGTAT
          1 GAGCTTATCGATTCTCAGCTCGTAT

                   *                   
       9687 GAGCTTACCGATT-TACAGCTCGTGA-
          1 GAGCTTATCGATTCT-CAGCTCGT-AT

                *                *    
       9712 GAGCATATCGATTCAT-AGCTAGTAT
          1 GAGCTTATCGATTC-TCAGCTCGTAT

                
       9737 GAGC
          1 GAGC

       9741 ATACATGTAC


Statistics
Matches: 80,  Mismatches: 15, Indels: 16
        0.72            0.14        0.14

Matches are distributed among these distances:
  24   20  0.25
  25   58  0.73
  26    1  0.01
  27    1  0.01

ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29


Consensus pattern (25 bp):   
GAGCTTATCGATTCTCAGCTCGTAT

Found at i:9679 original size:49 final size:49

Alignment explanation


    Indices: 9594--9744  Score: 178
    Period size: 49  Copynumber: 3.1  Consensus size: 49

       9584 CGTTAGGGAT

                     *    *           *                      
       9594 TACCGATTGTAGCTGGTGAGAGCTTACCGATTCTCAGCTCGTATGAGCA
          1 TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA

              *                 *       *  *                *
       9643 TATCGATTGCAGCTCGTGAGCGCTTATCAATACTCAGCTCGTATGAGCT
          1 TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA

                     *              *                *         
       9692 TACCGATTTACAGCTCGTGAGAGCATATCGATTCAT-AGCTAGTATGAGCA
          1 TACCGA-TTGCAGCTCGTGAGAGCTTATCGATTC-TCAGCTCGTATGAGCA

               
       9742 TAC
          1 TAC

       9745 ATGTACAGGA


Statistics
Matches: 84,  Mismatches: 16, Indels: 3
        0.82            0.16        0.03

Matches are distributed among these distances:
  49   46  0.55
  50   37  0.44
  51    1  0.01

ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29


Consensus pattern (49 bp):   
TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA
Done.