Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_307 ID=scaffold_307-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: 8577
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.32

Warning! 229 characters in sequence are not A, C, G, or T


Found at i:1789 original size:50 final size:50

Alignment explanation


    Indices: 1630--1920  Score: 302
    Period size: 50  Copynumber: 5.9  Consensus size: 50

       1620 GATAATAACA

                  *             *                   *  *    ***
       1630 TGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGA--TGTTTTCTATAC
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCT-CGG

                  *     *       *                **   *  *    
       1679 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATC-G
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG

                * *         * *            **                  
       1728 TGCCCATGCCATGTCCAAAACATGGTCTTACGGGGGACCT-TTCATCTCGG
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT-ATCTCGG

                  *                       *   *               
       1778 TGCCAAAGCCATGTCCCAGACATGGTCTTATATGAGACCTCTTATCTCGG
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG

              *          *                 *                  
       1828 TGTCAACGCCATGCCCCAGACATGGTCTTACTTGGGACCTCTTATCTCGG
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG

                                                       
       1878 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
          1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT

       1921 TACACAAATG


Statistics
Matches: 201,  Mismatches: 36, Indels: 9
        0.82            0.15        0.04

Matches are distributed among these distances:
  48    1  0.00
  49   70  0.35
  50  124  0.62
  51    6  0.03

ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29


Consensus pattern (50 bp):   
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG

Found at i:2291 original size:30 final size:30

Alignment explanation


    Indices: 2257--2314  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2247 CCTTGACTCG

                                          
       2257 AACTTTGGAAAAATTACAATTTTGCCCCTA
          1 AACTTTGGAAAAATTACAATTTTGCCCCTA

                  * * *       *         
       2287 AACTTTTGTATAATTACACTTTTGCCCC
          1 AACTTTGGAAAAATTACAATTTTGCCCC

       2315 AAAGCTCAAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACAATTTTGCCCCTA
Done.