Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_205 ID=scaffold_205-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: 9536
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32

Warning! 172 characters in sequence are not A, C, G, or T


Found at i:1795 original size:42 final size:42

Alignment explanation


    Indices: 1706--1846  Score: 212
    Period size: 42  Copynumber: 3.4  Consensus size: 42

       1696 GATCTTGGTA

                   *        *             *        *  
       1706 TCGCACATTTAGTGCCCGTTATTC-ACATCGTCATTTTAGTT
          1 TCGCACACTTAGTGCCTGTTATTCAACATCATCATTTTAATT

                       *                              
       1747 TCGCACACTTAATGCCTGTTATTCAACATCATCATTTTAATT
          1 TCGCACACTTAGTGCCTGTTATTCAACATCATCATTTTAATT

             *                                        
       1789 TTGCACACTTAGTGCCTGTTATTCAACATCATCATTTTAATT
          1 TCGCACACTTAGTGCCTGTTATTCAACATCATCATTTTAATT

              *             
       1831 TCCCACACTTAGTGCC
          1 TCGCACACTTAGTGCC

       1847 ATTCATATAG


Statistics
Matches: 90,  Mismatches: 9, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  41   21  0.23
  42   69  0.77

ACGTcount: A:0.24, C:0.26, G:0.11, T:0.40


Consensus pattern (42 bp):   
TCGCACACTTAGTGCCTGTTATTCAACATCATCATTTTAATT

Found at i:2983 original size:17 final size:15

Alignment explanation


    Indices: 2955--2987  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       2945 TTTAAAACAA

                           
       2955 AAATTTAGCACACAC
          1 AAATTTAGCACACAC

                           
       2970 AAATTTAGCACACAC
          1 AAATTTAGCACACAC

               
       2985 AAA
          1 AAA

       2988 AAGTAATTTT


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

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18


Consensus pattern (15 bp):   
AAATTTAGCACACAC
Done.