Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_945 ID=scaffold_945-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: 2610
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.33

Warning! 420 characters in sequence are not A, C, G, or T


Found at i:350 original size:11 final size:12

Alignment explanation


    Indices: 333--362  Score: 53
    Period size: 11  Copynumber: 2.6  Consensus size: 12

        323 TTTCTACATT

                        
        333 TTTCTTCAGTTC
          1 TTTCTTCAGTTC

                        
        345 -TTCTTCAGTTC
          1 TTTCTTCAGTTC

                   
        356 TTTCTTC
          1 TTTCTTC

        363 TTTAGTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  11   11  0.65
  12    6  0.35

ACGTcount: A:0.07, C:0.27, G:0.07, T:0.60


Consensus pattern (12 bp):   
TTTCTTCAGTTC

Found at i:362 original size:15 final size:14

Alignment explanation


    Indices: 342--375  Score: 50
    Period size: 15  Copynumber: 2.4  Consensus size: 14

        332 TTTTCTTCAG

                           
        342 TTCTTCTTCAGTTCT
          1 TTCTTCTTCAGTT-T

                    *     
        357 TTCTTCTTTAGTTT
          1 TTCTTCTTCAGTTT

                 
        371 TTCTT
          1 TTCTT

        376 TTTTCTTTCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14    6  0.33
  15   12  0.67

ACGTcount: A:0.06, C:0.21, G:0.06, T:0.68


Consensus pattern (14 bp):   
TTCTTCTTCAGTTT

Found at i:1528 original size:9 final size:9

Alignment explanation


    Indices: 1510--1602  Score: 132
    Period size: 9  Copynumber: 10.3  Consensus size: 9

       1500 TCAGTTGAAC

                     
       1510 TAAATCGGT
          1 TAAATCGGT

               *     
       1519 TAAGTCGGT
          1 TAAATCGGT

               *     
       1528 TAAGTCGGT
          1 TAAATCGGT

                     
       1537 TAAATCGGT
          1 TAAATCGGT

                 *   
       1546 TAAATTGGT
          1 TAAATCGGT

               *     
       1555 TAAGTCGGT
          1 TAAATCGGT

                  *  
       1564 TAAATCAGT
          1 TAAATCGGT

                     
       1573 TAAATCGGT
          1 TAAATCGGT

               *     
       1582 TAAGTCGGT
          1 TAAATCGGT

                     
       1591 TAAATCGGT
          1 TAAATCGGT

               
       1600 TAA
          1 TAA

       1603 TTTTTAACCA


Statistics
Matches: 74,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   9   74  1.00

ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34


Consensus pattern (9 bp):   
TAAATCGGT

Found at i:1540 original size:27 final size:27

Alignment explanation


    Indices: 1510--1602  Score: 159
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       1500 TCAGTTGAAC

                        *              
       1510 TAAATCGGTTAAGTCGGTTAAGTCGGT
          1 TAAATCGGTTAAATCGGTTAAGTCGGT

                          *            
       1537 TAAATCGGTTAAATTGGTTAAGTCGGT
          1 TAAATCGGTTAAATCGGTTAAGTCGGT

                  *                    
       1564 TAAATCAGTTAAATCGGTTAAGTCGGT
          1 TAAATCGGTTAAATCGGTTAAGTCGGT

                        
       1591 TAAATCGGTTAA
          1 TAAATCGGTTAA

       1603 TTTTTAACCA


Statistics
Matches: 61,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   61  1.00

ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34


Consensus pattern (27 bp):   
TAAATCGGTTAAATCGGTTAAGTCGGT

Found at i:1739 original size:12 final size:12

Alignment explanation


    Indices: 1722--1746  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       1712 TACTAATTCG

                        
       1722 GGTCGGTTAACC
          1 GGTCGGTTAACC

                        
       1734 GGTCGGTTAACC
          1 GGTCGGTTAACC

             
       1746 G
          1 G

       1747 AATGCACACC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24


Consensus pattern (12 bp):   
GGTCGGTTAACC
Done.