Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_408 ID=scaffold_408-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: 7398
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:1410 original size:14 final size:14

Alignment explanation


    Indices: 1391--1420  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1381 TTTATTATAT

                          
       1391 AATTTAATCAGTTA
          1 AATTTAATCAGTTA

                          
       1405 AATTTAATCAGTTA
          1 AATTTAATCAGTTA

              
       1419 AA
          1 AA

       1421 ATAAATAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40


Consensus pattern (14 bp):   
AATTTAATCAGTTA

Found at i:1551 original size:7 final size:7

Alignment explanation


    Indices: 1506--1561  Score: 53
    Period size: 7  Copynumber: 7.7  Consensus size: 7

       1496 ACGTTGTGTA

                   
       1506 TTTAATT
          1 TTTAATT

                    
       1513 TTT-ATAT
          1 TTTAAT-T

                   
       1520 TTTAATT
          1 TTTAATT

                     
       1527 TGATT-ATT
          1 T--TTAATT

                   
       1535 TTTAATT
          1 TTTAATT

                    
       1542 TTTAATTT
          1 TTTAA-TT

                 * 
       1550 TTTAAAT
          1 TTTAATT

                 
       1557 TTTAA
          1 TTTAA

       1562 AATTTCATGT


Statistics
Matches: 42,  Mismatches: 1, Indels: 12
        0.76            0.02        0.22

Matches are distributed among these distances:
   6    4  0.10
   7   23  0.55
   8   13  0.31
   9    2  0.05

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68


Consensus pattern (7 bp):   
TTTAATT

Found at i:1551 original size:15 final size:14

Alignment explanation


    Indices: 1506--1560  Score: 58
    Period size: 15  Copynumber: 3.8  Consensus size: 14

       1496 ACGTTGTGTA

                        * 
       1506 TTTAATTTTTATAT
          1 TTTAATTTTTATTT

                            
       1520 TTTAATTTGATTA-TT
          1 TTTAATTT--TTATTT

                           
       1535 TTTAATTTTTAATTT
          1 TTTAATTTTT-ATTT

                 *     
       1550 TTTAAATTTTA
          1 TTTAATTTTTA

       1561 AAATTTCATG


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
  13    2  0.06
  14   10  0.29
  15   20  0.57
  16    3  0.09

ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69


Consensus pattern (14 bp):   
TTTAATTTTTATTT

Found at i:4737 original size:37 final size:37

Alignment explanation


    Indices: 4696--4769  Score: 148
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       4686 ATTACATAGT

                                                 
       4696 TATTGGCCACAAGGCATTCTTTGGGTCTTCAACTGCC
          1 TATTGGCCACAAGGCATTCTTTGGGTCTTCAACTGCC

                                                 
       4733 TATTGGCCACAAGGCATTCTTTGGGTCTTCAACTGCC
          1 TATTGGCCACAAGGCATTCTTTGGGTCTTCAACTGCC

       4770 ATCGCTCTAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32


Consensus pattern (37 bp):   
TATTGGCCACAAGGCATTCTTTGGGTCTTCAACTGCC

Found at i:5441 original size:28 final size:28

Alignment explanation


    Indices: 5401--5498  Score: 124
    Period size: 28  Copynumber: 3.5  Consensus size: 28

       5391 GGTGATCTAA

                                        
       5401 TTTGGGGATTTTGAGTAAGGGTTTTGAT
          1 TTTGGGGATTTTGAGTAAGGGTTTTGAT

                                        
       5429 TTTGGGGATTTTGAGTAAGGGTTTTGAT
          1 TTTGGGGATTTTGAGTAAGGGTTTTGAT

               *  *     * * *         *  
       5457 TTTAGGAATTTTTATTTAGGGTTTTTAAT
          1 TTTGGGGATTTTGAGTAAGGG-TTTTGAT

                 *       
       5486 TTTGGAGATTTTG
          1 TTTGGGGATTTTG

       5499 GGGATTTCTC


Statistics
Matches: 59,  Mismatches: 10, Indels: 1
        0.84            0.14        0.01

Matches are distributed among these distances:
  28   44  0.75
  29   15  0.25

ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51


Consensus pattern (28 bp):   
TTTGGGGATTTTGAGTAAGGGTTTTGAT
Done.