Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_789 ID=scaffold_789-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: 5286
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.25

Warning! 1575 characters in sequence are not A, C, G, or T


Found at i:4425 original size:33 final size:33

Alignment explanation


    Indices: 4362--4436  Score: 89
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       4352 AGCACTCTCT

                *                 *  *       
       4362 TCTTCTTCACTCATTTCTTGTTGAAGCTCTCGC
          1 TCTTTTTCACTCATTTCTTGTTCAAACTCTCGC

                                            **
       4395 TCTTTTTCACTCAATTTCTT-TTCAAACTCTCTT
          1 TCTTTTTCACTC-ATTTCTTGTTCAAACTCTCGC

                     
       4428 TCTTTTTCA
          1 TCTTTTTCA

       4437 ATCTCTTTTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  33   29  0.81
  34    7  0.19

ACGTcount: A:0.15, C:0.28, G:0.05, T:0.52


Consensus pattern (33 bp):   
TCTTTTTCACTCATTTCTTGTTCAAACTCTCGC

Found at i:4453 original size:18 final size:17

Alignment explanation


    Indices: 4409--4463  Score: 65
    Period size: 18  Copynumber: 3.1  Consensus size: 17

       4399 TTTCACTCAA

                       *    *
       4409 TTTCTTTTCAAACTCTC
          1 TTTCTTTTCAATCTCTT

                              
       4426 TTTCTTTTTCAATCTCTT
          1 TTTC-TTTTCAATCTCTT

                       *      
       4444 TTTGCTTTTCACTCTCTT
          1 TTT-CTTTTCAATCTCTT

              
       4462 TT
          1 TT

       4464 GTTTTTGAAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  17    4  0.12
  18   28  0.85
  19    1  0.03

ACGTcount: A:0.11, C:0.25, G:0.02, T:0.62


Consensus pattern (17 bp):   
TTTCTTTTCAATCTCTT

Found at i:4516 original size:15 final size:15

Alignment explanation


    Indices: 4476--4522  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       4466 TTTTGAAATC

                      * *  
       4476 TCATTTTCATATATT
          1 TCATTTTCATTTCTT

              *            
       4491 TCTTTTTCATTTCTT
          1 TCATTTTCATTTCTT

                            
       4506 TCATTTTCATTTTCTT
          1 TCATTTTCA-TTTCTT

             
       4522 T
          1 T

       4523 ATTCTTTTCT


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  15   20  0.74
  16    7  0.26

ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68


Consensus pattern (15 bp):   
TCATTTTCATTTCTT

Found at i:5137 original size:14 final size:16

Alignment explanation


    Indices: 5118--5151  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5108 TAAACAACAG

                            
       5118 CAATTG-AA-CCTCAC
          1 CAATTGAAATCCTCAC

                            
       5132 CAATTGAAATCCTCAC
          1 CAATTGAAATCCTCAC

                
       5148 CAAT
          1 CAAT

       5152 CTCTCGCAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    6  0.33
  15    2  0.11
  16   10  0.56

ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24


Consensus pattern (16 bp):   
CAATTGAAATCCTCAC

Done.