Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_655 ID=scaffold_655-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: 6265
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.25

Warning! 1362 characters in sequence are not A, C, G, or T


Found at i:202 original size:17 final size:18

Alignment explanation


    Indices: 188--271  Score: 80
    Period size: 19  Copynumber: 4.4  Consensus size: 18

        178 ATAATCTTCG

                              
        188 AGGATATGCAATCTTAGA
          1 AGGATATGCAATCTTAGA

              *                
        206 TATGATATGCAATCTTAGA
          1 -AGGATATGCAATCTTAGA

                 *               
        225 TATGATATATGCAATCTTAGA
          1 -A-G-GATATGCAATCTTAGA

              *      *         
        246 TATGATATGTAATCTTAGA
          1 -AGGATATGCAATCTTAGA

                    
        265 A-GATATG
          1 AGGATATG

        272 ATTTTCTAAT


Statistics
Matches: 57,  Mismatches: 6, Indels: 6
        0.83            0.09        0.09

Matches are distributed among these distances:
  17    6  0.11
  18    1  0.02
  19   33  0.58
  21   17  0.30

ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36


Consensus pattern (18 bp):   
AGGATATGCAATCTTAGA

Found at i:214 original size:19 final size:19

Alignment explanation


    Indices: 190--264  Score: 123
    Period size: 19  Copynumber: 3.8  Consensus size: 19

        180 AATCTTCGAG

                               
        190 GATATGCAATCTTAGATAT
          1 GATATGCAATCTTAGATAT

                               
        209 GATATGCAATCTTAGATAT
          1 GATATGCAATCTTAGATAT

                                 
        228 GATATATGCAATCTTAGATAT
          1 G--ATATGCAATCTTAGATAT

                  *         
        249 GATATGTAATCTTAGA
          1 GATATGCAATCTTAGA

        265 AGATATGATT


Statistics
Matches: 53,  Mismatches: 1, Indels: 4
        0.91            0.02        0.07

Matches are distributed among these distances:
  19   34  0.64
  21   19  0.36

ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37


Consensus pattern (19 bp):   
GATATGCAATCTTAGATAT

Found at i:236 original size:21 final size:21

Alignment explanation


    Indices: 191--253  Score: 112
    Period size: 21  Copynumber: 3.1  Consensus size: 21

        181 ATCTTCGAGG

                                 
        191 ATATGCAATCTTAGATATG--
          1 ATATGCAATCTTAGATATGAT

                                 
        210 ATATGCAATCTTAGATATGAT
          1 ATATGCAATCTTAGATATGAT

                                 
        231 ATATGCAATCTTAGATATGAT
          1 ATATGCAATCTTAGATATGAT

              
        252 AT
          1 AT

        254 GTAATCTTAG


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   19  0.45
  21   23  0.55

ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38


Consensus pattern (21 bp):   
ATATGCAATCTTAGATATGAT

Found at i:489 original size:19 final size:21

Alignment explanation


    Indices: 465--503  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 21

        455 CTTATTGTTT

                  *              
        465 TTTTTTTCTT-TTT-CGATTA
          1 TTTTTTACTTATTTACGATTA

                                
        484 TTTTTTACTTATTTACGATT
          1 TTTTTTACTTATTTACGATT

        504 TTAAAAAAGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    9  0.53
  20    3  0.18
  21    5  0.29

ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69


Consensus pattern (21 bp):   
TTTTTTACTTATTTACGATTA

Done.