Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_588 ID=scaffold_588-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: 5598
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.31

Warning! 143 characters in sequence are not A, C, G, or T


Found at i:1360 original size:12 final size:12

Alignment explanation


    Indices: 1345--1415  Score: 56
    Period size: 12  Copynumber: 5.9  Consensus size: 12

       1335 TCACTCTCAT

                        
       1345 TTTCTTTTTCAA
          1 TTTCTTTTTCAA

                          
       1357 TTTCTTGTTTTC--
          1 TTTC-T-TTTTCAA

                * *    *
       1369 TTTCATGTTCAT
          1 TTTCTTTTTCAA

                        
       1381 TTTCTTTTTCAA
          1 TTTCTTTTTCAA

                     ***
       1393 TTTCTTTTTGTT
          1 TTTCTTTTTCAA

                       
       1405 TTTCTTTTTCA
          1 TTTCTTTTTCA

       1416 CATGCTATTT


Statistics
Matches: 45,  Mismatches: 10, Indels: 8
        0.71            0.16        0.13

Matches are distributed among these distances:
  10    4  0.09
  12   35  0.78
  13    1  0.02
  14    5  0.11

ACGTcount: A:0.10, C:0.15, G:0.04, T:0.70


Consensus pattern (12 bp):   
TTTCTTTTTCAA

Found at i:3904 original size:17 final size:19

Alignment explanation


    Indices: 3871--3916  Score: 53
    Period size: 18  Copynumber: 2.5  Consensus size: 19

       3861 TAAACCTGGA

                               
       3871 ATTTTTTTTCAACACTTC-
          1 ATTTTTTTTCAACACTTCG

                                
       3889 ATTTTTTTT-ATA-ACTTCG
          1 ATTTTTTTTCA-ACACTTCG

                      
       3907 TATTTTTTTT
          1 -ATTTTTTTT

       3917 TCTTTTTTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  17    6  0.24
  18   10  0.40
  19    9  0.36

ACGTcount: A:0.20, C:0.13, G:0.02, T:0.65


Consensus pattern (19 bp):   
ATTTTTTTTCAACACTTCG

Found at i:5251 original size:20 final size:20

Alignment explanation


    Indices: 5218--5262  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       5208 TAAATTCACA

                                 
       5218 TAATTAAAACAAGACAC-AAT
          1 TAATTAAAACAAGAC-CTAAT

                    **          
       5238 TAATTAAATTAAGACCTAAT
          1 TAATTAAAACAAGACCTAAT

                 
       5258 TAATT
          1 TAATT

       5263 CGGTTAGGAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    1  0.05
  20   21  0.95

ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31


Consensus pattern (20 bp):   
TAATTAAAACAAGACCTAAT
Done.