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MatrixPlot 1.2: MP format

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

The mp (matrix plot) format is also a column format. The identifiers (first word in a line) can either be R, B, I, and M. The "R" line provide the range (in horizontal and vertical directions) of the matrix plot. Four numbers are used: xstart, xend, ystart; "B" lines encode for the bars along the edges (max two); "I" lines encode for the sequence logo profile along the edges; "M" lines encode for the 2D positions in the matrix plot along with a value that is represented by a color on the plot. The first column in I and B lines must always indicate the position in sequence (alignment). In I lines the two following numbers must be the value of the sequence information and the frequency of gaps. The B lines can have arbitrarily many columns, but normally only the two first are used, either to encode a graphical bar (by numbers that correspond to colors) or by the text string given. However, all the columns of the B lines can be combined to one string that can be displayed along the edges of the matrixplot. The numbers that can be used for a bar are 0,1,...,8. These have fixed rgb values. Two examples are given below, a mutual information example and a distance matrix example.


Mutual information example:

R  1 25 1 25
I      1   2.000000  0.000000
I      2   2.000000  0.000000
I      3   1.016644  0.083333
I      4  -0.717765  0.583333
I      5   0.282235  0.166667
I      6   0.581704  0.000000
I      7   0.811278  0.000000
I      8   0.448902  0.000000
I      9   0.385995  0.000000
I     10   0.719328  0.000000
I     11  -0.311278  0.750000
I     12   0.219328  0.083333
I     13   1.586183  0.000000
I     14   1.586183  0.000000
I     15   2.000000  0.000000
I     16   2.000000  0.000000
I     17   1.586183  0.000000
I     18   0.615568  0.000000
I     19   2.000000  0.000000
I     20   1.349978  0.000000
I     21  -0.729574  0.500000
I     22   0.719328  0.000000
I     23   0.385995  0.000000
I     24   0.448902  0.000000
I     25   0.811278  0.000000
M      1     2    0.000000
M      1     3    0.000000
M      1     4    0.000000
M      1     5    0.000000
M      1     6    0.000000
M      1     7    0.000000
M      1     8    0.000000
M      1     9    0.000000
M      1    10    0.000000
M      1    11    0.000000
M      1    12    0.000000
M      1    13    0.000000
M      1    14    0.000000
M      1    15    0.000000
M      1    16    0.000000
M      1    17    0.000000
M      1    18    0.000000
M      1    19    0.000000
M      1    20    0.000000
M      1    21    0.000000
M      1    22    0.000000
M      1    23    0.000000
M      1    24    0.000000
M      1    25    0.000000
M      2     3    0.000000
M      2     4    0.000000
M      2     5    0.000000
M      2     6    0.000000
M      2     7    0.000000
M      2     8    0.000000
M      2     9    0.000000
M      2    10    0.000000
M      2    11    0.000000
M      2    12    0.000000
M      2    13    0.000000
M      2    14    0.000000
M      2    15    0.000000
M      2    16    0.000000
M      2    17    0.000000
M      2    18    0.000000
M      2    19    0.000000
M      2    20    0.000000
M      2    21    0.000000
M      2    22    0.000000
M      2    23    0.000000
M      2    24    0.000000
M      2    25    0.000000
M      3     4    0.008422
M      3     5    0.001736
M      3     6    0.003131
M      3     7    0.008111
M      3     8    0.008111
M      3     9    0.001277
M      3    10    0.049215
M      3    11    0.000000
M      3    12    0.001050
M      3    13    0.020859
M      3    14    0.000480
M      3    15    0.000000
M      3    16    0.000000
M      3    17    0.000480
M      3    18    0.006894
M      3    19    0.000000
M      3    20    0.001050
M      3    21    0.010721
M      3    22    0.032636
M      3    23    0.006249
M      3    24    0.002421
M      3    25    0.008961
M      4     5    0.042712
M      4     6    0.010721
M      4     7    0.029175
M      4     8    0.014755
M      4     9    0.144660
M      4    10    0.000188
M      4    11    0.093109
M      4    12    0.091428
M      4    13    0.026065
M      4    14    0.034659
M      4    15    0.000000
M      4    16    0.000000
M      4    17    0.034902
M      4    18    0.000000
M      4    19    0.000000
M      4    20    0.003131
M      4    21    0.360379
M      4    22    0.000000
M      4    23    0.124499
M      4    24    0.001612
M      4    25    0.038609
M      5     6    0.054893
M      5     7    0.091428
M      5     8    0.002117
M      5     9    0.072327
M      5    10    0.000000
M      5    11    0.093109
M      5    12    0.180353
M      5    13    0.030374
M      5    14    0.010693
M      5    15    0.000000
M      5    16    0.000000
M      5    17    0.010693
M      5    18    0.037010
M      5    19    0.000000
M      5    20    0.073450
M      5    21    0.108647
M      5    22    0.007094
M      5    23    0.151520
M      5    24    0.000183
M      5    25    0.052080
M      6     7    0.029175
M      6     8    0.013665
M      6     9    0.021555
M      6    10    0.017151
M      6    11    0.061401
M      6    12    0.038648
M      6    13    0.001658
M      6    14    0.005906
M      6    15    0.000000
M      6    16    0.000000
M      6    17    0.004964
M      6    18    0.062909
M      6    19    0.000000
M      6    20    0.038648
M      6    21    0.095268
M      6    22    0.311944
M      6    23    0.008422
M      6    24    0.020833
M      6    25    0.007094
M      7     8    0.023908
M      7     9    0.000557
M      7    10    0.017037
M      7    11    0.030374
M      7    12    0.349746
M      7    13    0.009462
M      7    14    0.009462
M      7    15    0.000000
M      7    16    0.000000
M      7    17    0.007094
M      7    18    0.006894
M      7    19    0.000000
M      7    20    0.021555
M      7    21    0.086424
M      7    22    0.008961
M      7    23    0.017037
M      7    24    0.020065
M      7    25    0.903138
M      8     9    0.124499
M      8    10    0.040343
M      8    11    0.093109
M      8    12    0.080130
M      8    13    0.002421
M      8    14    0.003131
M      8    15    0.000000
M      8    16    0.000000
M      8    17    0.000188
M      8    18    0.004067
M      8    19    0.000000
M      8    20    0.034902
M      8    21    0.000434
M      8    22    0.018178
M      8    23    0.041653
M      8    24    0.812373
M      8    25    0.008111
M      9    10    0.003531
M      9    11    0.079439
M      9    12    0.004964
M      9    13    0.083718
M      9    14    0.009462
M      9    15    0.000000
M      9    16    0.000000
M      9    17    0.003576
M      9    18    0.020065
M      9    19    0.000000
M      9    20    0.010515
M      9    21    0.114643
M      9    22    0.000618
M      9    23    1.061401
M      9    24    0.006851
M      9    25    0.057284
M     10    11    0.000000
M     10    12    0.042712
M     10    13    0.032636
M     10    14    0.040865
M     10    15    0.000000
M     10    16    0.000000
M     10    17    0.082462
M     10    18    0.008961
M     10    19    0.000000
M     10    20    0.019903
M     10    21    0.031313
M     10    22    0.980100
M     10    23    0.000576
M     10    24    0.045156
M     10    25    0.008989
M     11    12    0.061401
M     11    13    0.000000
M     11    14    0.079439
M     11    15    0.000000
M     11    16    0.000000
M     11    17    0.079439
M     11    18    0.026110
M     11    19    0.000000
M     11    20    0.061401
M     11    21    0.079439
M     11    22    0.030374
M     11    23    0.061401
M     11    24    0.030374
M     11    25    0.000000
M     12    13    0.000000
M     12    14    0.004964
M     12    15    0.000000
M     12    16    0.000000
M     12    17    0.004964
M     12    18    0.000139
M     12    19    0.000000
M     12    20    0.017040
M     12    21    0.072327
M     12    22    0.053444
M     12    23    0.038648
M     12    24    0.053444
M     12    25    0.118715
M     13    14    0.001050
M     13    15    0.000000
M     13    16    0.000000
M     13    17    0.010054
M     13    18    0.076244
M     13    19    0.000000
M     13    20    0.020178
M     13    21    0.030374
M     13    22    0.040865
M     13    23    0.032636
M     13    24    0.006851
M     13    25    0.008111
M     14    15    0.000000
M     14    16    0.000000
M     14    17    0.239188
M     14    18    0.028529
M     14    19    0.000000
M     14    20    0.003131
M     14    21    0.029175
M     14    22    0.040865
M     14    23    0.009462
M     14    24    0.003131
M     14    25    0.009462
M     15    16    0.000000
M     15    17    0.000000
M     15    18    0.000000
M     15    19    0.000000
M     15    20    0.000000
M     15    21    0.000000
M     15    22    0.000000
M     15    23    0.000000
M     15    24    0.000000
M     15    25    0.000000
M     16    17    0.000000
M     16    18    0.000000
M     16    19    0.000000
M     16    20    0.000000
M     16    21    0.000000
M     16    22    0.000000
M     16    23    0.000000
M     16    24    0.000000
M     16    25    0.000000
M     17    18    0.028529
M     17    19    0.000000
M     17    20    0.003131
M     17    21    0.001658
M     17    22    0.026065
M     17    23    0.007257
M     17    24    0.002421
M     17    25    0.040642
M     18    19    0.000000
M     18    20    0.055920
M     18    21    0.008012
M     18    22    0.020065
M     18    23    0.027369
M     18    24    0.040343
M     18    25    0.039710
M     19    20    0.000000
M     19    21    0.000000
M     19    22    0.000000
M     19    23    0.000000
M     19    24    0.000000
M     19    25    0.000000
M     20    21    0.006108
M     20    22    0.012774
M     20    23    0.029175
M     20    24    0.008012
M     20    25    0.082462
M     21    22    0.026065
M     21    23    0.077190
M     21    24    0.086424
M     21    25    0.103836
M     22    23    0.000139
M     22    24    0.051742
M     22    25    0.001302
M     23    24    0.109238
M     23    25    0.014007
M     24    25    0.011360


Distance matrix example:

R 1 61 1 61
B 1 0 MET
B 2 3 ASP
B 3 3 PRO
B 4 3 ASN
B 5 3 CYS
B 6 0 SER
B 7 0 CYS
B 8 0 ALA
B 9 0 THR
B 10 0 ASP
B 11 0 GLY
B 12 0 SER
B 13 0 CYS
B 14 0 SER
B 15 3 CYS
B 16 3 ALA
B 17 3 GLY
B 18 3 SER
B 19 0 CYS
B 20 0 LYS
B 21 3 CYS
B 22 3 LYS
B 23 3 GLN
B 24 3 CYS
B 25 0 LYS
B 26 3 CYS
B 27 3 THR
B 28 3 SER
B 29 3 CYS
B 30 0 LYS
B 31 0 LYS
B 32 0 SER
B 33 0 CYS
B 34 0 CYS
B 35 0 SER
B 36 0 CYS
B 37 0 CYS
B 38 3 PRO
B 39 3 VAL
B 40 3 GLY
B 41 3 CYS
B 42 1 ALA
B 43 1 LYS
B 44 3 CYS
B 45 3 SER
B 46 3 GLN
B 47 3 GLY
B 48 0 CYS
B 49 0 ILE
B 50 0 CYS
B 51 3 LYS
B 52 3 GLU
B 53 3 ALA
B 54 3 SER
B 55 0 ASP
B 56 0 LYS
B 57 0 CYS
B 58 1 SER
B 59 1 CYS
B 60 1 CYS
B 61 0 ALA
M 1 2 3.78584
M 1 3 6.65565
M 1 4 7.53659
M 1 5 5.39268
M 1 6 4.19479
M 1 7 5.35381
M 1 8 6.35822
M 1 9 6.75694
M 1 10 10.3962
M 1 11 12.1167
M 1 12 13.1617
M 1 13 11.6384
M 1 14 14.5411
M 1 15 13.291
M 1 16 15.9378
M 1 17 15.9077
M 1 18 15.6988
M 1 19 12.2591
M 1 20 12.1893
M 1 21 9.81419
M 1 22 11.6328
M 1 23 10.7819
M 1 24 9.28281
M 1 25 8.91772
M 1 26 10.7273
M 1 27 14.3726
M 1 28 15.5514
M 1 29 14.8265
M 1 30 17.5151
M 1 31 17.323
M 1 32 19.6786
M 1 33 19.2713
M 1 34 21.1731
M 1 35 22.5112
M 1 36 26.0724
M 1 37 25.9796
M 1 38 25.2386
M 1 39 22.8243
M 1 40 26.1192
M 1 41 27.7372
M 1 42 29.9209
M 1 43 30.0278
M 1 44 26.2307
M 1 45 25.6092
M 1 46 25.8724
M 1 47 23.7907
M 1 48 23.53
M 1 49 26.6949
M 1 50 26.4018
M 1 51 26.2612
M 1 52 23.1561
M 1 53 25.4718
M 1 54 24.3595
M 1 55 27.6796
M 1 56 29.5768
M 1 57 30.4987
M 1 58 33.7163
M 1 59 32.658
M 1 60 32.0455
M 1 61 34.5092
M 2 3 3.9436
M 2 4 5.38825
M 2 5 5.41153
M 2 6 6.28431
M 2 7 8.39598
M 2 8 9.85667
M 2 9 9.32764
M 2 10 13.0905
M 2 11 14.5086
M 2 12 16.152
M 2 13 14.5715
M 2 14 17.1931
M 2 15 15.5976
M 2 16 17.6738
M 2 17 17.0773
M 2 18 17.2848
M 2 19 13.6856
M 2 20 12.7831
M 2 21 9.78055
M 2 22 10.3203
M 2 23 9.39204
M 2 24 9.25577
M 2 25 9.17111
M 2 26 12.0994
M 2 27 15.5307
M 2 28 17.168
M 2 29 15.8625
M 2 30 17.9079
M 2 31 17.3485
M 2 32 19.0469
M 2 33 17.9234
M 2 34 19.8457
M 2 35 21.5521
M 2 36 24.9778
M 2 37 25.0441
M 2 38 24.7866
M 2 39 22.3903
M 2 40 25.6488
M 2 41 26.7956
M 2 42 28.7479
M 2 43 28.4212
M 2 44 24.5937
M 2 45 24.1952
M 2 46 24.0264
M 2 47 21.6852
M 2 48 21.4739
M 2 49 24.4401
M 2 50 24.2877
M 2 51 23.9494
M 2 52 21.0266
M 2 53 23.5724
M 2 54 22.9693
M 2 55 26.5424
M 2 56 28.3564
M 2 57 28.9247
M 2 58 31.9516
M 2 59 30.7584
M 2 60 30.5134
M 2 61 33.2664
M 3 4 3.80776
M 3 5 5.98182
M 3 6 7.02003
M 3 7 10.2935
M 3 8 12.6628
M 3 9 12.8137
M 3 10 16.6131
M 3 11 17.6925
M 3 12 18.9839
M 3 13 16.8008
M 3 14 18.8707
M 3 15 16.56
M 3 16 18.4744
M 3 17 17.089
M 3 18 16.9899
M 3 19 13.2484
M 3 20 11.32
M 3 21 8.64309
M 3 22 8.47725
M 3 23 8.92592
M 3 24 9.92004
M 3 25 11.1639
M 3 26 14.1532
M 3 27 17.6048
M 3 28 18.798
M 3 29 16.7936
M 3 30 18.3427
M 3 31 16.9506
M 3 32 18.1627
M 3 33 16.7078
M 3 34 17.9829
M 3 35 19.4293
M 3 36 22.8916
M 3 37 23.4966
M 3 38 23.7459
M 3 39 21.8296
M 3 40 25.2978
M 3 41 25.9946
M 3 42 28.1438
M 3 43 27.4604
M 3 44 23.6554
M 3 45 23.884
M 3 46 23.7918
M 3 47 20.9882
M 3 48 20.1745
M 3 49 22.7773
M 3 50 22.1521
M 3 51 21.3157
M 3 52 18.1929
M 3 53 20.4592
M 3 54 20.1382
M 3 55 23.786
M 3 56 25.8821
M 3 57 26.5635
M 3 58 29.6161
M 3 59 28.7452
M 3 60 28.82
M 3 61 31.7045
M 4 5 3.88682
M 4 6 6.7696
M 4 7 9.44501
M 4 8 12.3426
M 4 9 12.326
M 4 10 16.0462
M 4 11 16.2961
M 4 12 17.6685
M 4 13 15.191
M 4 14 16.7606
M 4 15 14.2731
M 4 16 15.5823
M 4 17 13.9764
M 4 18 14.4437
M 4 19 10.9297
M 4 20 9.1521
M 4 21 5.77055
M 4 22 5.07827
M 4 23 5.14572
M 4 24 6.58998
M 4 25 8.49545
M 4 26 11.5714
M 4 27 14.7772
M 4 28 15.906
M 4 29 13.5293
M 4 30 14.7272
M 4 31 13.282
M 4 32 14.4292
M 4 33 13.0626
M 4 34 14.6122
M 4 35 16.2797
M 4 36 19.6871
M 4 37 19.9829
M 4 38 20.0832
M 4 39 18.0517
M 4 40 21.4951
M 4 41 22.2612
M 4 42 24.4453
M 4 43 23.9283
M 4 44 20.1127
M 4 45 20.2642
M 4 46 20.4254
M 4 47 17.71
M 4 48 16.8677
M 4 49 19.7055
M 4 50 19.1842
M 4 51 18.8064
M 4 52 15.7704
M 4 53 18.3095
M 4 54 17.6189
M 4 55 21.2147
M 4 56 22.9868
M 4 57 23.5794
M 4 58 26.6606
M 4 59 25.6408
M 4 60 25.4477
M 4 61 28.2311
M 5 6 3.85901
M 5 7 5.66601
M 5 8 8.74549
M 5 9 9.16422
M 5 10 12.7451
M 5 11 12.8734
M 5 12 13.9035
M 5 13 11.3461
M 5 14 13.094
M 5 15 10.8651
M 5 16 12.6353
M 5 17 11.7061
M 5 18 12.0385
M 5 19 8.54771
M 5 20 8.02984
M 5 21 4.81543
M 5 22 6.48307
M 5 23 5.77151
M 5 24 4.59342
M 5 25 6.17117
M 5 26 8.45278
M 5 27 12.0215
M 5 28 12.8631
M 5 29 11.0128
M 5 30 13.0575
M 5 31 12.2783
M 5 32 14.3917
M 5 33 13.9886
M 5 34 15.8134
M 5 35 17.1998
M 5 36 20.7155
M 5 37 20.595
M 5 38 19.9749
M 5 39 17.7025
M 5 40 21.135
M 5 41 22.5638
M 5 42 24.9149
M 5 43 24.9856
M 5 44 21.204
M 5 45 20.8715
M 5 46 21.4689
M 5 47 19.2235
M 5 48 18.5892
M 5 49 21.7659
M 5 50 21.3095
M 5 51 21.371
M 5 52 18.2893
M 5 53 20.6773
M 5 54 19.3334
M 5 55 22.61
M 5 56 24.3143
M 5 57 25.2044
M 5 58 28.4475
M 5 59 27.4289
M 5 60 26.7232
M 5 61 29.1519
M 6 7 3.82953
M 6 8 6.94794
M 6 9 8.77428
M 6 10 12.1347
M 6 11 12.9346
M 6 12 13.1185
M 6 13 10.5142
M 6 14 12.576
M 6 15 10.4484
M 6 16 13.2314
M 6 17 12.69
M 6 18 11.945
M 6 19 8.35676
M 6 20 8.21891
M 6 21 6.57503
M 6 22 9.32653
M 6 23 9.48148
M 6 24 7.72263
M 6 25 8.87872
M 6 26 9.99826
M 6 27 13.7815
M 6 28 14.0067
M 6 29 12.7353
M 6 30 15.3696
M 6 31 14.6395
M 6 32 17.1762
M 6 33 17.222
M 6 34 18.6319
M 6 35 19.4451
M 6 36 23.1278
M 6 37 23.2365
M 6 38 22.4426
M 6 39 20.4221
M 6 40 23.9511
M 6 41 25.5958
M 6 42 28.1827
M 6 43 28.4125
M 6 44 24.6769
M 6 45 24.3976
M 6 46 25.2023
M 6 47 22.9781
M 6 48 22.1557
M 6 49 25.2535
M 6 50 24.4823
M 6 51 24.3035
M 6 52 20.9551
M 6 53 22.8916
M 6 54 21.3683
M 6 55 24.4487
M 6 56 26.5209
M 6 57 27.8331
M 6 58 31.2387
M 6 59 30.5301
M 6 60 29.7582
M 6 61 32.025
M 7 8 3.75216
M 7 9 6.11646
M 7 10 8.91449
M 7 11 9.4062
M 7 12 9.2939
M 7 13 6.81125
M 7 14 9.35296
M 7 15 8.11294
M 7 16 11.1403
M 7 17 11.676
M 7 18 11.2671
M 7 19 8.41296
M 7 20 9.8248
M 7 21 8.34998
M 7 22 11.4177
M 7 23 10.6349
M 7 24 7.65037
M 7 25 7.68176
M 7 26 7.48695
M 7 27 11.1628
M 7 28 11.277
M 7 29 10.9323
M 7 30 14.1655
M 7 31 14.3554
M 7 32 17.4267
M 7 33 18.0532
M 7 34 19.8943
M 7 35 20.7846
M 7 36 24.3267
M 7 37 23.8957
M 7 38 22.5078
M 7 39 20.1614
M 7 40 23.4249
M 7 41 25.5863
M 7 42 28.0856
M 7 43 28.7877
M 7 44 25.1468
M 7 45 24.3413
M 7 46 25.3445
M 7 47 23.6173
M 7 48 23.1761
M 7 49 26.542
M 7 50 26.075
M 7 51 26.3939
M 7 52 23.2346
M 7 53 25.313
M 7 54 23.4283
M 7 55 26.2795
M 7 56 28.0285
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M 29 39 10.7091
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M 29 41 16.262
M 29 42 18.7333
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M 29 46 18.0679
M 29 47 17.3757
M 29 48 17.1328
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M 29 53 22.4343
M 29 54 19.7526
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M 29 56 22.1771
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M 30 32 6.63704
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M 30 34 11.7703
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M 41 53 17.2159
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M 41 55 15.5875
M 41 56 13.0672
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M 43 52 15.3187
M 43 53 17.5312
M 43 54 16.8134
M 43 55 17.4689
M 43 56 14.6091
M 43 57 11.9019
M 43 58 11.9231
M 43 59 8.51761
M 43 60 6.645
M 43 61 8.53189
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M 44 46 5.77094
M 44 47 5.1505
M 44 48 4.44301
M 44 49 5.77142
M 44 50 7.9333
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M 44 54 14.7635
M 44 55 16.1445
M 44 56 13.9702
M 44 57 11.749
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M 45 47 5.38531
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M 45 49 9.09995
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M 45 51 15.119
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M 45 53 18.9322
M 45 54 17.8479
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M 45 58 16.5309
M 45 59 13.3938
M 45 60 11.5546
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M 46 52 16.6328
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