HDdist Sample Input File

The HDdist input file is the output from a gel scanner, which consists of two columns of information:

Column 1 is the pixel/position in the scan.

Column 2 is the strength of the signal (intensity) at that position.

***IMPORTANT: You must separate data from each lane in your gel with a blank line.

Also, the reference lane, which should contain your probe and essentially be a homoduplex band, needs to be represented as the first lane, or first data set. If you ran it as a later lane in the gel, move the data up to the top of the file, as if it were the first lane.

Here is an example of what an input file should look like:

0   14.496
1   10.04
2   6.48
3   2.328
4   0
5   0
6   0
7   0
8   0
9   0
10  0
11  0
12  0
13  0
14  0
15  0
16  0
17  0
18  0
19  0
20  0
21  0
22  0
23  0
24  0
25  0
26  0
27  0
28  0
29  0
30  0
31  0
32  0
33  0
34  0
35  0
36  0
37  0
38  0
39  0
40  0
41  0
42  0
43  0
44  0
45  0
46  0
47  0
48  0
49  0
50  0
51  0
52  0
53  0
54  0
55  0
56  0
57  0
58  0
59  0
60  0
61  0
62  0
63  0
64  0
65  0
66  0
67  0
68  0
69  0
70  0
71  0
72  0
73  0
74  0
75  0
76  0
77  0
78  0
79  0
80  0
81  0
82  0
83  0
84  0
85  0
86  0
87  0
88  0
89  0
90  0
91  0
92  0
93  0
94  0
95  0
96  0
97  0
98  0
99  0
100 0
101 0
102 0
103 0
104 0
105 0
106 0
107 0
108 0
109 0
110 0
111 0
112 0
113 0
114 0
115 0
116 0
117 0
118 0
119 0
120 0
121 0
122 0
123 0
124 0
125 0
126 0
127 0
128 0
129 0
130 0
131 0
132 0
133 0
134 0
135 0
136 0
137 0
138 0
139 0
140 0
141 0
142 0
143 0
144 0
145 0
146 0
147 0
148 0
149 0
150 0
151 0
152 0
153 0
154 0
155 0
156 0
157 0
158 0
159 0
160 0
161 0
162 0
163 0
164 0
165 0
166 0
167 0
168 0
169 0
170 0
171 0
172 0
173 0
174 0
175 0
176 0
177 0
178 0
179 0
180 0
181 0
182 0
183 0
184 0
185 0
186 0
187 0
188 0
189 0
190 0
191 0
192 0
193 0
194 0
195 0
196 0
197 0
198 0
199 0
200 0
201 0
202 0
203 0
204 0
205 0
206 0
207 0
208 0
209 0
210 0
211 0
212 0
213 0
214 0
215 0
216 0
217 0
218 0
219 0
220 0
221 0
222 0
223 0
224 0
225 0
226 0
227 0
228 0
229 0
230 0
231 0
232 0
233 0
234 0
235 0
236 0
237 0
238 0
239 0
240 0
241 0
242 0
243 0
244 0
245 0
246 0
247 0
248 0
249 0
250 0
251 0
252 0
253 0
254 0
255 0
256 0
257 0
258 0
259 0
260 0
261 0
262 0
263 0
264 0
265 0
266 0
267 0
268 0
269 0
270 0
271 0
272 0
273 0
274 0
275 0
276 0
277 0
278 0
279 1.164
280 4.851
281 3.748
282 0.04
283 4.718
284 6.289
285 6.342
286 7.812
287 9.179
288 11.422
289 12.093
290 15.065
291 21.195
292 22.4
293 20.518
294 19.863
295 23.899
296 24.364
297 26.637
298 30.073
299 32.916
300 39.389
301 39.99
302 47.274
303 46.191
304 51.721
305 55.528
306 57.715
307 59.83
308 66.298
309 65.993
310 69.394
311 72.263
312 76.433
313 84.11
314 86.623
315 83.01
316 92.942
317 97.808
318 102.296
319 112.885
320 125.333
321 132.773
322 135.608
323 147.855
324 155.004
325 168.062
326 176.328
327 184.322
328 199.315
329 207.514
330 221.139
331 237.585
332 254.995
333 277.966
334 292.453
335 313.242
336 340.596
337 372.909
338 391.335
339 416.687
340 436.728
341 470.342
342 519.183
343 573.061
344 615.689
345 653.782
346 696.161
347 735.633
348 776.59
349 820.619
350 874.784
351 929.408
352 981.612
353 1044.978
354 1108.962
355 1169.405
356 1225.055
357 1290.157
358 1339.174
359 1371.975
360 1417.53
361 1442.155
362 1439.664
363 1434.935
364 1440.328
365 1434.571
366 1398.236
367 1363.844
368 1315.025
369 1258.37
370 1184.579
371 1131.437
372 1045.553
    
0   36.633
1   39.989
2   34.81
3   32.823
4   32.808
5   33.222
6   31.828
7   25.559
8   27.978
9   23.471
10  23.074
11  18.768
12  16.112
13  17.764
14  14.882
15  14.456
16  11.957
17  8.656
18  8.434
19  8.549
20  7.551
21  1.77
22  4.42
23  4.591
24  3.815
25  3.537
26  5.02
27  2.688
28  7.627
29  7.491
30  0.698
31  0
32  1.063
33  2.028
34  2.03
35  0.205
36  0
37  0
38  0
39  0
40  0
41  0
42  0
43  0
44  0
45  0
46  0
47  0
48  0
49  0
50  0
51  0
52  0
53  0
54  0
55  0
56  0
57  0
58  0
59  0
60  0
61  0
62  0
63  0
64  0
65  0
66  0
67  0
68  0
69  0
70  0
71  0
72  0
73  0
74  0
75  0
76  0
77  0
78  0
79  0
80  0
81  0
82  0
83  0
84  0
85  0
86  0
87  0
88  0
89  0
90  0
91  0
92  0
93  0
94  0
95  0
96  0
97  0
98  0
99  0
100 0
101 0
102 0
103 0
104 0
105 0
106 0
107 0
108 0
109 0
110 0
111 0
112 0
113 0
114 0
115 0
116 0
117 0
118 0
119 0
120 0
121 0
122 0
123 0
124 0
125 0
126 0
127 0
128 0
129 0
130 0
131 0
132 0
133 0
134 0
135 0
136 0
137 0
138 0
139 0
140 0
141 0
142 0
143 0
144 0
145 0
146 0
147 0
148 2.76
149 9.487
150 3.4
151 4.096
152 5.826
153 7.096
154 3.5
155 5.963
156 6.874
157 7.912
158 8.087
159 9.66
160 5.596
161 3.194
162 0.146
163 0
164 0
165 0
166 0
167 0
168 0
169 0
170 0
171 0
172 0
173 0
174 0
175 0
176 0
177 0
178 0
179 0
180 0
181 0
182 4.198
183 2.309
184 4.457
185 4.775
186 1.476
187 0.683
188 0.17
189 0
190 0
191 0
192 0
193 0
194 0.625
195 0
196 0
197 0
198 0
199 0
200 0
201 0
202 0.733
203 0
204 0
205 0.632
206 1.466
207 0
208 1.778
209 0
210 0
211 1.117
212 2.846
213 0.893
214 5.908
215 5.448
216 3.833
217 4.916
218 0
219 0
220 0.507
221 3.053
222 2.112
223 8.842
224 7.455
225 10.349
226 10.717
227 13.94
228 11.437
229 9.369
230 12.573
231 15.984
232 20.834
233 19.502
234 24.958
235 27.318
236 29.122
237 33.007
238 34.158
239 34.873
240 28.677
241 30.401
242 31.007
243 32.955
244 33.752
245 34.153
246 35.31
247 40.1
248 39.073
249 40.277
250 38.161
251 40.734
252 35.247
253 36.276
254 37.996
255 41.741
256 42.575
257 49.144
258 49.716
259 52.58
260 62.35
261 58.53
262 60.146
263 67.262
264 72.462
265 77.055
266 83.815
267 94.456
268 110.734
269 114.087
270 120.309
271 129.621
272 144.876
273 155.534
274 174.894
275 189.637
276 195.322
277 215.821
278 232.2
279 264.335
280 282.125
281 301.724
282 330.153
283 353.378
284 374.169
285 392.591
286 407.989
287 436.116
288 445.353
289 457.186
290 476.366
291 486.162
292 510.021
293 533.574
294 554.43
295 563.788
296 583.523
297 599.276
298 598.285
299 588.859
300 579.999
301 583.239
302 573.592
303 544.783
304 516.654
305 482.457
306 444.045
307 390.036
308 337.894
309 295.11
310 248.124
311 208.957
312 164.772
313 142.144
314 111.599
315 89.788
316 67.019
317 56.099
318 44.988
319 30.482
320 19.139
321 11.517
322 6.745
323 9.32
324 7.652
325 3.449
326 0
327 0.788
328 2.706
329 1.397
330 4.505
331 1.169
332 2.887
333 6.226
334 5.926
335 3.745
336 5.708
337 7.758
338 14.053
339 14.222
340 16.827
341 19.635
342 21.346
343 22.888
344 26.911
345 31.924
346 31.526
347 38.101
348 51.339
349 62.535
350 69.273
351 71.848
352 81.708
353 95.751
354 104.237
355 117.271
356 121.132
357 130.371
358 147.152
359 169.238
360 181.851
361 187.18
362 193.112
363 191.025
364 187.214
365 177.735
366 155.2
367 143.241
368 122.433
369 94.271
370 75.449
371 49.451
372 37.055
    
0   50.353
1   49.425
2   52.662
3   62.802
4   62.624
5   70.934
6   70.554
7   72.146
8   80.12
9   81.729
10  68.984
11  70.315
12  63.969
13  55.901
14  53.678
15  48.191
16  42.37
17  35.135
18  33.932
19  31.857
20  26.079
21  30.223
22  30.246
23  33.555
24  28.393
25  29.983
26  32.899
27  34.354
28  38.075
29  32.597
30  29.78
31  27.267
32  26.613
33  22.057
34  19.728
35  18.529
36  10.731
37  5.297
38  5.136
39  1.7
40  0.627
41  0
42  0
43  0
44  0
45  1.957
46  5.07
47  7.125
48  2.308
49  0.722
50  2.28
51  1.01
52  0
53  0
54  0
55  3.653
56  2.202
57  1.518
58  0.561
59  1.706
60  1.682
61  2.629
62  3.134
63  8.323
64  10.872
65  10.607
66  17.372
67  20.185
68  21.063
69  21.151
70  21.808
71  20.249
72  17.452
73  22.088
74  28.327
75  33.428
76  36.84
77  43.362
78  45.368
79  44.283
80  41.945
81  49.91
82  55.992
83  64.125
84  68.434
85  74.681
86  77.699
87  83.543
88  93.956
89  103.742
90  117.203
91  121.711
92  133.488
93  155.151
94  171.992
95  177.13
96  197.008
97  207.348
98  217.976
99  237.418
100 247.212
101 253.28
102 266.109
103 275.531
104 279.788
105 277.574
106 275.931
107 283.005
108 276.715
109 270.934
110 251.731
111 227.984
112 207.017
113 191.405
114 181.268
115 172.78
116 167.745
117 170.499
118 168.616
119 163.635
120 168.146
121 169.637
122 183.708
123 190.923
124 189.861
125 194.881
126 207.736
127 210.824
128 228.117
129 238.964
130 259.621
131 289.746
132 322.126
133 350.661
134 372.106
135 404.067
136 427.069
137 460.548
138 496.971
139 540.62
140 594.662
141 634.927
142 695.973
143 758.236
144 831.14
145 897.667
146 986.038
147 1062.004
148 1136.906
149 1179.067
150 1203.229
151 1226.67
152 1221.755
153 1174.497
154 1110.423
155 1028.41
156 899.678
157 774.028
158 660.546
159 548.036
160 440.859
161 341.053
162 261.047
163 211.488
164 163.911
165 127.143
166 99.219
167 81.601
168 64.537
169 43.005
170 34.058
171 20.508
172 9.171
173 0
174 0
175 0
176 0
177 0
178 0
179 0
180 0
181 0
182 0
183 0
184 0
185 0
186 0
187 0
188 0
189 0
190 0
191 0
192 0
193 0
194 0
195 0
196 0
197 0
198 0
199 0
200 0
201 0
202 0
203 0
204 0
205 0
206 0
207 0
208 0
209 0
210 0
211 0
212 0
213 0
214 0
215 0
216 0
217 0
218 0
219 0
220 0
221 0
222 0
223 0
224 0
225 0
226 0
227 0
228 0
229 0
230 0
231 0
232 0
233 0
234 0
235 0
236 0
237 0
238 0
239 0
240 0
241 0
242 0
243 0
244 0
245 0
246 0
247 0
248 0
249 0
250 0
251 0
252 0
253 0
254 0
255 0
256 0
257 0
258 0
259 0
260 0
261 0
262 0
263 0
264 0
265 0
266 0
267 0
268 0
269 0
270 0
271 0
272 0
273 0
274 0
275 0
276 0
277 0
278 0
279 0
280 0
281 0
282 0
283 0
284 0
285 0
286 0
287 0
288 0
289 0
290 0
291 0
292 0
293 0
294 0
295 0
296 0
297 0
298 0
299 0
300 0
301 0
302 0
303 0
304 0
305 0
306 0
307 0
308 0
309 0
310 0
311 0
312 0
313 0
314 0
315 0
316 0
317 0
318 0
319 0
320 0
321 0
322 0
323 0
324 0
325 0
326 0
327 0
328 0
329 0
330 0
331 0
332 0
333 0
334 0
335 0
336 0
337 0
338 0
339 0
340 0
341 0
342 0
343 0
344 0
345 0
346 0
347 0
348 0
349 0
350 0
351 0
352 0
353 0
354 8.415
355 18.467
356 19.288
357 24.377
358 27.97
359 37.763
360 35.091
361 30.89
362 27.817
363 19.303
364 6.207
365 0
366 0
367 0
368 0
369 0
370 0
371 0
372 0
    
0   17.911
1   22.277
2   20.795
3   20.296
4   20.706
5   19.559
6   19.53
7   13.413
8   18.001
9   18.04
10  19.226
11  16.151
12  16.175
13  16.701
14  19.806
15  15.726
16  9.459
17  8.355
18  9.39
19  8.734
20  10.234
21  14.159
22  15.307
23  21.521
24  15.337
25  12.807
26  17.333
27  15.48
28  12.384
29  13.341
30  14.094
31  12.836
32  15.358
33  12.783
34  10.691
35  12.722
36  8.814
37  13.146
38  16.678
39  21.882
40  24.051
41  25.792
42  22.674
43  28.265
44  28.537
45  33.87
46  39.375
47  43.33
48  48.778
49  46.523
50  48.578
51  55.762
52  59.482
53  51.957
54  53.677
55  55.846
56  59.847
57  69.263
58  71.495
59  81.549
60  91.974
61  104.409
62  120.268
63  134.873
64  144.518
65  159.097
66  175.632
67  186.324
68  197.083
69  198.863
70  203.425
71  203.854
72  197.708
73  177.541
74  168.646
75  151.049
76  141.104
77  129.565
78  115.769
79  103.107
80  106.611
81  104.767
82  109.907
83  111.226
84  113.996
85  117.194
86  121.778
87  128.238
88  136.302
89  141.407
90  152.434
91  162.925
92  186.462
93  199.67
94  217.516
95  238.208
96  262.059
97  263.416
98  281.401
99  299.765
100 311.468
101 322.775
102 336.074
103 341.606
104 353.755
105 373.604
106 377.678
107 394.898
108 420.198
109 435.677
110 463.585
111 498.689
112 536.57
113 587.158
114 632.324
115 688.708
116 737.283
117 800.347
118 831.121
119 844.468
120 828.459
121 801.426
122 728.618
123 669.202
124 622.682
125 594.296
126 579.078
127 579.699
128 594.005
129 618.724
130 659.91
131 704.373
132 761.654
133 816.485
134 881.38
135 953.814
136 1036.509
137 1117.94
138 1183.572
139 1243.211
140 1295.683
141 1329.326
142 1331.604
143 1300.677
144 1250.554
145 1189.067
146 1122.751
147 1061.96
148 988.464
149 909.261
150 830.07
151 761.466
152 681.522
153 610.954
154 529.276
155 457.878
156 396.007
157 333.859
158 282.581
159 243.381
160 209.044
161 175.495
162 150.327
163 135.235
164 108.66
165 96.24
166 80.829
167 67.799
168 51.761
169 44.366
170 36.094
171 22.903
172 10.855
173 0
174 0
175 0
176 0
177 0
178 0
179 0
180 0
181 0
182 0
183 0
184 0
185 0
186 0
187 0
188 0
189 0
190 0
191 0
192 0
193 0
194 0
195 0
196 0
197 0
198 0
199 0
200 0
201 0
202 0
203 0
204 0
205 0
206 0
207 0
208 0
209 0
210 0
211 0
212 0
213 0
214 0
215 0
216 0
217 0
218 0
219 0
220 0
221 0
222 0
223 0
224 0
225 0
226 0
227 0
228 0
229 0
230 0
231 0
232 0
233 0
234 0
235 0
236 0
237 0
238 0
239 0
240 0
241 0
242 0
243 0
244 0
245 0
246 0
247 0
248 0
249 0
250 0
251 0
252 0
253 0
254 0
255 0
256 0
257 0
258 0
259 0
260 0
261 0
262 0
263 0
264 0
265 0
266 0
267 0
268 0
269 0
270 0
271 0
272 0
273 0
274 0
275 0
276 0
277 0
278 0
279 0
280 0
281 0
282 0
283 0
284 0
285 0
286 0
287 0
288 0
289 0
290 0
291 0
292 0
293 0
294 0
295 0
296 0
297 0
298 0
299 0
300 0
301 0
302 0
303 0
304 0
305 0
306 0
307 0
308 0
309 0
310 0
311 0
312 0
313 0
314 0
315 0
316 0
317 0
318 0
319 0
320 0
321 0
322 0
323 0
324 0
325 0
326 0
327 0
328 0
329 0
330 0
331 0
332 0
333 0
334 0
335 0
336 0
337 0
338 0
339 0
340 0
341 0
342 0
343 0
344 0
345 0
346 0
347 0
348 0
349 0
350 0
351 0
352 0
353 0
354 0
355 0
356 0
357 0
358 0
359 0
360 0
361 0
362 0
363 0
364 0
365 0
366 0
367 0
368 0
369 0
370 0
371 0
372 0
    
0   51.905
1   51.644
2   49.143
3   49.956
4   43.084
5   46.643
6   47.38
7   46.04
8   52.05
9   48.043
10  41.01
11  41.36
12  41.733
13  33.339
14  29.251
15  27.433
16  27.719
17  25.518
18  29.199
19  23.095
20  26.761
21  29.107
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0   20.629
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0   18.017
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0   34.896
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