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OPENSEQ.org
subFGnew
Genes: A B A+B
Length: 263 255 473
Sequences: 2115 2368 1459
Seq/Len: 8.04 9.29 3.08
MirrorTree (Pazo et al. 2001) 0.99
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.05 2.81
2 0.04 0.06 2.81
5 0.05 0.06 2.81
10 0.05 0.07 2.81
20 0.06 0.08 2.81
100 0.07 0.10 2.82
∞ 0.16 0.20 2.84
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
185_N 188_R 4.57 1.00 1.00
217_K 219_E 4.46 1.00 1.00
68_N 72_R 4.39 1.00 1.00
212_I 214_L 4.38 1.00 1.00
186_E 189_D 4.34 1.00 1.00
41_K 43_K 4.32 1.00 1.00
188_V 191_V 4.25 1.00 1.00
102_P 106_N 4.24 1.00 1.00
72_I 76_M 4.19 1.00 1.00
137_Y 141_Y 4.17 1.00 1.00
189_K 192_K 4.12 1.00 1.00
215_V 217_V 4.05 1.00 1.00
134_I 138_L 4.05 1.00 1.00
112_I 116_V 3.98 1.00 1.00
38_L 40_I 3.96 1.00 1.00
216_G 218_G 3.93 1.00 1.00
36_V 38_I 3.92 1.00 1.00
66_V 70_V 3.84 1.00 1.00
39_K 41_R 3.81 1.00 1.00
157_R 162_W 3.79 1.00 1.00
214_I 216_W 3.78 1.00 1.00
184_L 187_C 3.77 1.00 1.00
193_R 196_K 3.76 1.00 1.00
63_I 67_L 3.75 1.00 1.00
65_H 69_N 3.72 1.00 1.00
145_F 150_Y 3.71 1.00 1.00
42_T 44_D 3.71 1.00 1.00
105_V 109_L 3.70 1.00 1.00
98_V 102_N 3.70 1.00 1.00
100_D 104_G 3.70 1.00 1.00
46_L 48_F 3.69 1.00 1.00
103_L 107_I 3.68 1.00 1.00
70_I 74_V 3.65 1.00 1.00
135_A 139_G 3.62 1.00 1.00
85_C 89_A 3.62 1.00 1.00
86_N 90_D 3.59 1.00 1.00
106_S 110_K 3.58 1.00 1.00
154_F 159_Y 3.55 1.00 1.00
45_V 47_V 3.54 1.00 1.00
192_L 195_A 3.54 1.00 1.00
143_H 148_Q 3.54 1.00 1.00
210_V 212_L 3.53 1.00 1.00
90_Q 94_E 3.51 1.00 1.00
52_A 54_V 3.50 1.00 1.00
118_I 122_A 3.50 1.00 1.00
113_G 117_A 3.48 1.00 1.00
207_T 209_A 3.43 1.00 1.00
213_G 215_S 3.42 1.00 1.00
96_R 100_R 3.42 1.00 1.00
104_P 108_P 3.42 1.00 1.00
116_T 120_V 3.41 1.00 1.00
101_R 105_Y 3.39 1.00 1.00
159_M 164_C 3.38 1.00 1.00
53_Q 55_L 3.37 1.00 1.00
191_G 194_V 3.36 1.00 1.00
94_D 98_N 3.35 1.00 1.00
64_L 68_F 3.33 1.00 1.00
61_K 65_K 3.32 1.00 1.00
208_K 210_F 3.32 1.00 1.00
175_H 180_L 3.31 1.00 1.00
44_A 46_V 3.29 1.00 1.00
60_Q 64_N 3.28 1.00 1.00
177_S 182_M 3.27 1.00 1.00
155_D 160_G 3.27 1.00 1.00
167_S 172_A 3.25 1.00 1.00
197_E 200_I 3.25 1.00 1.00
196_R 199_Y 3.22 1.00 1.00
161_I 166_I 3.20 1.00 1.00
160_S 165_A 3.19 1.00 1.00
130_V 134_C 3.19 1.00 1.00
115_K 119_Y 3.18 1.00 1.00
40_S 42_C 3.16 1.00 1.00
206_T 208_K 3.16 1.00 1.00
69_H 73_H 3.15 1.00 1.00
147_T 152_I 3.15 1.00 1.00
183_N 186_T 3.13 1.00 1.00
114_S 118_M 3.12 1.00 1.00
47_V 49_G 3.12 1.00 1.00
109_V 113_A 3.12 1.00 1.00
152_N 157_V 3.11 1.00 1.00
166_Q 171_Q 3.11 1.00 1.00
218_D 220_L 3.11 1.00 1.00
170_T 175_T 3.09 1.00 1.00
110_S 114_D 3.09 1.00 1.00
153_Y 158_S 3.08 1.00 1.00
111_L 115_R 3.07 1.00 1.00
178_E 183_K 3.07 1.00 1.00
174_R 179_K 3.06 1.00 1.00
107_R 111_H 3.06 1.00 1.00
87_F 91_I 3.05 1.00 1.00
48_A 50_V 3.05 1.00 1.00
95_S 99_F 3.04 1.00 1.00
73_S 77_A 3.04 1.00 1.00
194_A 197_I 3.00 1.00 1.00
84_L 88_L 3.00 1.00 1.00
140_M 145_D 3.00 1.00 1.00
142_P 147_A 2.98 1.00 1.00
165_S 170_R 2.98 1.00 1.00
91_E 95_E 2.98 1.00 1.00
141_G 146_G 2.97 1.00 1.00
75_A 79_A 2.95 1.00 1.00
198_T 201_V 2.92 1.00 1.00
74_I 78_V 2.92 1.00 1.00
35_T 37_A 2.91 1.00 1.00
83_L 87_S 2.90 1.00 1.00
171_Y 176_E 2.88 1.00 1.00
169_R 174_K 2.88 1.00 1.00
71_G 75_G 2.87 1.00 1.00
133_L 137_M 2.85 1.00 1.00
182_C 185_M 2.84 1.00 1.00
190_H 193_E 2.84 1.00 1.00
97_F 101_S 2.84 1.00 1.00
132_L 136_F 2.83 1.00 1.00
176_M 181_Q 2.76 1.00 1.00
81_A 85_A 2.76 1.00 1.00
205_L 207_D 2.75 1.00 1.00
172_L 177_I 2.68 1.00 1.00
54_S 56_S 2.68 1.00 1.00
119_P 123_Y 2.68 1.00 1.00
78_T 82_L 2.67 1.00 1.00
187_L 190_I 2.66 1.00 1.00
211_S 213_E 2.65 1.00 1.00
59_H 63_S 2.63 1.00 1.00
139_D 143_V 2.63 1.00 1.00
79_A 83_A 2.62 1.00 1.00
168_A 173_A 2.61 1.00 1.00
181_E 184_E 2.61 1.00 1.00
29_V 31_V 2.60 1.00 1.00
125_R 129_V 2.57 1.00 1.00
200_P 203_D 2.56 1.00 1.00
146_Q 151_M 2.55 1.00 1.00
55_E 57_K 2.53 1.00 1.00
199_L 202_H 2.52 1.00 1.00
131_G 135_S 2.51 1.00 1.00
201_A 204_E 2.51 1.00 1.00
227_D 231_D 2.50 1.00 1.00
222_T 226_E 2.50 1.00 1.00
144_I 149_L 2.48 1.00 1.00
108_L 112_L 2.46 1.00 1.00
99_F 103_F 2.44 1.00 1.00
138_D 142_S 2.44 1.00 1.00
209_N 211_E 2.43 1.00 1.00
37_G 39_G 2.43 1.00 1.00
128_Y 132_F 2.41 1.00 1.00
195_L 198_I 2.39 1.00 0.99
50_K 52_K 2.38 1.00 0.99
163_A 168_K 2.35 1.00 0.99
164_R 169_A 2.35 1.00 0.99
77_L 81_L 2.35 1.00 0.99
88_M 92_A 2.34 1.00 0.99
93_L 97_S 2.32 1.00 0.99
34_A 36_T 2.31 1.00 0.99
51_R 53_L 2.30 1.00 0.99
92_C 96_A 2.29 1.00 0.99
89_R 93_R 2.28 1.00 0.99
122_R 126_Y 2.26 1.00 0.99
226_D 230_K 2.25 1.00 0.99
57_A 59_Y 2.22 1.00 0.99
67_D 71_D 2.19 1.00 0.99
82_R 86_R 2.14 1.00 0.99
148_C 153_D 2.12 1.00 0.99
156_C 161_Y 2.11 1.00 0.99
19_I 21_V 2.09 1.00 0.99
158_A 163_G 2.09 1.00 0.99
10_V 12_A 2.08 1.00 0.99
150_S 155_S 2.07 1.00 0.99
223_I 227_I 2.05 1.00 0.99
12_V 14_T 2.04 1.00 0.98
225_D 229_P 2.03 1.00 0.98
26_M 28_M 2.02 1.00 0.98
224_Y 228_V 2.00 1.00 0.98
123_Y 127_S 1.96 1.00 0.98
27_E 29_K 1.95 1.00 0.98
28_A 30_A 1.87 0.99 0.97
22_I 24_V 1.85 0.99 0.97
56_L 58_L 1.83 0.99 0.97
179_F 184_E 1.83 0.99 0.97
20_H 22_F 1.82 0.99 0.97
203_Q 206_K 1.77 0.99 0.96
173_E 178_E 1.77 0.99 0.96
58_A 62_G 1.75 0.99 0.96
16_Q 18_D 1.74 0.99 0.96
11_T 13_S 1.73 0.99 0.96
5_Q 7_G 1.70 0.98 0.95
30_K 32_E 1.70 0.98 0.95
13_W 15_F 1.63 0.98 0.94
180_M 185_M 1.62 0.98 0.94
49_L 51_E 1.60 0.97 0.93
9_D 11_S 1.59 0.97 0.93
58_A 60_E 1.58 0.97 0.93
221_F 225_H 1.58 0.97 0.93
149_P 154_P 1.57 0.97 0.92
32_G 34_S 1.56 0.97 0.92
229_V 233_R 1.54 0.97 0.91
136_G 140_S 1.52 0.96 0.91
31_Q 33_N 1.52 0.96 0.91
18_R 20_R 1.51 0.96 0.91
121_Q 125_L 1.49 0.96 0.90
57_A 61_E 1.46 0.95 0.88
117_Q 121_H 1.45 0.95 0.88
43_H 45_G 1.45 0.95 0.88
23_E 25_E 1.41 0.94 0.86
231_P 235_E 1.39 0.93 0.85
124_G 128_A 1.37 0.92 0.84
181_E 186_T 1.36 0.92 0.83
129_G 133_G 1.35 0.92 0.83
220_E 224_R 1.33 0.91 0.82
230_S 234_E 1.32 0.91 0.81
8_N 10_L 1.27 0.88 0.78
33_S 35_S 1.25 0.87 0.76
228_D 232_I 1.22 0.85 0.73
219_L 220_L 1.18 0.82 0.70
15_P 17_P 1.17 0.81 0.69
14_S 16_S 1.10 0.76 0.62
232_F 236_A 1.09 0.75 0.61
6_Y 8_Y 1.09 0.75 0.61
7_D 9_D 1.06 0.72 0.58
202_E 205_V 1.03 0.69 0.54
204_D 206_K 1.01 0.67 0.52
4_N 6_T 1.00 0.66 0.51
31_Q 34_S 0.99 0.64 0.49
126_R 130_R 0.97 0.62 0.46
120_T 124_T 0.95 0.60 0.45
62_K 66_R 0.92 0.56 0.40
24_Y 26_Y 0.87 0.50 0.35
80_D 84_D 0.83 0.45 0.30
59_H 61_E 0.81 0.42 0.27
219_L 223_G 0.76 0.36 0.23
151_A 156_G 0.74 0.34 0.21
139_D 144_N 0.71 0.31 0.18
127_P 131_P 0.69 0.29 0.17
140_M 144_N 0.66 0.26 0.14
25_A 27_A 0.63 0.23 0.12
203_Q 205_V 0.61 0.22 0.11
180_M 183_K 0.60 0.20 0.10
21_Q 23_Q 0.60 0.20 0.10
191_G 49_G 0.57 0.18 0.09
47_V 194_V 0.57 0.18 0.08
17_G 19_G 0.53 0.15 0.07
3_R 5_G 0.51 0.14 0.06
186_E 186_T 0.48 0.12 0.05
123_Y 126_Y 0.46 0.11 0.04
221_F 75_G 0.46 0.11 0.04
183_N 189_D 0.45 0.11 0.04
46_L 39_G 0.44 0.10 0.04
37_G 48_F 0.41 0.09 0.03
40_S 190_I 0.36 0.07 0.02
187_L 42_C 0.36 0.07 0.02
69_H 71_D 0.35 0.07 0.02
67_D 73_H 0.34 0.07 0.02
41_K 44_D 0.32 0.06 0.01
144_I 39_G 0.32 0.06 0.01
179_F 182_M 0.31 0.06 0.01
37_G 149_L 0.31 0.06 0.01
42_T 43_K 0.30 0.06 0.01
46_L 139_G 0.30 0.05 0.01
155_D 148_Q 0.30 0.05 0.01
143_H 160_G 0.29 0.05 0.01
135_A 48_F 0.29 0.05 0.01
18_R 25_E 0.29 0.05 0.01
191_G 40_I 0.29 0.05 0.01
23_E 20_R 0.29 0.05 0.01
38_L 194_V 0.28 0.05 0.01
178_E 181_Q 0.28 0.05 0.01
221_F 215_S 0.27 0.05 0.01
117_Q 124_T 0.27 0.05 0.01
9_D 10_L 0.26 0.04 0.01
8_N 11_S 0.26 0.04 0.01
15_P 8_Y 0.26 0.04 0.01
217_K 141_Y 0.26 0.04 0.01
96_R 71_D 0.26 0.04 0.01
67_D 100_R 0.26 0.04 0.01
141_G 145_D 0.26 0.04 0.01
105_V 140_S 0.25 0.04 0.01
120_T 121_H 0.25 0.04 0.01
140_M 146_G 0.25 0.04 0.01
136_G 109_L 0.25 0.04 0.01
4_N 7_G 0.25 0.04 0.01
6_Y 17_P 0.25 0.04 0.01
216_G 220_L 0.25 0.04 0.01
129_G 130_R 0.25 0.04 0.01
4_N 4_I 0.25 0.04 0.01
124_G 124_T 0.24 0.04 0.01
12_V 11_S 0.24 0.04 0.01
102_P 71_D 0.24 0.04 0.01
9_D 14_T 0.24 0.04 0.01
117_Q 125_L 0.24 0.04 0.01
126_R 133_G 0.24 0.04 0.01
141_G 148_Q 0.24 0.04 0.01
41_K 184_E 0.23 0.04 0.01
121_Q 121_H 0.23 0.04 0.01
40_S 44_D 0.23 0.04 0.01
141_G 142_S 0.23 0.04 0.01
42_T 42_C 0.23 0.04 0.01
137_Y 219_E 0.23 0.04 0.01
34_A 173_A 0.23 0.04 0.01
188_V 214_L 0.22 0.04 0.01
175_H 196_K 0.22 0.04 0.01
177_S 184_E 0.22 0.04 0.01
24_Y 27_A 0.22 0.04 0.01
66_V 76_M 0.22 0.04 0.01
233_L 199_Y 0.22 0.04 0.01
130_V 177_I 0.22 0.04 0.01
212_I 191_V 0.21 0.04 0.01
25_A 26_Y 0.21 0.04 0.01
175_H 193_E 0.21 0.04 0.01
67_D 106_N 0.21 0.04 0.01
213_G 225_H 0.21 0.04 0.01
172_L 134_C 0.21 0.04 0.01
149_P 155_S 0.21 0.04 0.01
162_G 167_G 0.21 0.04 0.01
35_T 77_A 0.21 0.04 0.01
168_A 36_T 0.21 0.04 0.01
3_R 7_G 0.21 0.04 0.01
120_T 125_L 0.21 0.04 0.01
150_S 154_P 0.21 0.04 0.01
6_Y 13_S 0.21 0.04 0.01
105_V 74_V 0.21 0.04 0.01
193_R 180_L 0.21 0.03 0.01
70_I 109_L 0.21 0.03 0.01
73_S 37_A 0.21 0.03 0.01
190_H 180_L 0.20 0.03 0.01
15_P 16_S 0.20 0.03 0.01
138_D 146_G 0.20 0.03 0.01
218_D 218_G 0.20 0.03 0.01
91_E 115_R 0.20 0.03 0.01
9_D 12_A 0.20 0.03 0.01
14_S 17_P 0.20 0.03 0.01
72_I 70_V 0.20 0.03 0.01
10_V 11_S 0.20 0.03 0.01
76_G 80_G 0.20 0.03 0.00
111_L 95_E 0.20 0.03 0.00
4_N 10_L 0.20 0.03 0.00
19_I 13_S 0.20 0.03 0.00
11_T 8_Y 0.19 0.03 0.00
20_H 16_S 0.19 0.03 0.00
232_F 191_V 0.19 0.03 0.00
2_F 7_G 0.19 0.03 0.00
14_S 22_F 0.19 0.03 0.00
143_H 146_G 0.19 0.03 0.00
25_A 30_A 0.19 0.03 0.00
121_Q 124_T 0.19 0.03 0.00
23_E 26_Y 0.19 0.03 0.00
21_Q 19_G 0.19 0.03 0.00
40_S 45_G 0.19 0.03 0.00
21_Q 26_Y 0.19 0.03 0.00
43_H 42_C 0.19 0.03 0.00
187_L 45_G 0.19 0.03 0.00
135_A 46_V 0.19 0.03 0.00
11_T 21_V 0.18 0.03 0.00
30_K 35_S 0.18 0.03 0.00
190_H 185_M 0.18 0.03 0.00
24_Y 23_Q 0.18 0.03 0.00
202_E 34_S 0.18 0.03 0.00
8_N 9_D 0.18 0.03 0.00
20_H 17_P 0.18 0.03 0.00
17_G 23_Q 0.18 0.03 0.00
102_P 73_H 0.18 0.03 0.00
24_Y 25_E 0.18 0.03 0.00
147_T 120_V 0.18 0.03 0.00
7_D 10_L 0.18 0.03 0.00
6_Y 9_D 0.18 0.03 0.00
10_V 13_S 0.18 0.03 0.00
133_L 166_I 0.18 0.03 0.00
4_N 5_G 0.18 0.03 0.00
11_T 12_A 0.18 0.03 0.00
43_H 190_I 0.18 0.03 0.00
181_E 43_K 0.17 0.03 0.00
21_Q 27_A 0.17 0.03 0.00
224_Y 216_W 0.17 0.03 0.00
10_V 10_L 0.17 0.03 0.00
143_H 142_S 0.17 0.03 0.00
148_C 157_V 0.17 0.03 0.00
15_P 22_F 0.17 0.03 0.00
202_E 35_S 0.17 0.03 0.00
69_H 106_N 0.17 0.03 0.00
28_A 27_A 0.17 0.03 0.00
25_A 23_Q 0.17 0.03 0.00
152_N 153_D 0.17 0.03 0.00
8_N 12_A 0.17 0.03 0.00
103_L 112_L 0.17 0.03 0.00
24_Y 19_G 0.17 0.03 0.00
44_A 45_G 0.17 0.03 0.00
13_W 21_V 0.17 0.03 0.00
5_Q 5_G 0.17 0.03 0.00
138_D 148_Q 0.17 0.03 0.00
198_T 169_A 0.17 0.03 0.00
17_G 15_F 0.17 0.03 0.00
161_I 137_M 0.17 0.03 0.00
129_G 154_P 0.17 0.03 0.00
161_I 79_A 0.17 0.03 0.00
19_I 15_F 0.17 0.03 0.00
235_G 192_K 0.17 0.03 0.00
126_R 84_D 0.16 0.03 0.00
5_Q 9_D 0.16 0.03 0.00
75_A 166_I 0.16 0.03 0.00
91_E 91_I 0.16 0.03 0.00
6_Y 16_S 0.16 0.03 0.00
225_D 228_V 0.16 0.03 0.00
155_D 150_Y 0.16 0.03 0.00
108_L 107_I 0.16 0.03 0.00
25_A 19_G 0.16 0.03 0.00
164_R 201_V 0.16 0.03 0.00
129_G 84_D 0.16 0.03 0.00
5_Q 8_Y 0.16 0.03 0.00
213_G 75_G 0.16 0.03 0.00
80_D 133_G 0.16 0.03 0.00
122_R 122_A 0.16 0.03 0.00
22_I 25_E 0.16 0.03 0.00
17_G 26_Y 0.16 0.03 0.00
7_D 8_Y 0.16 0.03 0.00
22_I 26_Y 0.16 0.03 0.00
116_T 152_I 0.16 0.03 0.00
149_P 133_G 0.16 0.03 0.00
70_I 138_L 0.16 0.03 0.00
4_N 11_S 0.16 0.03 0.00
27_E 32_E 0.15 0.03 0.00
23_E 24_V 0.15 0.03 0.00
224_Y 229_P 0.15 0.03 0.00
44_A 139_G 0.15 0.03 0.00
13_W 19_G 0.15 0.03 0.00
43_H 44_D 0.15 0.03 0.00
80_D 130_R 0.15 0.03 0.00
20_H 18_D 0.15 0.03 0.00
32_G 35_S 0.15 0.03 0.00
222_T 187_C 0.15 0.03 0.00
71_G 215_S 0.15 0.03 0.00
218_D 188_R 0.15 0.03 0.00
224_Y 214_L 0.15 0.03 0.00
179_F 181_Q 0.15 0.03 0.00
119_P 132_F 0.15 0.03 0.00
128_Y 123_Y 0.15 0.03 0.00
10_V 14_T 0.15 0.03 0.00
16_Q 22_F 0.15 0.03 0.00
76_G 167_G 0.15 0.03 0.00
20_H 20_R 0.15 0.03 0.00
43_H 46_V 0.15 0.03 0.00
12_V 12_A 0.15 0.03 0.00
182_C 34_S 0.15 0.03 0.00
185_N 220_L 0.15 0.03 0.00
18_R 22_F 0.15 0.03 0.00
17_G 27_A 0.15 0.03 0.00
7_D 7_G 0.15 0.03 0.00
23_E 27_A 0.15 0.03 0.00
74_I 83_A 0.15 0.03 0.00
17_G 16_S 0.15 0.03 0.00
222_T 216_W 0.15 0.03 0.00
119_P 129_V 0.15 0.03 0.00
24_Y 24_V 0.15 0.03 0.00
141_G 144_N 0.15 0.03 0.00
20_H 9_D 0.15 0.03 0.00
236_L 192_K 0.15 0.03 0.00
102_P 107_I 0.14 0.03 0.00
9_D 8_Y 0.14 0.03 0.00
8_N 18_D 0.14 0.03 0.00
211_S 52_K 0.14 0.03 0.00
162_G 80_G 0.14 0.03 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.15), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
ID Seq/Len Name Options I_Prob Status
6255 2.99 subFG00 Δgene:(0, 0) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 1.00 Done - Shared
6254 3.08 subFGnew Δgene:(0, 100) A:(1E-20, 4) B:(1E-20, 4) msa: HHblits (2015_06) 1.00 Done - Shared
6252 3.06 subFG Δgene:(0, ∞) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 1.00 Done - Shared
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