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OPENSEQ.org
cI_C_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 208 440 616
Sequences: 1081 3290 376
Seq/Len: 5.2 7.48 0.61
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.02
2 0.00 0.00 0.03
5 0.01 0.00 0.04
10 0.01 0.00 0.06
20 0.01 0.00 0.08
100 0.02 0.00 0.15
∞ 0.05 0.01 0.58
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
134_D 61_T 1.40 0.55 0.00
79_V 354_V 1.33 0.49 0.00
41_L 61_T 1.24 0.42 0.00
166_I 286_L 1.23 0.41 0.00
121_V 370_L 1.19 0.37 0.00
125_F 137_L 1.18 0.37 0.00
107_L 60_A 1.13 0.33 0.00
98_V 385_A 1.12 0.32 0.00
23_N 253_L 1.11 0.32 0.00
107_L 392_I 1.09 0.30 0.00
124_L 174_E 1.08 0.30 0.00
41_L 186_V 1.05 0.28 0.00
94_V 25_I 1.05 0.28 0.00
162_R 24_P 1.04 0.27 0.00
166_I 372_V 1.04 0.27 0.00
149_L 37_T 1.03 0.27 0.00
48_I 339_A 1.03 0.26 0.00
158_Y 167_G 1.03 0.26 0.00
92_I 398_A 1.00 0.24 0.00
159_V 25_I 0.99 0.24 0.00
92_I 366_W 0.98 0.24 0.00
108_I 171_G 0.98 0.23 0.00
21_R 169_I 0.97 0.23 0.00
173_E 88_N 0.97 0.23 0.00
95_K 266_I 0.96 0.23 0.00
130_S 395_A 0.96 0.22 0.00
171_V 399_Y 0.95 0.21 0.00
135_L 143_A 0.95 0.21 0.00
175_V 215_A 0.94 0.21 0.00
67_A 71_P 0.94 0.21 0.00
125_F 59_I 0.94 0.21 0.00
112_P 391_Y 0.93 0.21 0.00
19_L 375_V 0.93 0.21 0.00
37_V 354_V 0.93 0.20 0.00
131_G 413_I 0.93 0.20 0.00
111_F 160_T 0.92 0.20 0.00
106_S 386_E 0.92 0.20 0.00
138_I 264_F 0.92 0.20 0.00
25_V 365_W 0.92 0.20 0.00
39_A 414_I 0.91 0.19 0.00
112_P 267_V 0.90 0.19 0.00
165_D 137_L 0.90 0.19 0.00
66_T 397_S 0.90 0.19 0.00
41_L 411_L 0.89 0.18 0.00
182_R 200_L 0.89 0.18 0.00
127_I 304_I 0.88 0.18 0.00
80_V 240_D 0.88 0.18 0.00
65_I 44_W 0.88 0.18 0.00
14_A 164_G 0.88 0.18 0.00
181_Y 390_P 0.88 0.18 0.00
133_S 126_E 0.88 0.18 0.00
149_L 343_M 0.88 0.18 0.00
183_Q 171_G 0.88 0.18 0.00
26_I 375_V 0.87 0.18 0.00
122_F 44_W 0.87 0.18 0.00
68_V 63_I 0.86 0.17 0.00
42_S 416_K 0.86 0.17 0.00
98_V 269_F 0.86 0.17 0.00
44_V 411_L 0.86 0.17 0.00
172_Y 249_V 0.86 0.17 0.00
63_I 370_L 0.86 0.17 0.00
56_N 308_F 0.85 0.17 0.00
163_W 271_P 0.85 0.17 0.00
67_A 403_Y 0.85 0.17 0.00
161_V 72_H 0.85 0.17 0.00
16_H 27_S 0.85 0.17 0.00
100_E 138_M 0.85 0.17 0.00
180_E 237_A 0.85 0.17 0.00
106_S 65_L 0.84 0.16 0.00
173_E 262_V 0.84 0.16 0.00
171_V 93_L 0.84 0.16 0.00
125_F 338_G 0.84 0.16 0.00
52_R 126_E 0.84 0.16 0.00
173_E 131_V 0.84 0.16 0.00
158_Y 106_L 0.84 0.16 0.00
15_E 385_A 0.84 0.16 0.00
54_D 254_F 0.83 0.16 0.00
107_L 169_I 0.83 0.16 0.00
156_T 329_K 0.83 0.16 0.00
46_G 328_A 0.83 0.16 0.00
46_G 112_I 0.82 0.15 0.00
13_L 380_V 0.82 0.15 0.00
104_V 366_W 0.82 0.15 0.00
54_D 284_N 0.82 0.15 0.00
110_V 414_I 0.82 0.15 0.00
95_K 103_L 0.82 0.15 0.00
37_V 204_V 0.82 0.15 0.00
45_I 56_V 0.82 0.15 0.00
110_V 174_E 0.82 0.15 0.00
147_H 59_I 0.82 0.15 0.00
100_E 269_F 0.82 0.15 0.00
14_A 287_V 0.82 0.15 0.00
42_S 362_L 0.82 0.15 0.00
64_D 370_L 0.81 0.15 0.00
187_L 363_F 0.81 0.15 0.00
125_F 44_W 0.81 0.15 0.00
132_H 364_K 0.81 0.15 0.00
122_F 359_Y 0.81 0.15 0.00
186_F 367_F 0.81 0.15 0.00
29_Q 61_T 0.81 0.15 0.00
79_V 158_G 0.81 0.15 0.00
33_G 304_I 0.80 0.15 0.00
145_R 204_V 0.80 0.15 0.00
98_V 15_F 0.80 0.15 0.00
165_D 374_F 0.80 0.15 0.00
94_V 134_L 0.80 0.14 0.00
68_V 385_A 0.80 0.14 0.00
51_L 364_K 0.80 0.14 0.00
181_Y 163_T 0.80 0.14 0.00
142_Y 95_Y 0.79 0.14 0.00
35_L 107_A 0.79 0.14 0.00
82_H 392_I 0.79 0.14 0.00
175_V 350_D 0.79 0.14 0.00
122_F 16_E 0.79 0.14 0.00
75_A 362_L 0.79 0.14 0.00
169_R 403_Y 0.79 0.14 0.00
8_E 338_G 0.79 0.14 0.00
92_I 365_W 0.78 0.14 0.00
22_E 406_I 0.78 0.14 0.00
25_V 402_A 0.78 0.14 0.00
108_I 339_A 0.78 0.14 0.00
125_F 391_Y 0.78 0.14 0.00
127_I 29_V 0.78 0.14 0.00
86_M 51_L 0.78 0.14 0.00
127_I 339_A 0.78 0.14 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)
ID Seq/Len Name Options I_Prob Status
3008 0.62 cI_C_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2851 0.61 cI_C_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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