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OPENSEQ.org
cI_B_cIII_cytb
Genes: A B A+B
Length: 613 450 992
Sequences: 2092 3160 1079
Seq/Len: 3.41 7.02 1.09
MirrorTree (Pazo et al. 2001) 0.78
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 0.09
2 0.00 0.00 0.55
5 0.00 0.00 0.59
10 0.00 0.00 0.65
20 0.00 0.00 0.69
100 0.00 0.00 0.72
∞ 0.01 0.01 1.02
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
241_D 278_D 1.21 0.56 0.00
299_L 140_M 1.19 0.53 0.00
220_L 364_K 1.15 0.50 0.00
180_F 200_L 1.14 0.49 0.00
85_S 405_L 1.14 0.48 0.00
66_T 248_F 1.13 0.48 0.00
171_F 350_D 1.11 0.46 0.00
77_F 280_Y 1.11 0.46 0.00
136_L 356_S 1.07 0.42 0.00
95_V 80_V 1.06 0.42 0.00
384_A 80_V 1.05 0.40 0.00
283_V 344_A 1.04 0.40 0.00
396_F 379_W 1.01 0.37 0.00
333_F 18_W 1.01 0.36 0.00
44_V 371_A 1.00 0.36 0.00
222_L 349_L 1.00 0.36 0.00
141_L 406_I 0.99 0.35 0.00
437_F 88_N 0.98 0.34 0.00
220_L 93_L 0.98 0.34 0.00
392_V 54_C 0.97 0.34 0.00
122_L 278_D 0.97 0.34 0.00
56_G 412_G 0.97 0.34 0.00
8_I 197_L 0.96 0.33 0.00
333_F 404_F 0.96 0.33 0.00
388_A 384_P 0.95 0.32 0.00
100_H 122_K 0.94 0.31 0.00
222_L 222_N 0.93 0.30 0.00
388_A 298_F 0.92 0.29 0.00
325_V 407_I 0.92 0.29 0.00
194_T 103_L 0.92 0.29 0.00
213_N 342_V 0.92 0.29 0.00
109_G 254_F 0.91 0.29 0.00
325_V 280_Y 0.91 0.28 0.00
426_S 137_L 0.91 0.28 0.00
122_L 209_V 0.90 0.28 0.00
172_V 338_G 0.90 0.28 0.00
358_H 139_M 0.90 0.28 0.00
157_Y 364_K 0.90 0.28 0.00
103_A 207_A 0.90 0.28 0.00
420_V 60_A 0.90 0.28 0.00
73_F 204_V 0.90 0.28 0.00
280_L 357_G 0.89 0.27 0.00
459_V 345_L 0.89 0.27 0.00
73_F 375_V 0.88 0.27 0.00
299_L 141_G 0.88 0.26 0.00
149_C 282_E 0.87 0.26 0.00
38_V 172_V 0.87 0.26 0.00
207_H 172_V 0.87 0.26 0.00
263_V 123_A 0.87 0.25 0.00
430_F 96_L 0.86 0.25 0.00
323_L 418_D 0.86 0.25 0.00
286_V 169_I 0.86 0.25 0.00
397_F 363_F 0.86 0.25 0.00
44_V 116_L 0.86 0.25 0.00
172_V 59_I 0.85 0.24 0.00
220_L 284_N 0.85 0.24 0.00
186_F 60_A 0.84 0.24 0.00
333_F 418_D 0.84 0.23 0.00
367_G 371_A 0.84 0.23 0.00
362_I 174_E 0.84 0.23 0.00
171_F 122_K 0.84 0.23 0.00
75_I 138_M 0.84 0.23 0.00
437_F 43_W 0.83 0.23 0.00
75_I 108_V 0.83 0.23 0.00
122_L 218_T 0.83 0.23 0.00
219_T 136_Y 0.83 0.23 0.00
103_A 174_E 0.82 0.22 0.00
430_F 174_E 0.82 0.22 0.00
295_G 334_I 0.82 0.22 0.00
304_I 196_S 0.82 0.22 0.00
560_L 189_P 0.82 0.22 0.00
277_P 208_L 0.82 0.22 0.00
331_A 140_M 0.81 0.22 0.00
385_A 269_F 0.81 0.21 0.00
292_L 243_P 0.81 0.21 0.00
227_V 93_L 0.81 0.21 0.00
286_V 394_L 0.81 0.21 0.00
184_A 354_V 0.81 0.21 0.00
94_G 53_F 0.81 0.21 0.00
374_L 371_A 0.80 0.21 0.00
73_F 110_I 0.80 0.21 0.00
462_I 398_A 0.80 0.21 0.00
389_L 15_F 0.80 0.21 0.00
263_V 126_E 0.80 0.21 0.00
306_R 59_I 0.79 0.20 0.00
44_V 57_L 0.79 0.20 0.00
401_E 248_F 0.79 0.20 0.00
228_G 222_N 0.79 0.20 0.00
426_S 342_V 0.79 0.20 0.00
50_V 376_V 0.79 0.20 0.00
172_V 25_I 0.79 0.20 0.00
184_A 126_E 0.79 0.20 0.00
431_R 370_L 0.79 0.20 0.00
513_L 207_A 0.78 0.20 0.00
424_M 395_A 0.78 0.20 0.00
159_T 18_W 0.78 0.20 0.00
388_A 35_I 0.78 0.20 0.00
64_L 213_I 0.78 0.19 0.00
38_V 258_V 0.77 0.19 0.00
112_G 199_Y 0.77 0.19 0.00
105_W 126_E 0.77 0.19 0.00
294_A 357_G 0.77 0.19 0.00
493_L 71_P 0.77 0.19 0.00
84_L 272_N 0.77 0.19 0.00
80_V 88_N 0.77 0.19 0.00
137_L 208_L 0.77 0.19 0.00
298_A 196_S 0.77 0.19 0.00
267_A 126_E 0.77 0.19 0.00
228_G 89_G 0.76 0.19 0.00
20_F 143_A 0.76 0.18 0.00
378_C 71_P 0.76 0.18 0.00
14_G 336_M 0.76 0.18 0.00
364_K 158_G 0.76 0.18 0.00
65_W 286_L 0.76 0.18 0.00
43_L 414_I 0.76 0.18 0.00
358_H 71_P 0.76 0.18 0.00
426_S 248_F 0.76 0.18 0.00
283_V 350_D 0.75 0.18 0.00
502_V 407_I 0.75 0.18 0.00
499_V 60_A 0.75 0.18 0.00
283_V 103_L 0.75 0.18 0.00
103_A 280_Y 0.75 0.18 0.00
347_L 71_P 0.75 0.18 0.00
100_H 95_Y 0.75 0.18 0.00
501_A 60_A 0.75 0.18 0.00
439_G 209_V 0.75 0.18 0.00
227_V 387_G 0.75 0.18 0.00
183_F 103_L 0.75 0.18 0.00
389_L 378_M 0.75 0.18 0.00
17_L 172_V 0.75 0.18 0.00
181_L 56_V 0.75 0.18 0.00
349_S 84_M 0.75 0.18 0.00
220_L 169_I 0.75 0.18 0.00
269_T 356_S 0.75 0.18 0.00
292_L 412_G 0.75 0.18 0.00
179_V 300_P 0.75 0.18 0.00
388_A 291_H 0.74 0.18 0.00
103_A 57_L 0.74 0.17 0.00
495_I 96_L 0.74 0.17 0.00
17_L 334_I 0.74 0.17 0.00
87_T 243_P 0.74 0.17 0.00
233_L 403_Y 0.74 0.17 0.00
159_T 374_F 0.74 0.17 0.00
73_F 208_L 0.74 0.17 0.00
374_L 341_L 0.74 0.17 0.00
77_F 293_V 0.74 0.17 0.00
177_G 61_T 0.74 0.17 0.00
70_V 412_G 0.74 0.17 0.00
164_G 169_I 0.74 0.17 0.00
139_M 266_I 0.74 0.17 0.00
283_V 126_E 0.73 0.17 0.00
266_I 327_D 0.73 0.17 0.00
500_V 96_L 0.73 0.17 0.00
397_F 93_L 0.73 0.17 0.00
366_G 343_M 0.73 0.17 0.00
507_L 172_V 0.73 0.17 0.00
138_L 24_P 0.73 0.17 0.00
432_M 139_M 0.73 0.17 0.00
263_V 22_R 0.73 0.17 0.00
406_A 373_D 0.73 0.17 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)
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