evolutionary path: sequence table

Sequences Associated with Transitions [caption]

	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAAUGAUCUCGUGUGCCCAUUGCAUAUCCCGUACAGGA`
0	`((.(((((((((((((............(((....)))......)))))).))))))).))...(((......)))`
	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAAUGAUCUCGUGUGCCCAUUGCAUAUCCCGUACAGGA`
	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAAUGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
1	`..((((((..((((((............(((....)))......))))))(((((...)))))..)))))).....`
	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAAUGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
2	`..((((((..((((((.....((((...(((....))).)))).))))))(((((...)))))..)))))).....`
	`GUUAUGGGCGAUGAGGAGUAGUGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GUUAUGGGCGUUGAGGAGUAGUGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
3	`..((((((((((((.((................))..)))))).....(((((((...))))))))))))).....`
	`GUUAUGGGCGUUGAGGAGUAGUGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GUUAUGGGCGUUGAGGAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
4	`..((((((((((((.((....(((....)))..))..)))))).....(((((((...))))))))))))).....`
	`GUUAUGGGCGUUGAGGAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GGUAUGGGCGUUGAGGAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
5	`.(((((((((((((.((....(((....)))..))..)))))).....(((((((...))))))))))))))....`
	`GGUAUGGGCGUUGAGGAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GGUAUGGGCGUUGAGUAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
6	`.(((((((((((((.......(((....)))......)))))).....(((((((...))))))))))))))....`
	`GGUAUGGGCGUUGAGUAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUGCAUAUCCCGUACAGGA`
	`GGUAUGGGCGUUGAGUAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUUCAUAUCCCGUACAGGA`
7	`.(((((((((((((.......(((....)))......)))))).....(((((.......))))))))))))....`
	`GGUAUGGGCGUUGAAUAGUAGGGUUUAAACCAAUCGGUCAACGAUCUCGUGUGCGCAUUUCAUAUCCCGUACAGAA`
	`GGUAUGGGCGUUGAAUAGUAGGGUUUAAACCAAUCGGCCAACGAUCUCGUGUGCGCAUUUCAUAUCCCGUACAGAA`
8	`.((((((((((((........(((....))).......))))).....(((((.......))))))))))))....`
	`GGUAUGGGCGUUGAAUAAUAGGGUUUAAACCAAUCGGCCAACGAUCUCGUGUGCGCAUUUCAUAUCCCAUACAGAA`
	`GGUAUGGGCGUUGAAUAAUAGGGUUUAAACCAAUCGGCCAACGAUCUCGUGUGCGCAUUUCAUAUACCAUACAGAA`
9	`.((((((.(((((........(((....))).......))))).....(((((.......))))).))))))....`
	`UGGAUGGACGUUGAAUAACAAGGUAUCGACCAAACAACCAACGAGUAAGUGUGUACGCCCCACACACCGUCCCAAG`
	`UGGAUGGACGUUGAAUAACAAGGUAUCGACCAAACAACCAACGAGUAAGUGUGUACGCCCCACACAGCGUCCCAAG`
10	`.(((((..(((((........(((....))).......))))).....(((((.......)))))..)))))....`
	`UGGAUGGACGUUGAAUAACAAGGUAUCGACCAAACAACCAACGAGUAAGUGUGUACGCCCCACACAGCGUCCCAAG`
	`UGGAUGGACGUUGAAUAACAAGGUAUCGCCCAAACAACCAACGAGUAAGUGUGUACGCCCCACACAGCGUCCCAAG`
11	`.(((((..(((((........(((...)))........))))).....(((((.......)))))..)))))....`
	`UGGAUGGACGUUGAUUAACAAGGUAUCACCAAAACAACCAACGAGUAAGUGUGUACGCCCCACACAGCGUCCCAAG`
	`UGGAUGCACGUUGAUUAACAAGGUAUCACCAAAACAACCAACGAGUAAGUGUGUACGCCCCACACAGCGUCCCAAG`
12	`.((((((.(((((........(((...)))........))))).....(((((.......))))).))))))....`
	`UGGAUGCACGUUGACUAACAAGGUAUCACCAAAACAGCCAACGAGUACGUGUGUACGGCCCACACAGCGUCCCAAG`
	`GGGAUGCACGUUGACUAACAAGGUAUCACCAAAACAGCCAACGAGUACGUGUGUACGGCCCACACAGCGUCCCAAG`
13	`(((((((.(((((........(((...)))........))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUUGACGAAUAAGGUUUAACCAAGGCAGCUAACGAGUACGUGUGUACGGCCCACACCGCGUCCCAAG`
	`GGGAUGCACGUUGACGAAUAAGGUUUAAGCAAGGCAGCUAACGAGUACGUGUGUACGGCCCACACCGCGUCCCAAG`
14	`(((((((.(((((((.......)))..(((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUUGACGAAUAAGGUUUAAGCAAGGCAGCUAACGAGUACGUGUGUACAGCCCACACCGCGUCCCAAG`
	`GGGAUGCACGUUGACGAAUAAGGUUUAAGCAAGGCAGCUUACGAGUACGUGUGUACAGCCCACACCGCGUCCCAAG`
15	`(((((((.(((.(((.......))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUUGACGAAUAAGGUUUUAGCAAGGCAGCUAACGAGUAUGUGUGUACGGCCCACACCGCGUCCCAAG`
	`GGGAUGCACGUUGACGAAUAAGGUUAUAGCAAGGCAGCUAACGAGUAUGUGUGUACGGCCCACACCGCGUCCCAAG`
16	`(((((((.(((((((.......))))((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUUGACGAAUAAGGUUAUAGCAAGGCAGCUAACGAGUAUGUGUGUACGGCCCACACCGCGUCCCAAG`
	`GGGAUGCACGUUGACCAAUAAGGUUAUAGCAAGGCAGCUAACGAGUAUGUGUGUACGGCCCACACCGCGUCCCAAG`
17	`(((((((.((((((((.....)))))((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUUGACCAAUAAGGUUAUAGCAAGGCAGCUAACGAGUAUGUGUGUACGACCCACACCGCGUCCUAAG`
	`GGGAUGCACGUUGACCAAUAAGGUUGUAGCAAGGCAGCUAACGAGUAUGUGUGUACGACCCACACCGCGUCCUAAG`
18	`(((((((.(((.((((.....)))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUAGACCGAGAAGGUUGUAGCAAGGAAGCUAACGAGUAUGUGUGAAGGACCCACACCGCAUCCUAAG`
	`GGGAUGCACGUAGACCGAGAAGGCUGUAGCAAGGAAGCUAACGAGUAUGUGUGAAGGACCCACACCGCAUCCUAAG`
19	`(((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUAGACCGAGAAGGCUGUAGCAAGGAAGCUAACGAGUAUGUGUGAAGGACCCACACCGCAUCCUAAG`
	`GGGAUGAACGUAGACCGAGAAGGCUGUAGCAAGGAAGCUAACGAGUAUGUGUGAAGGACCCACACCGCAUCCUAAG`
20	`((((((..(((((.((.....)))).((((......))))))).....(((((.......)))))..))))))...`
	`GGGAUGGACGUAGACCGUGAAGGCUGUAGCAAGGAAGCUAACGAAUAUGUGUGAAGGACCCACACCGCAUCCUAAU`
	`GGGAUGGACGUAGACCGUGAAGGCUGUAGCUAGGAAGCUAACGAAUAUGUGUGAAGGACCCACACCGCAUCCUAAU`
21	`((((((..(((((.((.....)))).(((((....)))))))).....(((((.......)))))..))))))...`
	`GGGAUGGACGUAGACCGUGAAGGCUGUAGCUAGGAAGCUAACGAAUAUGUGUGAAGGACCCACACCGCAUCCUAAU`
	`GGGAUGGACGUAGACCGUGAAGGCUGUAGCAAGGAAGCUAACGAAUAUGUGUGAAGGACCCACACCGCAUCCUAAU`
22	`((((((..(((((.((.....)))).((((......))))))).....(((((.......)))))..))))))...`
	`GGGAUGCACGUAGACCGACAGGGCUAUAGCAAGGAAGCUAACGACUAUGUGUGAACGACCCACACCUCAUCCCAAA`
	`GGGAUGCACGUAGACCGACAGGGCUAUAGCUAGGAAGCUAACGACUAUGUGUGAACGACCCACACCUCAUCCCAAA`
23	`((((((..(((((.((.....)))).(((((....)))))))).....(((((.......)))))..))))))...`
	`GGGAUGCACGUAGACCGACAGGGCUAUAGCUAGGAAGCUAACGACUAUGUGUGAACGACCCACACUUCAUCCCAAA`
	`GGGAUGCACGUAGACCGACAGGGCUAUAGCGAGGAAGCUAACGACUAUGUGUGAACGACCCACACUUCAUCCCAAA`
24	`((((((..(((((.((.....)))).((((......))))))).....(((((.......)))))..))))))...`
	`GGGAUGCACGUGGACCGACAGGGCCAUAGCGCGGAAGCUAACGAAUACGUGUGAACGACCCACACCUCAUCCCAGA`
	`GGGAUGCACGUGGACCGACAGGGCCAUAGCGCGGAAGCUAACGAAUACGUGUGAACGACCCACACCGCAUCCCAGA`
25	`(((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUGGACCGACUGGGCUAUAGCGCGGAAGCUAACGACUACGUGUGAACGACCCACACCGCAUCCCAGA`
	`AGGAUGCACGUGGACCGACUGGGCUAUAGCGCGGAAGCUAACGACUACGUGUGAACGACCCACACCGCAUCCCAGA`
26	`.((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).))))))....`
	`GGGAUGUGCGUAGACCGAUCGGGCUGUAGCCAGGGAGCUAACGAAACCGUGUGAACCAUCCGCACUGCAUCUGACA`
	`CGGAUGUGCGUAGACCGAUCGGGCUGUAGCCAGGGAGCUAACGAAACCGUGUGAACCAUCCGCACUGCAUCUGACA`
27	`(((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUGGACCGGGAAGGCUGUAGCGAACGAGCUAACGAAAACGUGCAAGUGAAGUGCACUGCAUCCCCGG`
	`GGGAUGCACGUGGACCGGGAAGGCUGUAGCUAACGAGCUAACGAAAACGUGCAAGUGAAGUGCACUGCAUCCCCGG`
28	`(((((((.(((((.((.....)))).(((((....)))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUAGACCGGGAAGGCUGUAGCGAAGGCGCUAGCGAAGAUGUGCGAAUUUAAUGCACCGUGUCCCAAU`
	`AGGAUGCACGUAGACCGGGAAGGCUGUAGCGAAGGCGCUAGCGAAGAUGUGCGAAUUUAAUGCACCGUGUCCCAAU`
29	`.((((((.(((((.((.....)))).(((((....)))))))).....(((((.......))))).))))))....`
	`GGGAUGCACGUAGACCGGGAAGGCUGUAGCGAAGGCGCUAACGAAGUUGUGCGAAUCUAAUGCACCGUGUCCGAAU`
	`GGGAUGCACGUAGACCGGGAAGGCUGUAGCGAAGGAGCUAACGAAGUUGUGCGAAUCUAAUGCACCGUGUCCGAAU`
30	`.((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).))))))....`
	`GGGAUGCACGUAGACCGGGAAGGCUGUAGCGAUGUCGCUAACGAAGACGUGCGAACCUAAUGCACCGUGUCCAAGU`
	`GGGAUGCACGUAGCCCGGGAAGGCUGUAGCGAUGUCGCUAACGAAGACGUGCGAACCUAAUGCACCGUGUCCAAGU`
31	`.((((((.(((((((......)))).((((......))))))).....(((((.......))))).))))))....`
	`GGGAUGCACGUAGCCCGCGAAGGCUGUAGCGAUGUCGCUAACGAUUACGUGCGAAUCUAAUGCACCGUGUCCAAGU`
	`GGGAUGCACGUAGCCCGCGAAGGCUGUAGCGAUGUCGCUAACGAUUACGUGCGAAUCUAAUGCACCGUGUCCUAGU`
32	`(((((((.(((((((......)))).((((......))))))).....(((((.......))))).)))))))...`
	`GGGAUGCACGUAGCCCGCGAAGGCUGUAGCGAUGUCGCUAACGAUUAAGUGCGAAUCUAAUGCACCGUGUCCUAGU`
	`GGGAUGCACGUAGCCCGCGAAGGCUGUAGCGAUGGCGCUAACGAUUAAGUGCGAAUCUAAUGCACCGUGUCCUAGU`
33	`(((((((.(((((((......)))).(((((....)))))))).....(((((.......))))).)))))))...`
	`GGGAUACACGUGGCCCGUGAAGGCUGUAGCGCAACCGCUAACGAAAUAGUGCGAAUGUAAUGCACCGUGUCCCCGA`
	`GGGAUACACGUGGCCCGUGAACGCUGUAGCGCAACCGCUAACGAAAUAGUGCGAAUGUAAUGCACCGUGUCCCCGA`
34	`(((((((.((((((........))).(((((....)))))))).....(((((.......))))).)))))))...`
	`GGGAUACACGUGGCCCCUGAAAGCUGUAGCGCAACUGCUGACGAAAUAGUGCGAAUAGAAUGCACCGUGUCCCCGA`
	`GGGAUACACGUGGCCCCUGAAAGCUGUAGCGCAACUGCUGACGAAAUAGUGCGAAUAGAAUGCACCCUGUCCCCGA`
35	`((((((..((((((........))).(((((....)))))))).....(((((.......)))))..))))))...`
	`GGGAUACACGUGGCCCCUGAAAGCCGUAGCGCAACUGCUGACGAAACCGUGCGAAUAAUAUGCACCCUGUCCCCGG`
	`GGGAUACACGUGGCCCCUGAAGGCCGUAGCGCAACUGCUGACGAAACCGUGCGAAUAAUAUGCACCCUGUCCCCGG`
36	`((((((..(((((((......)))).(((((....)))))))).....(((((.......)))))..))))))...`
	`GGGAUACACGUGGCCCCUCAAGGCCGUAGCGCAACUGCUGAUGAAACCGUGCGAAUAAUCCGCACCCUGUCCCCGG`
	`GGGAUACACGUGGCCCCUCAAGGCCGUAGCGCAACUGCUGCUGAAACCGUGCGAAUAAUCCGCACCCUGUCCCCGG`
37	`((((((....(((((......)))))((((((....)).)))).....(((((.......)))))..))))))...`
	`GGGAUACACGUGGCCCCUCAAGGCCGUAGCGCAACUGCUGCUGAAACCGUGCGAAUAAUCCGCACCCUGUCCCCGG`
	`GGGAUACACGUGGCCCCUCAAGGCCGUAGCGAAACUGCUGCUGAAACCGUGCGAAUAAUCCGCACCCUGUCCCCGG`
38	`((((((....(((((......)))))(((((.......))))).....(((((.......)))))..))))))...`
	`GGGAUACAUGUGGCCCCUCAAGGCCGUAGCGAAACUGCUGCUGAAACCGUGUGAAUAAUCCGCACCCUGUCCCCGA`
	`GGGAUACAUGUGGCCCCUCAAGGCCCUAGCGAAACUGCUGCUGAAACCGUGUGAAUAAUCCGCACCCUGUCCCCGA`
39	`((((((.....((((......)))).(((((.......))))).....(((((.......)))))..))))))...`
	`GGGAUAUACGAGGCCCGUCAAGGCCGUAGCGAACCGACUGUUGAAACUGUGCGAAUAAUCCGCACCCUGUCCCGGG`
	`GGGAUAUACGGGGCCCGUCAAGGCCGUAGCGAACCGACUGUUGAAACUGUGCGAAUAAUCCGCACCCUGUCCCGGG`
40	`((((((...((((((......)))).(((((.......))))).....(((((.......)))))))))))))...`
	`GGGAUAUACGGGGCCCGUCAAGGCCGUAGCGAACCGACUGUUGAGACUGUGCGAAUAAUCCGCACCCUGUCCCGGG`
	`GGGAUAUACGGGCCCCGUCAAGGCCGUAGCGAACCGACUGUUGAGACUGUGCGAAUAAUCCGCACCCUGUCCCGGG`
41	`((((((....((((.......)))).(((((.......))))).....(((((.......)))))..))))))...`
	`GGGAUAUACGGGCCCCUUCAAGGCCAUAGCGAACCGACUGUUGAAACUGUGCGAAUAAUCCGCACCCUGUCCCGGA`
	`GGGAUAUACGGGCCCCUUCAAGCCCAUAGCGAACCGACUGUUGAAACUGUGCGAAUAAUCCGCACCCUGUCCCGGA`
42	`((((((...((((........)))).(((((.......))))).....(((((.......)))))..))))))...`
	`GGGAUGAUAGGGCGUGUGAUAGCCCAUAGCGAACCCCCCGCUGAGCUUGUGCGACGUUUGUGCACCCUGUCCCGCU`
	`GGGAAGAUAGGGCGUGUGAUAGCCCAUAGCGAACCCCCCGCUGAGCUUGUGCGACGUUUGUGCACCCUGUCCCGCU`
43	`((((((...((((........)))).(((((.......))))).....(((((.......))))).)).))))...`
	`GGGAAGAUAGGGCGUGUGAUAGCCCAUAGCGAACCCCCCGCUGAGCUUGUGCGACGUUUGUGCACCCUGUCCCGCU`
	`GGGCAGAUAGGGCGUGUGAUAGCCCAUAGCGAACCCCCCGCUGAGCUUGUGCGACGUUUGUGCACCCUGUCCCGCU`
44	`((((((...((((........)))).(((((.......))))).....(((((.......))))).))))))....`

The sample section

(a)	`CGGAUGUGCGUAGACCGAUCGGGCUGUAGCCAGGGAGCUAACGAAACCGUGUGAACCAUCCGCACUGCAUCUGACA`
27	`(((((((.(((((.((.....)))).((((......))))))).....(((((.......))))).)))))))...`
(b)	`GGGAUGCACGUGGACCGGGAAGGCUGUAGCGAACGAGCUAACGAAAACGUGCAAGUGAAGUGCACUGCAUCCCCGG`
(c)	`GGGAUGCACGUGGACCGGGAAGGCUGUAGCUAACGAGCUAACGAAAACGUGCAAGUGAAGUGCACUGCAUCCCCGG`
28	`(((((((.(((((.((.....)))).(((((....)))))))).....(((((.......))))).)))))))...`

shows the sequences underlying the transition from shape 27 on the evolutionary path of Figure 1A to shape 28. The shapes are represented by a balanced parentheses notation.

The first sequence (a) is derived from the preceding sequence folding into shape 26 (not shown) by a point mutation at the position indicated in red. (a) folds into shape 27, and innovates the reactor with that shape. The next sequence (b) also folds into 27. (b) mutated at the red position and gave rise to (c) innovating the reactor with shape 28. (a) and (b) are neutral sequences folding both into 27. They are separated by about 116 time units. (a) and (b) differ at the positions indicated in blue which show the accumulation of neutral mutations while the trajectory drifted for 116 time units on or close to the neutral sequence network associated with shape 27. With regard to Figure 1A (a) is the sequence associated with the green step to shape 27, and (b) is the sequence associated with the step away from it, leading to 28.

A printable file of this table is available for download [color postscript].