[Strategy Market][Switch] Penalize designs with listed stacks for R96 Same State NG 2

From DPAT3 penalize designs that have any of the following list of stacks in R96 Same State NG 2 since they are only predicted by Vienna 2 to exist in the MFE structure of poor performing designs only ( designs scoring bellow 80 only).  Here is an explanation from DPAT3’s documentation of the way the stacks are written)

’ If you wanted to look at a stack in the 2nd State with 3 pairs in it and the nucleotide pairs are 22 paired with 50, 23 paired with 49, and 24 paired with 48 then it would be written, “2ndState-22:50,23:49,24:48" ’

And here are the 2060 unique stacks predicted only in designs scoring under 80 in R96 Same State NG 2.

1stState-42:74,43:73,44:72
1stState-46:70
1stState-48:68
1stState-50:66,51:65,52:64
1stState-21:33,22:32,23:31
1stState-5:62,6:61,7:60
1stState-19:48,20:47,21:46,22:45,23:44,24:43
1stState-26:41,27:40,28:39
1stState-66:76,67:75,68:74
1stState-31:36
1stState-27:40,28:39
1stState-65:77,66:76,67:75,68:74
1stState-1:84,2:83,3:82
1stState-42:67,43:66,44:65
1stState-18:36,19:35,20:34,21:33,22:32,23:31
1stState-48:63,49:62,50:61,51:60
1stState-48:61,49:60,50:59
1stState-46:63
1stState-20:34,21:33,22:32,23:31
1stState-43:66,44:65
1stState-18:37,19:36
1stState-8:40,9:39,10:38,11:37
1stState-16:34,17:33,18:32,19:31
1stState-21:29,22:28
1stState-42:80,43:79,44:78,45:77
1stState-47:76,48:75,49:74
1stState-58:67,59:66,60:65
1stState-55:61,56:60
1stState-10:57,11:56
1stState-16:52,17:51,18:50
1stState-21:46,22:45,23:44,24:43
1stState-48:68,49:67,50:66
1stState-21:33,22:32,23:31,24:30,25:29
1stState-51:63,52:62,53:61,54:60
1stState-48:68,49:67
1stState-20:34,21:33,22:32,23:31,24:30,25:29
1stState-7:62,8:61,9:60,10:59,11:58
1stState-18:49,19:48,20:47,21:46,22:45,23:44,24:43
1stState-27:42,28:41,29:40,30:39
1stState-2:83,3:82,4:81,5:80,6:79
1stState-55:63,56:62
1stState-3:83,4:82,5:81,6:80,7:79,8:78
1stState-25:40,26:39,27:38,28:37,29:36,30:35
1stState-3:83,4:82,5:81,6:80,7:79
1stState-2:84,3:83,4:82,5:81,6:80,7:79
1stState-1:83,2:82,3:81
1stState-5:79,6:78,7:77
1stState-26:46,27:45,28:44
1stState-30:42,31:41,32:40,33:39
1stState-1:48,2:47,3:46,4:45
1stState-5:43,6:42,7:41,8:40
1stState-58:83,59:82,60:81,61:80,62:79,63:78
1stState-14:34,15:33,16:32,17:31,18:30,19:29,20:28,21:27
1stState-66:75
1stState-6:79,7:78,8:77,9:76,10:75,11:74
1stState-11:50,12:49
1stState-14:47,15:46
1stState-52:81,53:80,54:79,55:78,56:77
1stState-18:43,19:42,20:41,21:40
1stState-58:75,59:74
1stState-23:39,24:38,25:37,26:36
1stState-28:35,29:34
1stState-25:82,26:81,27:80,28:79
1stState-30:78,31:77,32:76,33:75
1stState-34:73,35:72
1stState-38:68,39:67,40:66
1stState-42:64,43:63
1stState-46:61,47:60,48:59,49:58
1stState-8:20,9:19,10:18,11:17,12:16
1stState-44:82,45:81,46:80,47:79
1stState-24:42,25:41,26:40,27:39,28:38
1stState-30:37,31:36
1stState-25:50,26:49,27:48,28:47,29:46,30:45,31:44
1stState-34:41,35:40
1stState-35:75,36:74,37:73,38:72
1stState-40:70
1stState-7:34,8:33,9:32
1stState-42:68,43:67,44:66,45:65,46:64,47:63
1stState-11:30
1stState-44:61,45:60
1stState-46:58,47:57,48:56,49:55
1stState-15:84,16:83,17:82,18:81,19:80,20:79
1stState-22:76,23:75
1stState-15:82,16:81,17:80,18:79,19:78
1stState-22:75,23:74
1stState-31:67,32:66,33:65
1stState-18:66,19:65,20:64,21:63,22:62,23:61,24:60,25:59
1stState-26:55,27:54,28:53,29:52,30:51,31:50
1stState-32:47,33:46,34:45,35:44
1stState-15:82,16:81,17:80,18:79,19:78,20:77,21:76
1stState-23:74
1stState-31:68
1stState-33:66,34:65
1stState-15:82,16:81,17:80,18:79,19:78,20:77,21:76,22:75,23:74
1stState-15:82,16:81,17:80,18:79,19:78,20:77,21:76,22:75
1stState-15:82,16:81,17:80,18:79
1stState-20:77,21:76,22:75
1stState-23:76,24:75
1stState-24:75
1stState-2:11,3:10,4:9
1stState-4:46,5:45,6:44
1stState-9:41,10:40,11:39,12:38
1stState-47:74,48:73,49:72
1stState-51:70
1stState-15:33,16:32,17:31,18:30,19:29,20:28
1stState-53:68,54:67
1stState-15:82,16:81,17:80,18:79,19:78,20:77
1stState-35:84,36:83,37:82,38:81,39:80
1stState-42:76,43:75,44:74,45:73
1stState-1:33,2:32,3:31,4:30,5:29
1stState-6:27,7:26
1stState-51:66,52:65,53:64
1stState-10:23,11:22,12:21,13:20,14:19
1stState-55:62,56:61
1stState-22:76
1stState-24:74,25:73,26:72,27:71
1stState-15:33,16:32,17:31,18:30,19:29
1stState-55:65,56:64
1stState-30:67,31:66,32:65,33:64
1stState-21:77,22:76,23:75
1stState-25:74,26:73,27:72
1stState-9:69,10:68,11:67,12:66,13:65
1stState-18:64,19:63,20:62,21:61,22:60
1stState-23:57,24:56,25:55,26:54
1stState-28:53,29:52,30:51,31:50
1stState-44:77,45:76,46:75,47:74,48:73,49:72
1stState-1:53,2:52,3:51,4:50,5:49
1stState-7:48
1stState-9:47,10:46,11:45,12:44
1stState-60:83,61:82,62:81,63:80
1stState-18:40,19:39,20:38,21:37,22:36,23:35
1stState-65:78,66:77,67:76
1stState-24:33,25:32
1stState-16:68,17:67,18:66
1stState-20:64,21:63,22:62,23:61,24:60,25:59
1stState-20:77,21:76,22:75,23:74
1stState-23:75,24:74,25:73,26:72,27:71
1stState-20:77,21:76
1stState-47:67,48:66,49:65
1stState-33:66
1stState-20:78,21:77,22:76
1stState-21:77,22:76
1stState-9:75,10:74,11:73
1stState-13:54,14:53,15:52,16:51,17:50,18:49,19:48,20:47
1stState-26:41,27:40,28:39,29:38
1stState-31:76,32:75,33:74,34:73,35:72
1stState-37:68,38:67,39:66
1stState-42:63,43:62,44:61,45:60,46:59,47:58,48:57,49:56,50:55
1stState-10:20,11:19,12:18
1stState-2:82,3:81
1stState-5:79,6:78
1stState-4:81,5:80,6:79,7:78,8:77,9:76,10:75,11:74
1stState-27:42,28:41,29:40,30:39,31:38
1stState-1:84,2:83
1stState-22:53,23:52,24:51,25:50,26:49
1stState-27:43,28:42,29:41,30:40
1stState-32:38,33:37
1stState-2:83,3:82,4:81
1stState-22:34,23:33,24:32,25:31
1stState-52:64,53:63,54:62,55:61,56:60
1stState-6:79,7:78
1stState-10:75,11:74
1stState-13:52,14:51,15:50,16:49,17:48,18:47,19:46,20:45,21:44
1stState-27:40,28:39,29:38
1stState-57:67,58:66,59:65
1stState-30:36
1stState-4:82,5:81
1stState-7:80,8:79,9:78
1stState-14:53,15:52,16:51,17:50,18:49,19:48,20:47
1stState-21:45
1stState-54:77,55:76,56:75,57:74,58:73
1stState-22:40,23:39,24:38,25:37,26:36,27:35
1stState-36:59,37:58,38:57
1stState-13:35,14:34
1stState-16:33,17:32,18:31,19:30,20:29
1stState-40:56,41:55,42:54,43:53
1stState-65:73,66:72,67:71
1stState-45:52,46:51
1stState-21:27,22:26
1stState-55:79,56:78
1stState-13:34,14:33,15:32,16:31
1stState-35:53,36:52,37:51,38:50,39:49
1stState-58:76,59:75,60:74,61:73,62:72
1stState-18:29,19:28
1stState-41:48,42:47
1stState-4:83,5:82
1stState-6:80,7:79
1stState-23:65,24:64,25:63,26:62
1stState-33:55,34:54,35:53,36:52,37:51,38:50
1stState-4:82,5:81,6:80,7:79,8:78
1stState-14:55,15:54,16:53,17:52,18:51,19:50,20:49,21:48
1stState-23:46
1stState-25:45,26:44
1stState-56:74,57:73,58:72,59:71,60:70,61:69
1stState-28:42,29:41,30:40,31:39
1stState-7:78
1stState-10:48,11:47,12:46,13:45
1stState-14:42,15:41,16:40,17:39,18:38,19:37,20:36,21:35
1stState-49:77,50:76,51:75,52:74
1stState-54:72
1stState-57:69,58:68
1stState-26:34,27:33,28:32
1stState-2:66,3:65
1stState-6:62,7:61,8:60,9:59,10:58
1stState-12:55,13:54
1stState-15:52,16:51,17:50,18:49,19:48,20:47,21:46,22:45,23:44,24:43
1stState-25:41,26:40
1stState-67:76,68:75,69:74
1stState-24:63,25:62
1stState-27:61,28:60
1stState-29:58
1stState-31:56,32:55
1stState-33:51,34:50,35:49,36:48,37:47
1stState-39:46,40:45
1stState-16:47,17:46,18:45,19:44,20:43,21:42
1stState-49:80,50:79
1stState-53:75,54:74,55:73,56:72
1stState-59:68,60:67,61:66
1stState-3:10,4:9
1stState-1:74,2:73,3:72
1stState-4:34,5:33,6:32
1stState-39:67,40:66,41:65
1stState-43:64
1stState-10:28
1stState-46:61,47:60,48:59,49:58,50:57
1stState-13:25,14:24,15:23,16:22,17:21
1stState-3:59,4:58,5:57,6:56,7:55
1stState-9:53,10:52
1stState-13:31,14:30,15:29,16:28,17:27,18:26,19:25,20:24
1stState-60:76,61:75,62:74,63:73,64:72
1stState-4:76,5:75,6:74,7:73,8:72
1stState-38:56,39:55,40:54,41:53,42:52
1stState-20:37,21:36,22:35,23:34,24:33,25:32
1stState-44:51,45:50
1stState-8:82,9:81
1stState-11:79,12:78,13:77,14:76,15:75
1stState-37:74,38:73,39:72
1stState-40:67,41:66,42:65,43:64,44:63
1stState-46:62,47:61,48:60,49:59
1stState-51:58,52:57
1stState-6:23,7:22,8:21,9:20,10:19
1stState-48:65,49:64
1stState-51:62,52:61,53:60,54:59
1stState-72:83
1stState-74:81,75:80
1stState-6:64,7:63
1stState-9:60,10:59
1stState-13:56,14:55,15:54,16:53,17:52,18:51,19:50
1stState-20:44,21:43
1stState-23:42,24:41,25:40,26:39,27:38,28:37
1stState-65:80,66:79,67:78
1stState-69:76,70:75
1stState-40:82,41:81,42:80,43:79
1stState-45:77,46:76,47:75,48:74,49:73,50:72
1stState-1:14,2:13,3:12
1stState-53:65,54:64,55:63,56:62
1stState-25:35,26:34,27:33,28:32
1stState-3:79,4:78,5:77
1stState-13:60,14:59,15:58,16:57,17:56,18:55,19:54,20:53
1stState-22:49,23:48,24:47,25:46
1stState-29:45,30:44,31:43,32:42,33:41
1stState-63:76,64:75
1stState-34:39
1stState-1:83,2:82,3:81,4:80
1stState-32:79,33:78,34:77,35:76,36:75,37:74,38:73
1stState-40:63,41:62,42:61
1stState-11:28,12:27,13:26,14:25,15:24,16:23
1stState-44:60,45:59,46:58,47:57
1stState-49:56,50:55
1stState-4:81,5:80,6:79
1stState-22:63,23:62
1stState-26:59,27:58,28:57
1stState-29:53,30:52,31:51,32:50,33:49,34:48,35:47,36:46
1stState-51:84,52:83,53:82,54:81,55:80,56:79,57:78,58:77,59:76,60:75
1stState-62:73,63:72
1stState-6:16,7:15,8:14,9:13
1stState-44:80,45:79,46:78,47:77
1stState-4:39,5:38,6:37,7:36,8:35
1stState-48:75,49:74,50:73,51:72
1stState-13:31,14:30,15:29,16:28
1stState-54:70
1stState-56:68,57:67,58:66,59:65
1stState-17:25,18:24,19:23
1stState-54:79,55:78,56:77,57:76,58:75,59:74,60:73,61:72
1stState-10:29,11:28
1stState-34:52,35:51,36:50,37:49,38:48
1stState-13:27,14:26,15:25
1stState-40:47,41:46
1stState-8:60,9:59,10:58,11:57
1stState-13:55,14:54,15:53,16:52,17:51,18:50
1stState-21:47,22:46
1stState-61:78,62:77,63:76,64:75
1stState-65:73
1stState-4:81,5:80,6:79,7:78
1stState-27:63,28:62,29:61
1stState-33:60,34:59,35:58,36:57
1stState-4:69,5:68,6:67
1stState-7:26,8:25,9:24,10:23
1stState-39:57,40:56,41:55,42:54,43:53
1stState-72:82,73:81,74:80,75:79
1stState-13:20,14:19
1stState-37:81,38:80
1stState-40:78,41:77
1stState-43:76,44:75,45:74,46:73,47:72
1stState-14:34,15:33,16:32
1stState-48:62,49:61,50:60,51:59,52:58,53:57
1stState-18:30,19:29,20:28,21:27
1stState-4:13,5:12,6:11
1stState-33:61,34:60,35:59,36:58
1stState-37:55,38:54,39:53,40:52,41:51
1stState-43:50,44:49
1stState-8:81,9:80,10:79,11:78,12:77,13:76,14:75
1stState-18:68,19:67,20:66,21:65,22:64,23:63
1stState-29:62,30:61
1stState-31:59,32:58,33:57
1stState-23:46,24:45,25:44
1stState-59:78,60:77,61:76,62:75,63:74
1stState-26:42,27:41,28:40,29:39
1stState-8:22,9:21,10:20,11:19,12:18
1stState-31:38,32:37
1stState-65:72,66:71
1stState-44:80,45:79,46:78,47:77,48:76
1stState-4:25,5:24,6:23,7:22
1stState-52:70,53:69
1stState-28:41,29:40,30:39,31:38,32:37
1stState-54:67,55:66,56:65,57:64,58:63
1stState-12:21,13:20
1stState-3:84
1stState-5:82,6:81,7:80
1stState-9:79,10:78
1stState-29:76,30:75,31:74,32:73,33:72
1stState-39:66,40:65,41:64,42:63,43:62
1stState-45:61,46:60,47:59,48:58
1stState-50:57,51:56
1stState-6:32,7:31,8:30,9:29,10:28
1stState-36:60,37:59
1stState-62:84,63:83,64:82
1stState-66:80,67:79
1stState-11:23,12:22,13:21,14:20
1stState-45:51
1stState-1:81,2:80,3:79,4:78,5:77
1stState-7:75,8:74,9:73,10:72,11:71
1stState-28:58,29:57,30:56
1stState-31:49,32:48,33:47,34:46,35:45
1stState-37:44,38:43
1stState-2:22,3:21,4:20,5:19,6:18,7:17,8:16,9:15,10:14
1stState-45:63,46:62,47:61,48:60,49:59
1stState-67:81,68:80,69:79,70:78,71:77
1stState-23:35,24:34,25:33,26:32
1stState-54:83,55:82,56:81
1stState-4:28,5:27,6:26,7:25
1stState-30:53,31:52,32:51
1stState-59:79,60:78,61:77
1stState-34:50,35:49,36:48,37:47
1stState-8:23,9:22,10:21
1stState-63:75,64:74,65:73,66:72
1stState-12:19,13:18
1stState-3:39,4:38,5:37
1stState-6:34,7:33,8:32,9:31,10:30
1stState-55:76,56:75,57:74,58:73,59:72
1stState-11:28,12:27,13:26
1stState-40:54,41:53,42:52
1stState-14:24,15:23,16:22
1stState-5:80,6:79
1stState-8:61,9:60,10:59,11:58,12:57,13:56
1stState-14:32,15:31,16:30,17:29,18:28
1stState-63:73,64:72,65:71
1stState-24:80,25:79,26:78,27:77,28:76,29:75
1stState-31:73,32:72
1stState-53:70,54:69,55:68,56:67,57:66,58:65
1stState-36:52,37:51,38:50,39:49
1stState-1:55,2:54,3:53,4:52,5:51
1stState-18:50,19:49,20:48
1stState-21:46,22:45,23:44
1stState-58:81,59:80,60:79,61:78,62:77,63:76,64:75
1stState-66:74
1stState-2:70,3:69
1stState-5:67,6:66,7:65
1stState-8:63,9:62,10:61
1stState-12:59,13:58
1stState-14:56,15:55,16:54,17:53,18:52,19:51
1stState-26:48,27:47,28:46,29:45
1stState-30:43,31:42,32:41,33:40,34:39
1stState-73:84,74:83,75:82,76:81
1stState-1:82,2:81,3:80
1stState-40:76,41:75,42:74
1stState-44:72
1stState-47:69,48:68,49:67,50:66
1stState-7:24,8:23,9:22,10:21,11:20,12:19,13:18
1stState-25:39,26:38,27:37
1stState-52:64,53:63
1stState-54:61
1stState-6:47,7:46,8:45
1stState-10:43,11:42
1stState-58:79,59:78,60:77,61:76,62:75
1stState-64:73,65:72
1stState-1:83,2:82
1stState-13:59,14:58,15:57,16:56,17:55,18:54,19:53
1stState-21:49,22:48
1stState-25:46,26:45
1stState-3:81,4:80,5:79
1stState-24:63
1stState-26:62,27:61,28:60
1stState-29:58,30:57
1stState-13:59,14:58,15:57,16:56,17:55,18:54
1stState-21:52,22:51,23:50,24:49
1stState-26:48,27:47
1stState-29:46,30:45,31:44,32:43,33:42
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1stState-24:61,25:60
1stState-36:56,37:55,38:54,39:53,40:52,41:51
1stState-19:37,20:36,21:35,22:34,23:33
1stState-19:37,20:36,21:35,22:34,23:33,24:32
1stState-25:61
1stState-27:59,28:58,29:57
1stState-46:70,47:69,48:68
1stState-35:64,36:63,37:62,38:61
1stState-35:64,36:63,37:62,38:61,39:60
1stState-21:30,22:29,23:28
1stState-32:67
1stState-20:31,21:30,22:29,23:28
1stState-40:57,41:56,42:55,43:54,44:53,45:52,46:51
1stState-32:67,33:66
1stState-25:42,26:41
1stState-1:77,2:76,3:75,4:74,5:73
1stState-7:41,8:40,9:39,10:38,11:37
1stState-42:62,43:61,44:60,45:59,46:58,47:57,48:56
1stState-17:31,18:30,19:29,20:28
1stState-26:46,27:45,28:44,29:43,30:42,31:41,32:40
1stState-2:42,3:41,4:40,5:39
1stState-48:83,49:82,50:81,51:80,52:79,53:78
1stState-7:37,8:36
1stState-10:34,11:33
1stState-55:77,56:76,57:75
1stState-59:73,60:72
1stState-15:27,16:26,17:25,18:24,19:23
1stState-3:46,4:45,5:44,6:43,7:42
1stState-48:83,49:82,50:81,51:80
1stState-17:37,18:36,19:35,20:34
1stState-22:31
1stState-4:34,5:33,6:32,7:31,8:30
1stState-52:78,53:77,54:76,55:75
1stState-56:73,57:72
1stState-60:69
1stState-2:55,3:54,4:53
1stState-5:50,6:49
1stState-8:47,9:46,10:45,11:44
1stState-56:76,57:75
1stState-5:50,6:49,7:48,8:47,9:46,10:45,11:44
1stState-1:43,2:42,3:41,4:40,5:39
1stState-1:43,2:42,3:41,4:40,5:39,6:38,7:37,8:36,9:35,10:34,11:33
1stState-55:77
1stState-57:75
1stState-1:43,2:42,3:41,4:40
1stState-7:37,8:36,9:35
1stState-11:33
1stState-1:43,2:42,3:41,4:40,5:39,6:38,7:37,8:36,9:35
1stState-8:48,9:47,10:46,11:45
1stState-57:84,58:83,59:82,60:81,61:80,62:79,63:78,64:77
1stState-48:83,49:82,50:81,51:80,52:79,53:78,54:77,55:76,56:75
1stState-1:33,2:32,3:31,4:30,5:29,6:28,7:27
1stState-8:24,9:23
1stState-57:73
1stState-59:70,60:69
1stState-11:21,12:20,13:19
1stState-34:42,35:41
1stState-2:54,3:53,4:52,5:51,6:50,7:49,8:48
1stState-10:46,11:45
1stState-59:82,60:81,61:80,62:79,63:78,64:77
1stState-3:53,4:52,5:51,6:50,7:49,8:48
1stState-7:49,8:48,9:47,10:46,11:45
1stState-38:84,39:83,40:82,41:81,42:80,43:79
1stState-45:78,46:77
1stState-6:37,7:36,8:35,9:34
1stState-13:31
1stState-16:28,17:27,18:26,19:25,20:24
1stState-48:57,49:56
1stState-27:47,28:46
1stState-7:25,8:24,9:23
1stState-31:43,32:42
1stState-45:83,46:82,47:81
1stState-6:38,7:37,8:36,9:35
1stState-50:78,51:77,52:76
1stState-55:73
1stState-59:68,60:67
1stState-54:78,55:77
1stState-10:33,11:32,12:31,13:30,14:29,15:28
1stState-16:26,17:25,18:24
1stState-2:66,3:65,4:64,5:63,6:62,7:61,8:60
1stState-71:84,72:83,73:82
1stState-45:79,46:78
1stState-48:76,49:75,50:74,51:73,52:72
1stState-56:68,57:67
1stState-1:8,2:7
1stState-1:73,2:72,3:71,4:70,5:69
1stState-6:46,7:45,8:44
1stState-10:42
1stState-1:44,2:43,3:42,4:41,5:40,6:39,7:38,8:37,9:36
1stState-59:79,60:78
1stState-25:57,26:56,27:55,28:54,29:53
1stState-44:84,45:83,46:82,47:81,48:80,49:79,50:78
1stState-56:72
1stStat

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