| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 2 I | 6 2 3 | 7 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_69353.6_Instance_1 HL_69353.6_HL_4ZT0_005_C55_G58 | C | U | A | G | ||||||||
| HL_69353.6_Sequence_1 HL_69353.6_HL_4ZT0_005_C55_G58 | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_69353.6_Instance_2 HL_69353.6_HL_5B2T_002_C55_G58 | C | U | A | G | ||||||||
| HL_69353.6_Sequence_2 HL_69353.6_HL_5B2T_002_C55_G58 | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_69353.6_Instance_3 HL_69353.6_HL_5FQ5_002_C55_G58 | C | U | A | G | ||||||||
| HL_69353.6_Sequence_3 HL_69353.6_HL_5FQ5_002_C55_G58 | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_69353.6_Instance_4 HL_69353.6_HL_2F8K_001_U6_A9 | U | U | G | A | ||||||||
| HL_69353.6_Sequence_4 HL_69353.6_HL_2F8K_001_U6_A9 | U | U | G | A | true | 86 | 0 | 0 | 1.28 | |||
| HL_69353.6_Instance_5 HL_69353.6_HL_5VW1_002_C55_G58 | C | U | A | G | ||||||||
| HL_69353.6_Sequence_5 HL_69353.6_HL_5VW1_002_C55_G58 | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_69353.6_Instance_6 HL_69353.6_HL_4Y4O_141_C1565_G1568 | C | A | A | G | ||||||||
| HL_69353.6_Sequence_6 HL_69353.6_HL_4Y4O_141_C_1565_G_1568 | C | A | A | G | true | 92 | 0 | 0 | 0.74 | |||
| HL_69353.6_Instance_7 HL_69353.6_HL_5J7L_172_C1565_G1568 | C | A | G | G | ||||||||
| HL_69353.6_Sequence_7 HL_69353.6_HL_5J7L_172_C_1565_G_1568 | C | A | G | G | true | 83 | 0 | 0 | 1.62 | |||
| HL_69353.6_Instance_8 HL_69353.6_HL_5U30_001_U4_A7 | U | A | G | A | ||||||||
| HL_69353.6_Sequence_8 HL_69353.6_HL_5U30_001_U4_A7 | U | A | G | A | true | 79 | 0 | 0 | 2.02 | |||
| HL_69353.6_Instance_9 HL_69353.6_HL_5TBW_040_C1792_G1796 | C | CG | U | G | ||||||||
| HL_69353.6_Sequence_9 HL_69353.6_HL_5TBW_040_C_1792_G_1796 | C | C | G | U | G | true | 39 | 0 | 0 | 5.83 | ||
| HL_69353.6_Instance_10 HL_69353.6_HL_7A0S_039_C1581_G1584 | C | A | A | G | ||||||||
| HL_69353.6_Sequence_10 HL_69353.6_HL_7A0S_039_C_1581_G_1584 | C | A | A | G | true | 92 | 0 | 0 | 0.74 | |||
| HL_69353.6_Instance_11 HL_69353.6_HL_5F9R_002_C73_G76 | C | U | A | G | ||||||||
| HL_69353.6_Sequence_11 HL_69353.6_HL_5F9R_002_C73_G76 | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_69353.6_Instance_12 HL_69353.6_HL_6JOO_002_C58_G61 | C | U | C | G | ||||||||
| HL_69353.6_Sequence_12 HL_69353.6_HL_6JOO_002_C58_G61 | C | U | C | G | true | 87 | 0 | 0 | 1.22 | |||
| HL_69353.6_Instance_13 HL_69353.6_HL_4V9F_041_C1651_G1655 | C | CA | U | G | ||||||||
| HL_69353.6_Sequence_13 HL_69353.6_HL_4V9F_041_C_1651_G_1655 | C | C | A | U | G | true | 48 | 0 | 0 | 4.95 | ||
| HL_69353.6_Instance_14 HL_69353.6_HL_5TBW_071_C3350_G3353 | C | U | U | G | ||||||||
| HL_69353.6_Sequence_14 HL_69353.6_HL_5TBW_071_C_3350_G_3353 | C | U | U | G | true | 93 | 0 | 0 | 0.64 | |||
| HL_69353.6_Instance_15 HL_69353.6_HL_4V88_192_C276_G279 | C | U | U | G | ||||||||
| HL_69353.6_Sequence_15 HL_69353.6_HL_4V88_192_C276_G279 | C | U | U | G | true | 93 | 0 | 0 | 0.64 | |||
| HL_69353.6_Instance_16 HL_69353.6_HL_5SWD_005_U47_A52 | U | UU | C | U | A | |||||||
| HL_69353.6_Sequence_16 HL_69353.6_HL_5SWD_005_U47_A52 | U | UU | C | U | A | true | 24 | 0 | 0 | 7.22 | ||
| HL_69353.6_Instance_17 HL_69353.6_HL_4WF9_037_C1612_G1615 | C | G | A | G | ||||||||
| HL_69353.6_Sequence_17 HL_69353.6_HL_4WF9_037_C_1612_G_1615 | C | G | A | G | true | 84 | 0 | 0 | 1.53 |
1 2 s35 1 3 cWW 2 3 s55JAR3D SCFG/MRF model for HL_69353.6:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [3] // Initial node C55 - G58 from junction BasepairNode | Deletion Probability [0.0000000352713031] | Pair Probability [[0.008236672,0.014977105,0.009395839,0.172923817,0.000000000],[0.017948791,0.008485807,0.299996653,0.011600188,0.000000000],[0.009487208,0.175712836,0.001814837,0.020393308,0.000000000],[0.201661815,0.011135483,0.027419546,0.008810094,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.002407629,0.819109693,0.177820580,0.000636302,0.000025796] | Left Letter Distribution [0.250000000,0.113636364,0.113636364,0.522727273,0.000000000] | Right Length Distribution [0.938289488,0.061391483,0.000310406,0.000008622] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C55 - G58 cWW HairpinNode | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A57:A57 Interaction | Interacting Bases [1,1] | Pair Probability [[0.447368421,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.131578947,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.184210526,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.236842105,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A57Sequences of instances from HL_69353.6:
> HL_69353.6 HL_4ZT0_005 C 55 G 58 CUAG > HL_69353.6 HL_5B2T_002 C 55 G 58 CUAG > HL_69353.6 HL_5FQ5_002 C 55 G 58 CUAG > HL_69353.6 HL_2F8K_001 U 6 A 9 UUGA > HL_69353.6 HL_5VW1_002 C 55 G 58 CUAG > HL_69353.6 HL_4Y4O_141 C 1565 G 1568 CAAG > HL_69353.6 HL_5J7L_172 C 1565 G 1568 CAGG > HL_69353.6 HL_5U30_001 U 4 A 7 UAGA > HL_69353.6 HL_5TBW_040 C 1792 G 1796 CCGUG > HL_69353.6 HL_7A0S_039 C 1581 G 1584 CAAG > HL_69353.6 HL_5F9R_002 C 73 G 76 CUAG > HL_69353.6 HL_6JOO_002 C 58 G 61 CUCG > HL_69353.6 HL_4V9F_041 C 1651 G 1655 CCAUG > HL_69353.6 HL_5TBW_071 C 3350 G 3353 CUUG > HL_69353.6 HL_4V88_192 C 276 G 279 CUUG > HL_69353.6 HL_5SWD_005 U 47 A 52 UUUCUA > HL_69353.6 HL_4WF9_037 C 1612 G 1615 CGAG