| 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 5 2 | 5 5 I | 6 6 3 | 7 6 I | 8 7 4 | 9 7 I | 10 8 | 11 7 I | 12 7 5 | 13 6 I | 14 6 6 | 15 5 I | 16 5 7 | 17 4 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_31555.5_Instance_1 IL_31555.5_IL_4FAW_010_U172_G194 | U | G | A | G | C | A | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_1 IL_31555.5_IL_4FAW_010_U172_G194 | U | G | A | G | * | C | A | A | A | G | true | 95 | 0 | 0 | 0.52 | |||||||||||
| IL_31555.5_Instance_2 IL_31555.5_IL_4A1B_026_U571_A598 | U | G | A | G | C | A | A | A | A | |||||||||||||||||
| IL_31555.5_Sequence_2 IL_31555.5_IL_4A1B_026_U571_A598 | U | G | A | G | * | C | A | A | A | A | true | 90 | 0 | 0 | 0.91 | |||||||||||
| IL_31555.5_Instance_3 IL_31555.5_IL_4A1B_022_U499_G479 | U | G | A | G | C | A | G | A | G | |||||||||||||||||
| IL_31555.5_Sequence_3 IL_31555.5_IL_4A1B_022_U499_G479 | U | G | A | G | * | C | A | G | A | G | true | 97 | 0 | 0 | 0.33 | |||||||||||
| IL_31555.5_Instance_4 IL_31555.5_IL_1X8W_002_U205_G116 | U | A | A | C | G | A | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_4 IL_31555.5_IL_1X8W_002_U205_G116 | U | A | A | C | * | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_31555.5_Instance_5 IL_31555.5_IL_1GID_010_U205_G116 | U | A | A | C | G | A | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_5 IL_31555.5_IL_1GID_010_U205_G116 | U | A | A | C | * | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_31555.5_Instance_6 IL_31555.5_IL_1GID_003_U205_G116 | U | A | A | C | G | A | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_6 IL_31555.5_IL_1GID_003_U205_G116 | U | A | A | C | * | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_31555.5_Instance_7 IL_31555.5_IL_3FTM_001_U46_A4 | U | G | A | G | C | G | G | A | A | |||||||||||||||||
| IL_31555.5_Sequence_7 IL_31555.5_IL_3FTM_001_U46_A4 | U | G | A | G | * | C | G | G | A | A | true | 90 | 0 | 0 | 0.95 | |||||||||||
| IL_31555.5_Instance_8 IL_31555.5_IL_4A1B_120_U3043_G3077 | U | A | A | A | U | A | U | G | A | A | G | |||||||||||||||
| IL_31555.5_Sequence_8 IL_31555.5_IL_4A1B_120_U_3043_G_3077 | U | A | A | A | U | A | * | U | G | A | A | G | true | 29 | 0 | 0 | 6.77 | |||||||||
| IL_31555.5_Instance_9 IL_31555.5_IL_3FS0_001_U46_A4 | U | G | A | G | C | G | G | A | A | |||||||||||||||||
| IL_31555.5_Sequence_9 IL_31555.5_IL_3FS0_001_U46_A4 | U | G | A | G | * | C | G | G | A | A | true | 90 | 0 | 0 | 0.95 | |||||||||||
| IL_31555.5_Instance_10 IL_31555.5_IL_3LOA_001_G1401_C1501 | G | C | C | C | G | U | A | A | C | |||||||||||||||||
| IL_31555.5_Sequence_10 IL_31555.5_IL_3LOA_001_G_1401_C_1501 | G | C | C | C | * | G | U | A | A | C | true | 87 | 0 | 0 | 1.24 | |||||||||||
| IL_31555.5_Instance_11 IL_31555.5_IL_3BNT_002_C6_G18 | C | A | C | C | G | C | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_11 IL_31555.5_IL_3BNT_002_C6_G18 | C | A | C | C | * | G | C | A | A | G | true | 91 | 0 | 0 | 0.89 | |||||||||||
| IL_31555.5_Instance_12 IL_31555.5_IL_3BNT_005_C6_G18 | C | A | C | C | G | C | A | A | G | |||||||||||||||||
| IL_31555.5_Sequence_12 IL_31555.5_IL_3BNT_005_C6_G18 | C | A | C | C | * | G | C | A | A | G | true | 91 | 0 | 0 | 0.89 | |||||||||||
| IL_31555.5_Instance_13 IL_31555.5_IL_3CUN_001_C22_G49 | C | A | G | G | U | A | U | U | G | G | ||||||||||||||||
| IL_31555.5_Sequence_13 IL_31555.5_IL_3CUN_001_C22_G49 | C | A | G | G | * | U | A | U | U | G | G | true | -3 | 0 | 0 | 9.79 |
1 2 s35 1 9 cWW 2 3 s35 2 6 s33 2 7 tSH 3 4 s35 3 6 tHS 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 7 8 s35 8 9 s35 3 6 6BRJAR3D SCFG/MRF model for IL_31555.5:
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 [9] // Initial node U172 - G194 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010119758,0.015381041,0.011773713,0.112831708,0.000000000],[0.142681571,0.011045710,0.145037150,0.013259572,0.000000000],[0.011944510,0.123602112,0.002515582,0.018248559,0.000000000],[0.144091318,0.012444267,0.213280671,0.011742757,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair U172 - G194 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.033333333,0.100000000,0.033333333,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000105840881771] | Pair Probability [[0.172671224,0.085919845,0.001808419,0.104872879,0.000000000],[0.114691441,0.055711829,0.001808419,0.001808419,0.000000000],[0.106569534,0.001808419,0.128790389,0.037772399,0.000000000],[0.093027893,0.089122053,0.001808419,0.001808419,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G173 - A192 tSH BasepairNode | Deletion Probability [0.0000160934329480] | Pair Probability [[0.177077827,0.121481100,0.141533733,0.119606275,0.000000000],[0.111119146,0.107057298,0.001305849,0.133418568,0.000000000],[0.019569829,0.001305849,0.009851328,0.001305849,0.000000000],[0.009110720,0.001305849,0.043644933,0.001305849,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A174 - A191 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009506456,0.037620190,0.010717425,0.174190618,0.000000000],[0.017026146,0.007935753,0.231011961,0.012191369,0.000000000],[0.010702666,0.222205897,0.002030899,0.054241435,0.000000000],[0.164390525,0.012266178,0.022436068,0.011526414,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [4] | Right Index [5] // Basepair G175 - C190 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_31555.5:
> IL_31555.5 IL_4FAW_010 U 172 G 194 UGAG*CAAAG > IL_31555.5 IL_4A1B_026 U 571 A 598 UGAG*CAAAA > IL_31555.5 IL_4A1B_022 U 499 G 479 UGAG*CAGAG > IL_31555.5 IL_1X8W_002 U 205 G 116 UAAC*GAAAG > IL_31555.5 IL_1GID_010 U 205 G 116 UAAC*GAAAG > IL_31555.5 IL_1GID_003 U 205 G 116 UAAC*GAAAG > IL_31555.5 IL_3FTM_001 U 46 A 4 UGAG*CGGAA > IL_31555.5 IL_4A1B_120 U 3043 G 3077 UAAAUA*UGAAG > IL_31555.5 IL_3FS0_001 U 46 A 4 UGAG*CGGAA > IL_31555.5 IL_3LOA_001 G 1401 C 1501 GCCC*GUAAC > IL_31555.5 IL_3BNT_002 C 6 G 18 CACC*GCAAG > IL_31555.5 IL_3BNT_005 C 6 G 18 CACC*GCAAG > IL_31555.5 IL_3CUN_001 C 22 G 49 CAGG*UAUUGG