| 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 2 2 | 5 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 2 I | 12 2 6 | 13 2 I | 14 2 7 | 15 2 I | 16 2 8 | 17 2 I | 18 2 9 | 19 2 I | 20 2 10 | 21 2 I | 22 2 11 | 23 2 I | 24 2 12 | 25 2 I | 26 2 13 | 27 3 I | 28 4 14 | 29 4 I | 30 5 | 31 4 I | 32 4 15 | 33 3 I | 34 2 16 | 35 2 I | 36 2 17 | 37 2 I | 38 2 18 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_75283.2_Instance_1 IL_75283.2,IL_3U4M_003,C2161_G2127 | C | G | C | C | G | G | U | G | A | A | A | U | A | C | G | G | A | G | ||||||||||||||||||||||||||
| IL_75283.2_Sequence_1 IL_75283.23U4M_C_2161_G_2127 | C | G | C | C | G | G | U | G | A | A | A | U | A | C | * | G | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_75283.2_Instance_2 IL_75283.2,IL_5ML7_007,C2206_G2168 | C | A | A | C | A | G | U | G | A | A | A | U | A | C | G | G | A | G | ||||||||||||||||||||||||||
| IL_75283.2_Sequence_2 IL_75283.25ML7_C_2206_G_2168 | C | A | A | C | A | G | U | G | A | A | A | U | A | C | * | G | G | A | G | true | 94 | 0 | 0 | 1.53 | ||||||||||||||||||||
| IL_75283.2_Instance_3 IL_75283.2,IL_1MZP_003,C32_G23 | C | G | C | C | G | G | U | G | A | A | A | U | A | C | G | G | A | G | ||||||||||||||||||||||||||
| IL_75283.2_Sequence_3 IL_75283.21MZP_C32_G23 | C | G | C | C | G | G | U | G | A | A | A | U | A | C | * | G | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 18 cWW 2 3 s35 2 18 s55 3 4 s35 4 5 s35 5 6 s35 6 7 s35 6 12 tWH 7 8 s35 7 11 tWH 8 10 s33 8 11 s55 9 10 s35 11 12 s35 13 14 s35 13 16 tHS 13 17 s55 13 18 tSS 14 15 cWW 14 16 s55 15 16 s35 4 3 7BPh 8 11 6BPh 16 12 6BPh 14 13 7BPh 10 8 7BR 13 16 6BRJAR3D SCFG/MRF model for IL_75283.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [18] // Initial node ClusterNode | Deletion Probability [0.000000000000000000000000000000000000152587890625000050301882] | Num Left Bases [13] | Num Right Bases [3] | Left Index [1] | Right Index [18] | Norm Constant [0.126798550564041] // Cluster node 3U4M|1|B|C|2161:3U4M|1|B|A|2173 and 3U4M|1|B|G|2125:3U4M|1|B|G|2127 Interaction | Interacting Bases [13,14] | Pair Probability [[0.043273743,0.043595236,0.392756919,0.048305054,0.000000000],[0.045811089,0.045705009,0.003636307,0.045458262,0.000000000],[0.000519472,0.000519472,0.017776750,0.000519472,0.000000000],[0.002448275,0.000519472,0.308635994,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3U4M|1|B|A|2173 - 3U4M|1|B|G|2125 tHS Interaction | Interacting Bases [1,16] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3U4M|1|B|C|2161 - 3U4M|1|B|G|2127 cWW Interaction | Interacting Bases [13,16] | Pair Probability [[0.219748591,0.219222758,0.300871829,0.207896374,0.000000000],[0.000451027,0.000451027,0.004673648,0.000451027,0.000000000],[0.003536468,0.000451027,0.003683468,0.036758648,0.000000000],[0.000451027,0.000451027,0.000451027,0.000451027,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3U4M|1|B|A|2173 - 3U4M|1|B|G|2127 tSS Interaction | Interacting Bases [7,11] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3U4M|1|B|U|2167 - 3U4M|1|B|A|2171 tWH Interaction | Interacting Bases [6,12] | Pair Probability [[0.043222547,0.004038099,0.323955368,0.004038099,0.000000000],[0.037222380,0.019018019,0.004038099,0.004038099,0.000000000],[0.004038099,0.007058475,0.040666371,0.432936133,0.000000000],[0.017960075,0.004038099,0.015639489,0.038092549,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3U4M|1|B|G|2166 - 3U4M|1|B|U|2172 tWH Interaction | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|G|2162 Interaction | Interacting Bases [3,3] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|C|2163 Interaction | Interacting Bases [4,4] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.934782609,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|C|2164 Interaction | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|G|2165 Interaction | Interacting Bases [8,8] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|G|2168 Interaction | Interacting Bases [9,9] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|A|2169 Interaction | Interacting Bases [10,10] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3U4M|1|B|A|2170 Interaction | Interacting Bases [15,15] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 3U4M|1|B|A|2126 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [15] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003708089,0.006649494,0.004262905,0.077294868,0.000000000],[0.055188220,0.026436068,0.597914779,0.037535311,0.000000000],[0.004310778,0.078960365,0.000812555,0.009124318,0.000000000],[0.078296919,0.005166364,0.010409412,0.003929554,0.000000000],[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 [14] | Right Index [15] // Basepair C2174 - G2124 cWW HairpinNode | Num Bases [1] | Left Index [15] | Right Index [15] | 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_75283.2:
> IL_75283.2 3U4M C 2161 G 2127 CGCCGGUGAAAUAC*GGAG > IL_75283.2 5ML7 C 2206 G 2168 CAACAGUGAAAUAC*GGAG > IL_75283.2 1MZP C 32 G 23 CGCCGGUGAAAUAC*GGAG