| 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 5 3 | 7 5 I | 8 5 4 | 9 6 I | 10 7 5 | 11 8 I | 12 15 6 | 13 15 I | 14 16 | 15 15 I | 16 15 7 | 17 14 I | 18 18 8 | 19 19 I | 20 20 9 | 21 21 I | 22 22 10 | 23 23 I | 24 24 11 | 25 25 I | 26 26 12 | 27 27 I | 28 28 13 | 29 28 I | 30 29 | 31 28 I | 32 28 14 | 33 12 I | 34 11 15 | 35 10 I | 36 9 16 | 37 6 I | 38 5 17 | 39 5 I | 40 5 18 | 41 4 I | 42 3 19 | 43 2 I | 44 2 20 | 45 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_08394.2_Instance_1 J3_08394.2,J3_4LFB_007,C1063_G1193 | C | G | U | C | A | G | C | G | C | A | A | C | C | G | A | C | G | A | C | G | ||||||||||||||||||||||||||||||
| J3_08394.2_Sequence_1 J3_08394.24LFB_C_1063_G_1193 | C | G | U | C | A | G | * | C | G | C | A | A | C | C | * | G | A | C | G | A | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||
| J3_08394.2_Instance_2 J3_08394.2,J3_5J7L_008,C1063_G1193 | C | G | U | C | A | G | C | G | C | A | A | C | C | G | A | U | G | A | C | G | ||||||||||||||||||||||||||||||
| J3_08394.2_Sequence_2 J3_08394.25J7L_C_1063_G_1193 | C | G | U | C | A | G | * | C | G | C | A | A | C | C | * | G | A | U | G | A | C | G | true | 98 | 0 | 0 | 0.51 | |||||||||||||||||||||||
| J3_08394.2_Instance_3 J3_08394.2,J3_6CZR_023,C1046_G1175 | C | G | U | C | A | G | C | G | C | A | A | C | C | G | A | C | G | A | C | G | ||||||||||||||||||||||||||||||
| J3_08394.2_Sequence_3 J3_08394.26CZR_C_1046_G_1175 | C | G | U | C | A | G | * | C | G | C | A | A | C | C | * | G | A | C | G | A | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s33 1 20 cWW 2 4 s55 2 17 tSS 3 16 s33 4 5 s35 4 18 tWH 5 6 perp 5 18 s55 6 7 cWW 6 8 s55 6 18 perp 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35 13 14 cWW 14 15 s35 15 16 s35 18 19 s35 19 20 s35 17 3 6BPh 3 9 6BPh 13 12 7BPh 2 18 6BPh 4 3 7BRJAR3D SCFG/MRF model for J3_08394.2:
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 [20] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | 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]] | 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 [1] | Right Index [20] // Basepair C1063 - G1193 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [19] // Fixed node on right for 4LFB|1|A|C|1192 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [18] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [18] | Norm Constant [0.999999999999999] // Cluster node 4LFB|1|A|G|1064:4LFB|1|A|C|1066 and 4LFB|1|A|G|1190:4LFB|1|A|A|1191 Interaction | Interacting Bases [1,4] | Pair Probability [[0.001209665,0.001012520,0.008096436,0.000727275,0.000000000],[0.000141626,0.000141626,0.087194218,0.000141626,0.000000000],[0.096373775,0.000991379,0.723091243,0.079462358,0.000000000],[0.000141626,0.000141626,0.000991379,0.000141626,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|1064 - 4LFB|1|A|G|1190 tSS Interaction | Interacting Bases [3,5] | Pair Probability [[0.011141843,0.001301708,0.037237822,0.001301708,0.000000000],[0.726212202,0.047418907,0.006508539,0.006508539,0.000000000],[0.001301708,0.004544633,0.011705676,0.011998879,0.000000000],[0.013090387,0.001301708,0.005852505,0.112573236,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|C|1066 - 4LFB|1|A|A|1191 tWH Interaction | Interacting Bases [2,2] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.934782609,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|U|1065 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 [5] | Right Index [16] // Initial node 4LFB|1|A|A|1067 - 4LFB|1|A|C|1189 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [16] // Fixed node on left for 4LFB|1|A|A|1067 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [6] | Right Index [16] // Fixed node on right for 4LFB|1|A|C|1189 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [6] | Right Index [15] // Fixed node on right for 4LFB|1|A|A|1188 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [14] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [6] | Right Index [14] // Junction node G1068 - G1187 ID J2784 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair G1068 - C1107 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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 truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [14] // Initial node 4LFB|1|A|G|1108 - 4LFB|1|A|G|1187 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [14] // Fixed node on left for 4LFB|1|A|G|1108 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [9] | Right Index [14] // Fixed node on left for 4LFB|1|A|C|1109 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [10] | Right Index [14] // Fixed node on left for 4LFB|1|A|A|1110 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [11] | Right Index [14] // Fixed node on left for 4LFB|1|A|A|1111 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [12] | Right Index [14] // Fixed node on left for 4LFB|1|A|C|1112 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // Basepair C1113 - G1187 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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 J3_08394.2:
> J3_08394.2 4LFB C 1063 G 1193 CGUCAG*CGCAACC*GACGACG > J3_08394.2 5J7L C 1063 G 1193 CGUCAG*CGCAACC*GAUGACG > J3_08394.2 6CZR C 1046 G 1175 CGUCAG*CGCAACC*GACGACG