| 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 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 6 I | 16 7 | 17 6 I | 18 5 8 | 19 4 I | 20 9 9 | 21 9 I | 22 10 10 | 23 10 I | 24 11 | 25 10 I | 26 10 11 | 27 9 I | 28 9 12 | 29 2 I | 30 2 13 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_28621.2_Instance_1 J3_28621.2,J3_4V9F_004,U1185_A1161 | U | C | U | A | A | G | A | U | A | C | G | G | A | |||||||||||||||||||||||
| J3_28621.2_Sequence_1 J3_28621.24V9F_U_1185_A_1161 | U | C | U | A | A | G | A | * | U | A | C | * | G | G | A | true | 98 | 0 | 0 | 0.36 | ||||||||||||||||
| J3_28621.2_Instance_2 J3_28621.2,J3_6PRV_001,U1081_A1057 | U | U | U | A | A | A | G | C | A | C | G | G | A | |||||||||||||||||||||||
| J3_28621.2_Sequence_2 J3_28621.26PRV_U_1081_A_1057 | U | U | U | A | A | A | G | * | C | A | C | * | G | G | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| J3_28621.2_Instance_3 J3_28621.2,J3_1MMS_001,U1081_A1057 | U | U | U | A | A | A | G | C | A | C | G | G | A | |||||||||||||||||||||||
| J3_28621.2_Sequence_3 J3_28621.21MMS_U_1081_A_1057 | U | U | U | A | A | A | G | * | C | A | C | * | G | G | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| J3_28621.2_Instance_4 J3_28621.2,J3_5D8H_001,U1191_A1167 | U | U | U | A | A | A | G | C | A | C | G | G | A | |||||||||||||||||||||||
| J3_28621.2_Sequence_4 J3_28621.25D8H_U_1191_A_1167 | U | U | U | A | A | A | G | * | C | A | C | * | G | G | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| J3_28621.2_Instance_5 J3_28621.2,J3_5TBW_007,G1256_C1232 | G | C | U | A | A | G | G | C | A | C | G | A | C | |||||||||||||||||||||||
| J3_28621.2_Sequence_5 J3_28621.25TBW_G_1256_C_1232 | G | C | U | A | A | G | G | * | C | A | C | * | G | A | C | true | 96 | 0 | 0 | 0.67 | ||||||||||||||||
| J3_28621.2_Instance_6 J3_28621.2,J3_5J7L_040,U1081_A1057 | U | U | U | A | A | A | G | C | A | C | G | G | A | |||||||||||||||||||||||
| J3_28621.2_Sequence_6 J3_28621.25J7L_U_1081_A_1057 | U | U | U | A | A | A | G | * | C | A | C | * | G | G | A | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 3 s35 2 6 tWW 2 13 s55 3 5 tSH 4 5 s35 5 6 s33 5 10 cSS 5 11 tSS 6 13 s55 7 8 cWW 7 9 s55 8 9 s35 8 12 s33 9 10 s35 9 12 tHS 10 11 cWW 10 12 s55 11 12 s35 3 6 6BPh 9 7 2BPh 10 9 7BPh 9 12 6BRJAR3D SCFG/MRF model for J3_28621.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008805578,0.017320049,0.009724403,0.189714638,0.000000000],[0.020418805,0.009414670,0.190517887,0.010987213,0.000000000],[0.009720160,0.198876750,0.001974330,0.022774049,0.000000000],[0.242969588,0.010530429,0.046498791,0.009752660,0.000000000],[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 [13] // Basepair U1185 - A1161 cWW JunctionNode | Branches [2] | Left Index [2] | Right Index [12] // Junction node C1186 - G1160 ID J6557 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 [8] // Initial node 4V9F|1|0|C|1186 - 4V9F|1|0|U|1206 from node ClusterNode | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [6] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node 4V9F|1|0|C|1186:4V9F|1|0|A|1191 and 4V9F|1|0|U|1206:4V9F|1|0|U|1206 Interaction | Interacting Bases [6,7] | Pair Probability [[0.009294090,0.019785678,0.010478215,0.203605867,0.000000000],[0.016519773,0.009190356,0.193944205,0.012313588,0.000000000],[0.010376412,0.246249955,0.002002721,0.029996924,0.000000000],[0.190808126,0.012824690,0.022503671,0.010105729,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|1191 - 4V9F|1|0|U|1206 cWW Interaction | Interacting Bases [2,4] | Pair Probability [[0.043836710,0.040040618,0.000486824,0.002394787,0.000000000],[0.044006054,0.041405452,0.000486824,0.000486824,0.000000000],[0.045269111,0.000486824,0.003008812,0.040415433,0.000000000],[0.415878478,0.314981716,0.003407767,0.003407767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|U|1187 - 4V9F|1|0|A|1189 tSH Interaction | Interacting Bases [1,5] | Pair Probability [[0.017052940,0.016778513,0.004341174,0.034743286,0.000000000],[0.035093026,0.033054476,0.234795927,0.031706602,0.000000000],[0.004341174,0.017933689,0.018317643,0.017961687,0.000000000],[0.277443849,0.036683610,0.192514291,0.027238116,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|C|1186 - 4V9F|1|0|G|1190 tWW Interaction | Interacting Bases [3,3] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|A|1188 InitialNode | 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 [8] | Right Index [7] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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 [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [9] | Right Index [12] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.213455812,0.182908896,0.287582345,0.202669487,0.000000000],[0.027457967,0.027394385,0.000311358,0.027246492,0.000000000],[0.000311358,0.000311358,0.001522131,0.000311358,0.000000000],[0.001467432,0.000311358,0.026426904,0.000311358,0.000000000],[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 [9] | Right Index [12] // Basepair A1207 - G1160 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004532070,0.008127091,0.005210173,0.094470710,0.000000000],[0.047940450,0.022964267,0.550694352,0.032605866,0.000000000],[0.005268685,0.096506299,0.000993115,0.011151850,0.000000000],[0.095695428,0.006314392,0.012722507,0.004802747,0.000000000],[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 [10] | Right Index [11] // Basepair C1208 - G1159 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_28621.2:
> J3_28621.2 4V9F U 1185 A 1161 UCUAAGA*UAC*GGA > J3_28621.2 6PRV U 1081 A 1057 UUUAAAG*CAC*GGA > J3_28621.2 1MMS U 1081 A 1057 UUUAAAG*CAC*GGA > J3_28621.2 5D8H U 1191 A 1167 UUUAAAG*CAC*GGA > J3_28621.2 5TBW G 1256 C 1232 GCUAAGG*CAC*GAC > J3_28621.2 5J7L U 1081 A 1057 UUUAAAG*CAC*GGA