| 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 3 I | 12 4 6 | 13 5 I | 14 6 7 | 15 6 I | 16 7 8 | 17 7 I | 18 8 | 19 7 I | 20 7 9 | 21 6 I | 22 6 10 | 23 3 I | 24 2 11 | 25 2 I | 26 2 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_99692.2_Instance_1 IL_99692.2,IL_5J7L_284,C1043_G1112 | C | C | C | A | G | A | C | A | G | U | C | G | A | G | ||||||||||||||||||||
| IL_99692.2_Sequence_1 IL_99692.25J7L_C_1043_G_1112 | C | C | C | A | G | A | C | A | G | * | U | C | G | A | G | true | 97 | 0 | 0 | 0.57 | ||||||||||||||
| IL_99692.2_Instance_2 IL_99692.2,IL_4V9F_042,C1147_G1216 | C | C | U | A | G | A | C | A | G | C | C | G | A | G | ||||||||||||||||||||
| IL_99692.2_Sequence_2 IL_99692.24V9F_C_1147_G_1216 | C | C | U | A | G | A | C | A | G | * | C | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_99692.2_Instance_3 IL_99692.2,IL_8CRE_057,U1214_A1283 | U | C | U | A | G | A | C | A | G | C | C | G | A | A | ||||||||||||||||||||
| IL_99692.2_Sequence_3 IL_99692.28CRE_U_1214_A_1283 | U | C | U | A | G | A | C | A | G | * | C | C | G | A | A | true | 100 | 0 | 0 | 0.07 | ||||||||||||||
| IL_99692.2_Instance_4 IL_99692.2,IL_9DFE_041,C1043_G1112 | C | G | A | A | G | A | C | A | G | U | C | G | A | G | ||||||||||||||||||||
| IL_99692.2_Sequence_4 IL_99692.29DFE_C_1043_G_1112 | C | G | A | A | G | A | C | A | G | * | U | C | G | A | G | true | 99 | 0 | 0 | 0.16 | ||||||||||||||
| IL_99692.2_Instance_5 IL_99692.2,IL_8P9A_282,U1218_A1287 | U | C | U | A | G | A | C | A | G | C | C | G | A | A | ||||||||||||||||||||
| IL_99692.2_Sequence_5 IL_99692.28P9A_U_1218_A_1287 | U | C | U | A | G | A | C | A | G | * | C | C | G | A | A | true | 100 | 0 | 0 | 0.07 | ||||||||||||||
| IL_99692.2_Instance_6 IL_99692.2,IL_5D8H_001,C1153_G1222 | C | U | A | A | G | A | C | A | G | U | C | G | A | G | ||||||||||||||||||||
| IL_99692.2_Sequence_6 IL_99692.25D8H_C_1153_G_1222 | C | U | A | A | G | A | C | A | G | * | U | C | G | A | G | true | 98 | 0 | 0 | 0.41 |
1 2 s35 1 13 cWW 2 12 tSS 2 13 s55 3 4 s55 3 12 s53 4 11 s33 4 12 tSH 5 6 s35 5 11 tHS 5 12 s55 5 13 tSS 6 7 s35 7 8 s35 7 10 bif 8 9 cWW 9 10 s35 10 11 s35 11 12 s35 11 5 6BPh 11 4 6BRJAR3D SCFG/MRF model for IL_99692.2:
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 ClusterNode | Deletion Probability [0.000000000000000000001944664658252592206548044411245326895476] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.030346452643607] // Cluster node 5J7L|1|DA|C|1043:5J7L|1|DA|A|1048 and 5J7L|1|DA|G|1110:5J7L|1|DA|G|1112 Interaction | Interacting Bases [5,6] | Pair Probability [[0.042049014,0.042361408,0.409943044,0.046937930,0.000000000],[0.044514549,0.044411471,0.003533393,0.044171708,0.000000000],[0.000504770,0.000504770,0.017273635,0.000504770,0.000000000],[0.002378984,0.000504770,0.299901013,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1048 - 5J7L|1|DA|G|1110 tHS Interaction | Interacting Bases [2,7] | Pair Probability [[0.057806141,0.057806141,0.057806141,0.057806141,0.000000000],[0.095541990,0.057806141,0.057806141,0.057806141,0.000000000],[0.085738069,0.057806141,0.057806141,0.057806141,0.000000000],[0.067240104,0.057806141,0.057806141,0.057806141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1044 - 5J7L|1|DA|A|1111 tSS Interaction | Interacting Bases [4,7] | Pair Probability [[0.108491223,0.114852581,0.001302365,0.006138049,0.000000000],[0.109297235,0.114586629,0.001302365,0.001302365,0.000000000],[0.186840254,0.001302365,0.006366848,0.110539801,0.000000000],[0.121105178,0.113968012,0.001302365,0.001302365,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1047 - 5J7L|1|DA|A|1111 tSH Interaction | Interacting Bases [1,8] | Pair Probability [[0.009015611,0.016598259,0.010211877,0.190496184,0.000000000],[0.020078202,0.009384364,0.234978378,0.012389530,0.000000000],[0.010297061,0.192647257,0.001996300,0.022446401,0.000000000],[0.213616688,0.011851437,0.034268488,0.009723963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1043 - 5J7L|1|DA|G|1112 cWW Interaction | Interacting Bases [5,8] | Pair Probability [[0.242283528,0.165842281,0.236924871,0.157273858,0.000000000],[0.001706013,0.001706013,0.017678100,0.001706013,0.000000000],[0.013376713,0.001706013,0.013932741,0.139039806,0.000000000],[0.001706013,0.001706013,0.001706013,0.001706013,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1048 - 5J7L|1|DA|G|1112 tSS Interaction | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|C|1045 Insertion | Location [3] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node 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 [6] | Right Index [10] // Initial node 5J7L|1|DA|C|1049 - 5J7L|1|DA|C|1109 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 5J7L|1|DA|A|1048 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.027418842,0.725623265,0.006690195,0.006690195,0.000000000],[0.030801564,0.078351263,0.006690195,0.006690195,0.000000000],[0.006690195,0.006690195,0.028073232,0.006690195,0.000000000],[0.006690195,0.006690195,0.042829885,0.006690195,0.000000000],[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 [7] | Right Index [10] // Basepair A1050 - C1109 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012304240,0.152595251,0.012221578,0.137557369,0.000000000],[0.014828613,0.010745729,0.115211142,0.013322044,0.000000000],[0.012014775,0.148821138,0.002566200,0.197277540,0.000000000],[0.113221234,0.014204047,0.018215096,0.024894003,0.000000000],[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 [8] | Right Index [9] // Basepair G1051 - U1108 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_99692.2:
> IL_99692.2 5J7L C 1043 G 1112 CCCAGACAG*UCGAG > IL_99692.2 4V9F C 1147 G 1216 CCUAGACAG*CCGAG > IL_99692.2 8CRE U 1214 A 1283 UCUAGACAG*CCGAA > IL_99692.2 9DFE C 1043 G 1112 CGAAGACAG*UCGAG > IL_99692.2 8P9A U 1218 A 1287 UCUAGACAG*CCGAA > IL_99692.2 5D8H C 1153 G 1222 CUAAGACAG*UCGAG