| 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_34363.2_Instance_1 IL_34363.2_IL_1S72_043_C1147_G1216 | C | C | U | A | G | A | C | A | G | C | C | G | A | G | ||||||||||||||||||||
| IL_34363.2_Sequence_1 IL_34363.2_IL_1S72_043_C_1147_G_1216 | C | C | U | A | G | A | C | A | G | * | C | C | G | A | G | true | 99 | 0 | 0 | 0.16 | ||||||||||||||
| IL_34363.2_Instance_2 IL_34363.2_IL_3U5H_059_U1218_A1287 | U | C | U | A | G | A | C | A | G | C | C | G | A | A | ||||||||||||||||||||
| IL_34363.2_Sequence_2 IL_34363.2_IL_3U5H_059_U_1218_A_1287 | U | C | U | A | G | A | C | A | G | * | C | C | G | A | A | true | 97 | 0 | 0 | 0.62 | ||||||||||||||
| IL_34363.2_Instance_3 IL_34363.2_IL_2QBG_042_C1043_G1112 | C | C | C | A | G | A | C | A | G | U | C | G | A | G | ||||||||||||||||||||
| IL_34363.2_Sequence_3 IL_34363.2_IL_2QBG_042_C_1043_G_1112 | C | C | C | A | G | A | C | A | G | * | U | C | G | A | G | true | 97 | 0 | 0 | 0.68 | ||||||||||||||
| IL_34363.2_Instance_4 IL_34363.2_IL_4IOA_039_C1054_G1123 | C | A | U | A | G | A | C | A | G | U | C | G | A | G | ||||||||||||||||||||
| IL_34363.2_Sequence_4 IL_34363.2_IL_4IOA_039_C_1054_G_1123 | C | A | U | A | G | A | C | A | G | * | U | C | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 5 cSS 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 12 13 cSS 11 5 6BPh 12 2 6BR 11 4 6BRJAR3D SCFG/MRF model for IL_34363.2:
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 [13] // Initial node C1147 - G1216 from junction ClusterNode | Deletion Probability [0.000000000000000000001940553474955695100000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.000558380037188] // Cluster node C1147:A1152 and G1214:G1216 Interaction | Interacting Bases [5,6] | Pair Probability [[0.042875527,0.043256990,0.400078329,0.046604180,0.000000000],[0.049976915,0.045339634,0.003616168,0.044897183,0.000000000],[0.000516595,0.000516595,0.017519574,0.000516595,0.000000000],[0.002459961,0.000516595,0.300792562,0.000516595,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1214 tHS Interaction | Interacting Bases [2,7] | Pair Probability [[0.107954545,0.054632867,0.054632867,0.054632867,0.000000000],[0.127185315,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1148 - A1215 tSS Interaction | Interacting Bases [4,7] | Pair Probability [[0.185166390,0.043167026,0.000446204,0.002124765,0.000000000],[0.186813816,0.039161625,0.000446204,0.000446204,0.000000000],[0.261563424,0.000446204,0.002161764,0.037115194,0.000000000],[0.201269312,0.038779462,0.000446204,0.000446204,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1151 - A1215 tSH Interaction | Interacting Bases [1,8] | Pair Probability [[0.009613617,0.017593128,0.010983027,0.192350441,0.000000000],[0.021287894,0.008639455,0.234523700,0.012787711,0.000000000],[0.011096459,0.200570476,0.002109537,0.023296342,0.000000000],[0.204768830,0.012284769,0.027115440,0.010979173,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - G1216 cWW Interaction | Interacting Bases [5,8] | Pair Probability [[0.204273875,0.182392691,0.228460848,0.175009089,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.010954656,0.012643890,0.019492821,0.150802954,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1216 tSS Interaction | Interacting Bases [1,5] | Pair Probability [[0.056456460,0.057489227,0.055785276,0.056733612,0.000000000],[0.136969236,0.057810615,0.007079764,0.053147720,0.000000000],[0.060169857,0.061092715,0.055484166,0.061453996,0.000000000],[0.111667921,0.056875119,0.054584017,0.057200297,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - A1152 cSS Interaction | Interacting Bases [7,8] | Pair Probability [[0.195141897,0.160173003,0.197628067,0.154493037,0.000000000],[0.029233204,0.029516469,0.003600697,0.030054980,0.000000000],[0.029730386,0.030050892,0.013725809,0.030122553,0.000000000],[0.029973668,0.007433790,0.028524377,0.030597170,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1215 - G1216 cSS Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1149 Insertion | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node C1153 - C1213 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [0.0000239574126029] | Pair Probability [[0.018665872,0.615612422,0.004897383,0.004897383,0.000000000],[0.021553581,0.253036378,0.004897383,0.004897383,0.000000000],[0.004897383,0.004897383,0.018574216,0.004897383,0.000000000],[0.004897383,0.004897383,0.023583701,0.004897383,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A1154 - C1213 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013091073,0.162345844,0.013424526,0.116783626,0.000000000],[0.015534003,0.009786201,0.120926247,0.014071788,0.000000000],[0.013182666,0.146362737,0.002747701,0.202112848,0.000000000],[0.112925662,0.015211513,0.019098011,0.022395553,0.000000000],[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 G1155 - C1212 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_34363.2:
> IL_34363.2 IL_1S72_043 C 1147 G 1216 CCUAGACAG*CCGAG > IL_34363.2 IL_3U5H_059 U 1218 A 1287 UCUAGACAG*CCGAA > IL_34363.2 IL_2QBG_042 C 1043 G 1112 CCCAGACAG*UCGAG > IL_34363.2 IL_4IOA_039 C 1054 G 1123 CAUAGACAG*UCGAG