| 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 3 2 | 5 4 I | 6 5 3 | 7 5 I | 8 6 | 9 5 I | 10 5 4 | 11 2 I | 12 2 5 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_56465.4_Instance_1 IL_56465.4_IL_4IOA_005_A189_U161 | A | A | G | C | U | |||||||||||||
| IL_56465.4_Sequence_1 IL_56465.4_IL_4IOA_005_A189_U161 | A | A | G | * | C | U | true | 95 | 0 | 0 | 0.47 | |||||||
| IL_56465.4_Instance_2 IL_56465.4_IL_4A1B_001_G54_C26 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_2 IL_56465.4_IL_4A1B_001_G54_C26 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_3 IL_56465.4_IL_3V2F_005_G212_C184 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_3 IL_56465.4_IL_3V2F_005_G212_C184 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_4 IL_56465.4_IL_3V2F_024_G940_C838 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_4 IL_56465.4_IL_3V2F_024_G940_C838 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_5 IL_56465.4_IL_3U5H_004_G56_C28 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_5 IL_56465.4_IL_3U5H_004_G56_C28 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_6 IL_56465.4_IL_4IOA_021_G951_C851 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_6 IL_56465.4_IL_4IOA_021_G951_C851 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_7 IL_56465.4_IL_2QBG_010_G212_C184 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_7 IL_56465.4_IL_2QBG_010_G212_C184 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_8 IL_56465.4_IL_1S72_005_G182_C154 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_8 IL_56465.4_IL_1S72_005_G182_C154 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_9 IL_56465.4_IL_2QBG_027_G940_C838 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_9 IL_56465.4_IL_2QBG_027_G940_C838 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_10 IL_56465.4_IL_1S72_079_U2436_A2455 | U | A | G | C | A | |||||||||||||
| IL_56465.4_Sequence_10 IL_56465.4_IL_1S72_079_U_2436_A_2455 | U | A | G | * | C | A | true | 96 | 0 | 0 | 0.33 | |||||||
| IL_56465.4_Instance_11 IL_56465.4_IL_2QBG_090_C2498_G2454 | C | C | U | A | G | |||||||||||||
| IL_56465.4_Sequence_11 IL_56465.4_IL_2QBG_090_C_2498_G_2454 | C | C | U | * | A | G | true | 73 | 0 | 0 | 2.61 | |||||||
| IL_56465.4_Instance_12 IL_56465.4_IL_4IOA_056_A1463_U1478 | A | A | G | C | U | |||||||||||||
| IL_56465.4_Sequence_12 IL_56465.4_IL_4IOA_056_A_1463_U_1478 | A | A | G | * | C | U | true | 95 | 0 | 0 | 0.47 | |||||||
| IL_56465.4_Instance_13 IL_56465.4_IL_2AW7_047_G1041_C999 | G | A | G | C | C | |||||||||||||
| IL_56465.4_Sequence_13 IL_56465.4_IL_2AW7_047_G_1041_C999 | G | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_56465.4_Instance_14 IL_56465.4_IL_3U5H_009_C163_G258 | C | A | A | U | G | |||||||||||||
| IL_56465.4_Sequence_14 IL_56465.4_IL_3U5H_009_C163_G258 | C | A | A | * | U | G | true | 99 | 0 | 0 | 0.14 | |||||||
| IL_56465.4_Instance_15 IL_56465.4_IL_3U5H_146_C47_G30 | C | U | G | C | G | |||||||||||||
| IL_56465.4_Sequence_15 IL_56465.4_IL_3U5H_146_C47_G30 | C | U | G | * | C | G | true | 87 | 0 | 0 | 1.20 | |||||||
| IL_56465.4_Instance_16 IL_56465.4_IL_2O3X_001_G42_C7 | G | U | C | G | U | C | ||||||||||||
| IL_56465.4_Sequence_16 IL_56465.4_IL_2O3X_001_G42_C7 | G | U | C | * | G | U | C | true | 39 | 0 | 0 | 5.84 | ||||||
| IL_56465.4_Instance_17 IL_56465.4_IL_1O9M_001_G1494_C1407 | G | U | C | G | U | C | ||||||||||||
| IL_56465.4_Sequence_17 IL_56465.4_IL_1O9M_001_G_1494_C_1407 | G | U | C | * | G | U | C | true | 39 | 0 | 0 | 5.84 | ||||||
| IL_56465.4_Instance_18 IL_56465.4_IL_4M30_001_U25_A2 | U | U | A | U | A | |||||||||||||
| IL_56465.4_Sequence_18 IL_56465.4_IL_4M30_001_U25_A2 | U | U | A | * | U | A | true | 80 | 0 | 0 | 1.95 | |||||||
| IL_56465.4_Instance_19 IL_56465.4_IL_4A1B_073_U1802_A1695 | U | U | G | C | A | |||||||||||||
| IL_56465.4_Sequence_19 IL_56465.4_IL_4A1B_073_U_1802_A_1695 | U | U | G | * | C | A | true | 82 | 0 | 0 | 1.68 | |||||||
| IL_56465.4_Instance_20 IL_56465.4_IL_2QBG_029_G926_C851 | G | A | A | U | C | |||||||||||||
| IL_56465.4_Sequence_20 IL_56465.4_IL_2QBG_029_G926_C851 | G | A | A | * | U | C | true | 97 | 0 | 0 | 0.27 | |||||||
| IL_56465.4_Instance_21 IL_56465.4_IL_4A1B_042_U1138_A995 | U | A | G | C | A | |||||||||||||
| IL_56465.4_Sequence_21 IL_56465.4_IL_4A1B_042_U_1138_A995 | U | A | G | * | C | A | true | 96 | 0 | 0 | 0.33 | |||||||
| IL_56465.4_Instance_22 IL_56465.4_IL_1FJG_046_G1143_C1128 | G | G | C | G | C | |||||||||||||
| IL_56465.4_Sequence_22 IL_56465.4_IL_1FJG_046_G_1143_C_1128 | G | G | C | * | G | C | true | 79 | 0 | 0 | 2.03 | |||||||
| IL_56465.4_Instance_23 IL_56465.4_IL_4IOA_085_C2477_G2433 | C | C | U | A | G | |||||||||||||
| IL_56465.4_Sequence_23 IL_56465.4_IL_4IOA_085_C_2477_G_2433 | C | C | U | * | A | G | true | 73 | 0 | 0 | 2.61 | |||||||
| IL_56465.4_Instance_24 IL_56465.4_IL_2AW7_024_C477_G455 | C | A | U | G | G | |||||||||||||
| IL_56465.4_Sequence_24 IL_56465.4_IL_2AW7_024_C477_G455 | C | A | U | * | G | G | true | 79 | 0 | 0 | 2.03 | |||||||
| IL_56465.4_Instance_25 IL_56465.4_IL_3U5H_037_U1111_A970 | U | A | G | C | A | |||||||||||||
| IL_56465.4_Sequence_25 IL_56465.4_IL_3U5H_037_U_1111_A970 | U | A | G | * | C | A | true | 96 | 0 | 0 | 0.33 | |||||||
| IL_56465.4_Instance_26 IL_56465.4_IL_3V2F_088_C2498_G2454 | C | C | U | A | G | |||||||||||||
| IL_56465.4_Sequence_26 IL_56465.4_IL_3V2F_088_C_2498_G_2454 | C | C | U | * | A | G | true | 73 | 0 | 0 | 2.61 | |||||||
| IL_56465.4_Instance_27 IL_56465.4_IL_1ZX7_001_C26_G10 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_27 IL_56465.4_IL_1ZX7_001_C26_G10 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_28 IL_56465.4_IL_4IOA_046_G1241_C1234 | G | A | G | U | A | C | ||||||||||||
| IL_56465.4_Sequence_28 IL_56465.4_IL_4IOA_046_G_1241_C_1234 | G | A | G | * | U | A | C | true | 59 | 0 | 0 | 3.86 | ||||||
| IL_56465.4_Instance_29 IL_56465.4_IL_3MOJ_004_C2540_G2523 | C | A | A | U | G | |||||||||||||
| IL_56465.4_Sequence_29 IL_56465.4_IL_3MOJ_004_C_2540_G_2523 | C | A | A | * | U | G | true | 99 | 0 | 0 | 0.14 | |||||||
| IL_56465.4_Instance_30 IL_56465.4_IL_3T4B_001_U287_G137 | U | A | C | G | A | G | ||||||||||||
| IL_56465.4_Sequence_30 IL_56465.4_IL_3T4B_001_U287_G137 | U | A | C | * | G | A | G | true | 62 | 0 | 0 | 3.61 | ||||||
| IL_56465.4_Instance_31 IL_56465.4_IL_4A1B_009_U173_G246 | U | A | A | U | G | |||||||||||||
| IL_56465.4_Sequence_31 IL_56465.4_IL_4A1B_009_U173_G246 | U | A | A | * | U | G | true | 81 | 0 | 0 | 1.78 | |||||||
| IL_56465.4_Instance_32 IL_56465.4_IL_4A1B_018_U466_G512 | U | A | A | U | G | |||||||||||||
| IL_56465.4_Sequence_32 IL_56465.4_IL_4A1B_018_U466_G512 | U | A | A | * | U | G | true | 81 | 0 | 0 | 1.78 | |||||||
| IL_56465.4_Instance_33 IL_56465.4_IL_1ZX7_007_C26_G10 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_33 IL_56465.4_IL_1ZX7_007_C26_G10 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_34 IL_56465.4_IL_2O3X_003_C30_G19 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_34 IL_56465.4_IL_2O3X_003_C30_G19 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_35 IL_56465.4_IL_2AW7_025_U472_A459 | U | U | G | U | A | |||||||||||||
| IL_56465.4_Sequence_35 IL_56465.4_IL_2AW7_025_U472_A459 | U | U | G | * | U | A | true | 63 | 0 | 0 | 3.49 | |||||||
| IL_56465.4_Instance_36 IL_56465.4_IL_2QBG_084_A2184_U2105 | A | U | G | C | C | U | ||||||||||||
| IL_56465.4_Sequence_36 IL_56465.4_IL_2QBG_084_A_2184_U_2105 | A | U | G | * | C | C | U | true | 42 | 0 | 0 | 5.46 | ||||||
| IL_56465.4_Instance_37 IL_56465.4_IL_2QWY_002_C43_G22 | C | U | A | U | G | |||||||||||||
| IL_56465.4_Sequence_37 IL_56465.4_IL_2QWY_002_C43_G22 | C | U | A | * | U | G | true | 84 | 0 | 0 | 1.48 | |||||||
| IL_56465.4_Instance_38 IL_56465.4_IL_1T0E_001_C16_G10 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_38 IL_56465.4_IL_1T0E_001_C16_G10 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_39 IL_56465.4_IL_1MWL_003_C28_G18 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_39 IL_56465.4_IL_1MWL_003_C28_G18 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_40 IL_56465.4_IL_1MWL_002_C6_G40 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_40 IL_56465.4_IL_1MWL_002_C6_G40 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_41 IL_56465.4_IL_2O3X_002_C7_G42 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_41 IL_56465.4_IL_2O3X_002_C7_G42 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_42 IL_56465.4_IL_1O9M_002_C1407_G1494 | C | A | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_42 IL_56465.4_IL_1O9M_002_C_1407_G_1494 | C | A | C | * | G | AA | G | true | 84 | 0 | 0 | 1.48 | ||||||
| IL_56465.4_Instance_43 IL_56465.4_IL_4IOA_102_G2818_C2849 | G | G | C | G | GA | C | ||||||||||||
| IL_56465.4_Sequence_43 IL_56465.4_IL_4IOA_102_G_2818_C_2849 | G | G | C | * | G | GA | C | true | 32 | 0 | 0 | 6.51 | ||||||
| IL_56465.4_Instance_44 IL_56465.4_IL_1DUH_001_C66_G43 | C | A | A | U | ACCA | G | ||||||||||||
| IL_56465.4_Sequence_44 IL_56465.4_IL_1DUH_001_C66_G43 | C | A | A | * | U | ACCA | G | true | 24 | 0 | 0 | 7.21 | ||||||
| IL_56465.4_Instance_45 IL_56465.4_IL_1DUH_005_C66_G43 | C | A | A | U | ACCA | G | ||||||||||||
| IL_56465.4_Sequence_45 IL_56465.4_IL_1DUH_005_C66_G43 | C | A | A | * | U | ACCA | G | true | 24 | 0 | 0 | 7.21 | ||||||
| IL_56465.4_Instance_46 IL_56465.4_IL_3TD1_002_C7_G42 | C | G | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_46 IL_56465.4_IL_3TD1_002_C7_G42 | C | G | C | * | G | AA | G | true | 64 | 0 | 0 | 3.46 | ||||||
| IL_56465.4_Instance_47 IL_56465.4_IL_3TD1_005_C30_G19 | C | G | C | G | AA | G | ||||||||||||
| IL_56465.4_Sequence_47 IL_56465.4_IL_3TD1_005_C30_G19 | C | G | C | * | G | AA | G | true | 64 | 0 | 0 | 3.46 |
1 2 s35 1 5 cWW 2 3 s35 2 5 s55 3 4 cWW 4 5 s35JAR3D SCFG/MRF model for IL_56465.4:
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 [5] // Initial node A189 - U161 from junction BasepairNode | Deletion Probability [0.0000004752076360] | Pair Probability [[0.007013269,0.013200437,0.008049529,0.149653816,0.000000000],[0.027041859,0.006359192,0.273371709,0.009196872,0.000000000],[0.008076843,0.238547761,0.001552997,0.017140816,0.000000000],[0.170808705,0.009069603,0.052955769,0.007960824,0.000000000],[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 [0.616195094,0.107125059,0.233832083,0.000299453,0.042500850,0.000045200,0.000002260] | Right Letter Distribution [0.743243243,0.148648649,0.040540541,0.067567568,0.000000000] | Left Index [1] | Right Index [5] // Basepair A189 - U161 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.663265306,0.071428571,0.091836735,0.173469388,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left 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 [3] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007092369,0.022541509,0.007972059,0.192002477,0.000000000],[0.017778225,0.006243616,0.237874688,0.008951255,0.000000000],[0.007961221,0.251860467,0.001550452,0.040958339,0.000000000],[0.150342859,0.009001170,0.028902739,0.008966555,0.000000000],[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 [3] | Right Index [4] // Basepair G191 - C160 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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_56465.4:
> IL_56465.4 IL_4IOA_005 A 189 U 161 AAG*CU > IL_56465.4 IL_4A1B_001 G 54 C 26 GAG*CC > IL_56465.4 IL_3V2F_005 G 212 C 184 GAG*CC > IL_56465.4 IL_3V2F_024 G 940 C 838 GAG*CC > IL_56465.4 IL_3U5H_004 G 56 C 28 GAG*CC > IL_56465.4 IL_4IOA_021 G 951 C 851 GAG*CC > IL_56465.4 IL_2QBG_010 G 212 C 184 GAG*CC > IL_56465.4 IL_1S72_005 G 182 C 154 GAG*CC > IL_56465.4 IL_2QBG_027 G 940 C 838 GAG*CC > IL_56465.4 IL_1S72_079 U 2436 A 2455 UAG*CA > IL_56465.4 IL_2QBG_090 C 2498 G 2454 CCU*AG > IL_56465.4 IL_4IOA_056 A 1463 U 1478 AAG*CU > IL_56465.4 IL_2AW7_047 G 1041 C 999 GAG*CC > IL_56465.4 IL_3U5H_009 C 163 G 258 CAA*UG > IL_56465.4 IL_3U5H_146 C 47 G 30 CUG*CG > IL_56465.4 IL_2O3X_001 G 42 C 7 GUC*GUC > IL_56465.4 IL_1O9M_001 G 1494 C 1407 GUC*GUC > IL_56465.4 IL_4M30_001 U 25 A 2 UUA*UA > IL_56465.4 IL_4A1B_073 U 1802 A 1695 UUG*CA > IL_56465.4 IL_2QBG_029 G 926 C 851 GAA*UC > IL_56465.4 IL_4A1B_042 U 1138 A 995 UAG*CA > IL_56465.4 IL_1FJG_046 G 1143 C 1128 GGC*GC > IL_56465.4 IL_4IOA_085 C 2477 G 2433 CCU*AG > IL_56465.4 IL_2AW7_024 C 477 G 455 CAU*GG > IL_56465.4 IL_3U5H_037 U 1111 A 970 UAG*CA > IL_56465.4 IL_3V2F_088 C 2498 G 2454 CCU*AG > IL_56465.4 IL_1ZX7_001 C 26 G 10 CAC*GAAG > IL_56465.4 IL_4IOA_046 G 1241 C 1234 GAG*UAC > IL_56465.4 IL_3MOJ_004 C 2540 G 2523 CAA*UG > IL_56465.4 IL_3T4B_001 U 287 G 137 UAC*GAG > IL_56465.4 IL_4A1B_009 U 173 G 246 UAA*UG > IL_56465.4 IL_4A1B_018 U 466 G 512 UAA*UG > IL_56465.4 IL_1ZX7_007 C 26 G 10 CAC*GAAG > IL_56465.4 IL_2O3X_003 C 30 G 19 CAC*GAAG > IL_56465.4 IL_2AW7_025 U 472 A 459 UUG*UA > IL_56465.4 IL_2QBG_084 A 2184 U 2105 AUG*CCU > IL_56465.4 IL_2QWY_002 C 43 G 22 CUA*UG > IL_56465.4 IL_1T0E_001 C 16 G 10 CAC*GAAG > IL_56465.4 IL_1MWL_003 C 28 G 18 CAC*GAAG > IL_56465.4 IL_1MWL_002 C 6 G 40 CAC*GAAG > IL_56465.4 IL_2O3X_002 C 7 G 42 CAC*GAAG > IL_56465.4 IL_1O9M_002 C 1407 G 1494 CAC*GAAG > IL_56465.4 IL_4IOA_102 G 2818 C 2849 GGC*GGAC > IL_56465.4 IL_1DUH_001 C 66 G 43 CAA*UACCAG > IL_56465.4 IL_1DUH_005 C 66 G 43 CAA*UACCAG > IL_56465.4 IL_3TD1_002 C 7 G 42 CGC*GAAG > IL_56465.4 IL_3TD1_005 C 30 G 19 CGC*GAAG