| 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 3 I | 6 4 3 | 7 4 I | 8 5 | 9 4 I | 10 4 4 | 11 3 I | 12 2 5 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_44540.4_Instance_1 IL_44540.4_IL_1S72_035_U1009_A957 | U | C | C | G | A | |||||||||||||
| IL_44540.4_Sequence_1 IL_44540.4_IL_1S72_035_U_1009_A957 | U | C | C | * | G | A | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_44540.4_Instance_2 IL_44540.4_IL_3V2F_028_U913_A863 | U | C | C | G | A | |||||||||||||
| IL_44540.4_Sequence_2 IL_44540.4_IL_3V2F_028_U913_A863 | U | C | C | * | G | A | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_44540.4_Instance_3 IL_44540.4_IL_4IOA_027_U925_A876 | U | C | C | G | A | |||||||||||||
| IL_44540.4_Sequence_3 IL_44540.4_IL_4IOA_027_U925_A876 | U | C | C | * | G | A | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_44540.4_Instance_4 IL_44540.4_IL_2QBG_008_U434_A44 | U | C | C | G | A | |||||||||||||
| IL_44540.4_Sequence_4 IL_44540.4_IL_2QBG_008_U434_A44 | U | C | C | * | G | A | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_44540.4_Instance_5 IL_44540.4_IL_1Y0Q_003_A120_U193 | A | C | G | C | U | |||||||||||||
| IL_44540.4_Sequence_5 IL_44540.4_IL_1Y0Q_003_A120_U193 | A | C | G | * | C | U | true | 80 | 0 | 0 | 1.94 | |||||||
| IL_44540.4_Instance_6 IL_44540.4_IL_3V2F_078_U2438_A2071 | U | A | C | C | G | A | ||||||||||||
| IL_44540.4_Sequence_6 IL_44540.4_IL_3V2F_078_U_2438_A_2071 | U | A | C | C | * | G | A | true | 84 | 0 | 0 | 1.53 | ||||||
| IL_44540.4_Instance_7 IL_44540.4_IL_1S72_075_U2473_A2112 | U | A | C | C | G | A | ||||||||||||
| IL_44540.4_Sequence_7 IL_44540.4_IL_1S72_075_U_2473_A_2112 | U | A | C | C | * | G | A | true | 84 | 0 | 0 | 1.53 | ||||||
| IL_44540.4_Instance_8 IL_44540.4_IL_2QBG_081_U2438_A2071 | U | A | C | U | A | A | ||||||||||||
| IL_44540.4_Sequence_8 IL_44540.4_IL_2QBG_081_U_2438_A_2071 | U | A | C | U | * | A | A | true | 82 | 0 | 0 | 1.69 | ||||||
| IL_44540.4_Instance_9 IL_44540.4_IL_3U5F_029_A518_U533 | A | C | A | U | U | |||||||||||||
| IL_44540.4_Sequence_9 IL_44540.4_IL_3U5F_029_A518_U533 | A | C | A | * | U | U | true | 75 | 0 | 0 | 2.35 | |||||||
| IL_44540.4_Instance_10 IL_44540.4_IL_4IOA_076_U2417_A2054 | U | A | C | C | G | A | ||||||||||||
| IL_44540.4_Sequence_10 IL_44540.4_IL_4IOA_076_U_2417_A_2054 | U | A | C | C | * | G | A | true | 84 | 0 | 0 | 1.53 | ||||||
| IL_44540.4_Instance_11 IL_44540.4_IL_3U5H_041_U1050_A998 | U | U | U | A | A | |||||||||||||
| IL_44540.4_Sequence_11 IL_44540.4_IL_3U5H_041_U_1050_A998 | U | U | U | * | A | A | true | 71 | 0 | 0 | 2.75 | |||||||
| IL_44540.4_Instance_12 IL_44540.4_IL_4A1B_096_U2795_A2408 | U | A | C | C | G | A | ||||||||||||
| IL_44540.4_Sequence_12 IL_44540.4_IL_4A1B_096_U_2795_A_2408 | U | A | C | C | * | G | A | true | 84 | 0 | 0 | 1.53 | ||||||
| IL_44540.4_Instance_13 IL_44540.4_IL_1FJG_038_C1226_G954 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_13 IL_44540.4_IL_1FJG_038_C_1226_G954 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_14 IL_44540.4_IL_3U5H_099_U2807_A2413 | U | A | C | C | G | A | ||||||||||||
| IL_44540.4_Sequence_14 IL_44540.4_IL_3U5H_099_U_2807_A_2413 | U | A | C | C | * | G | A | true | 84 | 0 | 0 | 1.53 | ||||||
| IL_44540.4_Instance_15 IL_44540.4_IL_1U6B_007_G128_C178 | G | A | G | C | C | |||||||||||||
| IL_44540.4_Sequence_15 IL_44540.4_IL_1U6B_007_G128_C178 | G | A | G | * | C | C | true | 79 | 0 | 0 | 2.01 | |||||||
| IL_44540.4_Instance_16 IL_44540.4_IL_4BPP_069_C1278_G1290 | C | U | G | C | G | |||||||||||||
| IL_44540.4_Sequence_16 IL_44540.4_IL_4BPP_069_C_1278_G_1290 | C | U | G | * | C | G | true | 82 | 0 | 0 | 1.66 | |||||||
| IL_44540.4_Instance_17 IL_44540.4_IL_2AW7_045_C1226_G954 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_17 IL_44540.4_IL_2AW7_045_C_1226_G954 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_18 IL_44540.4_IL_4BPP_059_C1430_G1151 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_18 IL_44540.4_IL_4BPP_059_C_1430_G_1151 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_19 IL_44540.4_IL_4IOA_003_U447_A43 | U | C | C | G | A | |||||||||||||
| IL_44540.4_Sequence_19 IL_44540.4_IL_4IOA_003_U447_A43 | U | C | C | * | G | A | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_44540.4_Instance_20 IL_44540.4_IL_2GDI_003_C23_G36 | C | C | U | A | G | |||||||||||||
| IL_44540.4_Sequence_20 IL_44540.4_IL_2GDI_003_C23_G36 | C | C | U | * | A | G | true | 66 | 0 | 0 | 3.22 | |||||||
| IL_44540.4_Instance_21 IL_44540.4_IL_4A1B_128_U3338_A3282 | U | C | U | A | A | |||||||||||||
| IL_44540.4_Sequence_21 IL_44540.4_IL_4A1B_128_U_3338_A_3282 | U | C | U | * | A | A | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_22 IL_44540.4_IL_4A1B_020_C470_G507 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_22 IL_44540.4_IL_4A1B_020_C470_G507 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_23 IL_44540.4_IL_2QWY_006_U40_A24 | U | A | G | C | A | |||||||||||||
| IL_44540.4_Sequence_23 IL_44540.4_IL_2QWY_006_U40_A24 | U | A | G | * | C | A | true | 85 | 0 | 0 | 1.43 | |||||||
| IL_44540.4_Instance_24 IL_44540.4_IL_2QWY_003_U40_A24 | U | A | G | C | A | |||||||||||||
| IL_44540.4_Sequence_24 IL_44540.4_IL_2QWY_003_U40_A24 | U | A | G | * | C | A | true | 85 | 0 | 0 | 1.43 | |||||||
| IL_44540.4_Instance_25 IL_44540.4_IL_2GDI_007_C23_G36 | C | C | U | A | G | |||||||||||||
| IL_44540.4_Sequence_25 IL_44540.4_IL_2GDI_007_C23_G36 | C | C | U | * | A | G | true | 66 | 0 | 0 | 3.22 | |||||||
| IL_44540.4_Instance_26 IL_44540.4_IL_2AW7_035_A746_U659 | A | A | G | C | U | |||||||||||||
| IL_44540.4_Sequence_26 IL_44540.4_IL_2AW7_035_A746_U659 | A | A | G | * | C | U | true | 77 | 0 | 0 | 2.21 | |||||||
| IL_44540.4_Instance_27 IL_44540.4_IL_3U5F_071_C1306_G1318 | C | U | G | C | G | |||||||||||||
| IL_44540.4_Sequence_27 IL_44540.4_IL_3U5F_071_C_1306_G_1318 | C | U | G | * | C | G | true | 82 | 0 | 0 | 1.66 | |||||||
| IL_44540.4_Instance_28 IL_44540.4_IL_2AW7_067_U1440_G1461 | U | A | G | C | G | |||||||||||||
| IL_44540.4_Sequence_28 IL_44540.4_IL_2AW7_067_U_1440_G_1461 | U | A | G | * | C | G | true | 78 | 0 | 0 | 2.09 | |||||||
| IL_44540.4_Instance_29 IL_44540.4_IL_4A1B_049_G1039_C1063 | G | A | C | U | A | C | ||||||||||||
| IL_44540.4_Sequence_29 IL_44540.4_IL_4A1B_049_G_1039_C_1063 | G | A | C | U | * | A | C | true | 55 | 0 | 0 | 4.30 | ||||||
| IL_44540.4_Instance_30 IL_44540.4_IL_3V2F_070_G1846_C1894 | G | A | A | G | C | C | ||||||||||||
| IL_44540.4_Sequence_30 IL_44540.4_IL_3V2F_070_G_1846_C_1894 | G | A | A | G | * | C | C | true | 63 | 0 | 0 | 3.54 | ||||||
| IL_44540.4_Instance_31 IL_44540.4_IL_3IWN_001_G89_C3 | G | A | U | A | C | |||||||||||||
| IL_44540.4_Sequence_31 IL_44540.4_IL_3IWN_001_G89_C3 | G | A | U | * | A | C | true | 79 | 0 | 0 | 1.97 | |||||||
| IL_44540.4_Instance_32 IL_44540.4_IL_1X8W_004_G129_C193 | G | U | U | A | C | |||||||||||||
| IL_44540.4_Sequence_32 IL_44540.4_IL_1X8W_004_G129_C193 | G | U | U | * | A | C | true | 56 | 0 | 0 | 4.22 | |||||||
| IL_44540.4_Instance_33 IL_44540.4_IL_3RW6_001_U53_A8 | U | A | A | U | A | A | ||||||||||||
| IL_44540.4_Sequence_33 IL_44540.4_IL_3RW6_001_U53_A8 | U | A | A | U | * | A | A | true | 69 | 0 | 0 | 2.92 | ||||||
| IL_44540.4_Instance_34 IL_44540.4_IL_4BPP_005_C49_G421 | C | A | U | A | G | |||||||||||||
| IL_44540.4_Sequence_34 IL_44540.4_IL_4BPP_005_C49_G421 | C | A | U | * | A | G | true | 97 | 0 | 0 | 0.32 | |||||||
| IL_44540.4_Instance_35 IL_44540.4_IL_3U5F_005_C50_G429 | C | A | U | A | G | |||||||||||||
| IL_44540.4_Sequence_35 IL_44540.4_IL_3U5F_005_C50_G429 | C | A | U | * | A | G | true | 97 | 0 | 0 | 0.32 | |||||||
| IL_44540.4_Instance_36 IL_44540.4_IL_3U5F_062_C1459_G1179 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_36 IL_44540.4_IL_3U5F_062_C_1459_G_1179 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_37 IL_44540.4_IL_1S72_033_U942_G1024 | U | A | G | C | G | |||||||||||||
| IL_44540.4_Sequence_37 IL_44540.4_IL_1S72_033_U942_G_1024 | U | A | G | * | C | G | true | 78 | 0 | 0 | 2.09 | |||||||
| IL_44540.4_Instance_38 IL_44540.4_IL_1FJG_004_C54_G357 | C | A | U | A | G | |||||||||||||
| IL_44540.4_Sequence_38 IL_44540.4_IL_1FJG_004_C54_G357 | C | A | U | * | A | G | true | 97 | 0 | 0 | 0.32 | |||||||
| IL_44540.4_Instance_39 IL_44540.4_IL_2AW7_004_C54_G357 | C | A | U | A | G | |||||||||||||
| IL_44540.4_Sequence_39 IL_44540.4_IL_2AW7_004_C54_G357 | C | A | U | * | A | G | true | 97 | 0 | 0 | 0.32 | |||||||
| IL_44540.4_Instance_40 IL_44540.4_IL_1FJG_052_C1260_G1274 | C | A | C | G | G | |||||||||||||
| IL_44540.4_Sequence_40 IL_44540.4_IL_1FJG_052_C_1260_G_1274 | C | A | C | * | G | G | true | 98 | 0 | 0 | 0.16 | |||||||
| IL_44540.4_Instance_41 IL_44540.4_IL_1FJG_051_G1274_C1260 | G | A | G | C | C | |||||||||||||
| IL_44540.4_Sequence_41 IL_44540.4_IL_1FJG_051_G_1274_C_1260 | G | A | G | * | C | C | true | 79 | 0 | 0 | 2.01 | |||||||
| IL_44540.4_Instance_42 IL_44540.4_IL_2AW7_050_U1199_G1058 | U | CA | U | C | G | G | ||||||||||||
| IL_44540.4_Sequence_42 IL_44540.4_IL_2AW7_050_U_1199_G_1058 | U | CA | U | C | * | G | G | true | 21 | 0 | 0 | 7.50 | ||||||
| IL_44540.4_Instance_43 IL_44540.4_IL_1FJG_042_U1199_G1058 | U | CA | G | C | G | G | ||||||||||||
| IL_44540.4_Sequence_43 IL_44540.4_IL_1FJG_042_U_1199_G_1058 | U | CA | G | C | * | G | G | true | -12 | 0 | 0 | 10.68 |
1 2 cSH 1 3 s35 1 5 cWW 2 3 s35 2 5 tHS 3 4 cWW 3 5 s55 4 5 s35JAR3D SCFG/MRF model for IL_44540.4:
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 U1009 - A957 from junction ClusterNode | Deletion Probability [0.0000000250261143] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.026353112417028] // Cluster node U1009:C1010 and A957:A957 Interaction | Interacting Bases [1,3] | Pair Probability [[0.007087812,0.013604265,0.008008610,0.153195201,0.000000000],[0.035070638,0.006885220,0.232591707,0.008978534,0.000000000],[0.008055311,0.175121578,0.001625852,0.016955527,0.000000000],[0.246453501,0.008762438,0.068720802,0.008883005,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1009 - A957 cWW Interaction | Interacting Bases [2,3] | Pair Probability [[0.095591915,0.106824167,0.178277454,0.088940395,0.000000000],[0.177764611,0.079495179,0.019247943,0.088356483,0.000000000],[0.001148396,0.001148396,0.028598932,0.001148396,0.000000000],[0.028336673,0.010198169,0.093774496,0.001148396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1010 - A957 tHS Interaction | Interacting Bases [1,2] | Pair Probability [[0.071009696,0.093309902,0.007442406,0.005625961,0.000000000],[0.146912668,0.074881625,0.001218629,0.076253838,0.000000000],[0.062794928,0.037675486,0.014189529,0.069006930,0.000000000],[0.088994680,0.163818414,0.010445824,0.076419484,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1009 - C1010 cSH Insertion | Location [1] | Length Distribution [0.743300802,0.209903027,0.046727319,0.000066152,0.000002700] | Letter Distribution [0.766666667,0.166666667,0.033333333,0.033333333,0.000000000]// Insertion after nucleotide 1, position 1 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 [3] | Right Index [4] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006974620,0.013674620,0.007915035,0.148008959,0.000000000],[0.014958019,0.006302134,0.273084914,0.008986373,0.000000000],[0.007935635,0.223147879,0.001534242,0.017694250,0.000000000],[0.233663470,0.008895267,0.018972439,0.008252145,0.000000000],[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 C1011 - G956 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_44540.4:
> IL_44540.4 IL_1S72_035 U 1009 A 957 UCC*GA > IL_44540.4 IL_3V2F_028 U 913 A 863 UCC*GA > IL_44540.4 IL_4IOA_027 U 925 A 876 UCC*GA > IL_44540.4 IL_2QBG_008 U 434 A 44 UCC*GA > IL_44540.4 IL_1Y0Q_003 A 120 U 193 ACG*CU > IL_44540.4 IL_3V2F_078 U 2438 A 2071 UACC*GA > IL_44540.4 IL_1S72_075 U 2473 A 2112 UACC*GA > IL_44540.4 IL_2QBG_081 U 2438 A 2071 UACU*AA > IL_44540.4 IL_3U5F_029 A 518 U 533 ACA*UU > IL_44540.4 IL_4IOA_076 U 2417 A 2054 UACC*GA > IL_44540.4 IL_3U5H_041 U 1050 A 998 UUU*AA > IL_44540.4 IL_4A1B_096 U 2795 A 2408 UACC*GA > IL_44540.4 IL_1FJG_038 C 1226 G 954 CAC*GG > IL_44540.4 IL_3U5H_099 U 2807 A 2413 UACC*GA > IL_44540.4 IL_1U6B_007 G 128 C 178 GAG*CC > IL_44540.4 IL_4BPP_069 C 1278 G 1290 CUG*CG > IL_44540.4 IL_2AW7_045 C 1226 G 954 CAC*GG > IL_44540.4 IL_4BPP_059 C 1430 G 1151 CAC*GG > IL_44540.4 IL_4IOA_003 U 447 A 43 UCC*GA > IL_44540.4 IL_2GDI_003 C 23 G 36 CCU*AG > IL_44540.4 IL_4A1B_128 U 3338 A 3282 UCU*AA > IL_44540.4 IL_4A1B_020 C 470 G 507 CAC*GG > IL_44540.4 IL_2QWY_006 U 40 A 24 UAG*CA > IL_44540.4 IL_2QWY_003 U 40 A 24 UAG*CA > IL_44540.4 IL_2GDI_007 C 23 G 36 CCU*AG > IL_44540.4 IL_2AW7_035 A 746 U 659 AAG*CU > IL_44540.4 IL_3U5F_071 C 1306 G 1318 CUG*CG > IL_44540.4 IL_2AW7_067 U 1440 G 1461 UAG*CG > IL_44540.4 IL_4A1B_049 G 1039 C 1063 GACU*AC > IL_44540.4 IL_3V2F_070 G 1846 C 1894 GAAG*CC > IL_44540.4 IL_3IWN_001 G 89 C 3 GAU*AC > IL_44540.4 IL_1X8W_004 G 129 C 193 GUU*AC > IL_44540.4 IL_3RW6_001 U 53 A 8 UAAU*AA > IL_44540.4 IL_4BPP_005 C 49 G 421 CAU*AG > IL_44540.4 IL_3U5F_005 C 50 G 429 CAU*AG > IL_44540.4 IL_3U5F_062 C 1459 G 1179 CAC*GG > IL_44540.4 IL_1S72_033 U 942 G 1024 UAG*CG > IL_44540.4 IL_1FJG_004 C 54 G 357 CAU*AG > IL_44540.4 IL_2AW7_004 C 54 G 357 CAU*AG > IL_44540.4 IL_1FJG_052 C 1260 G 1274 CAC*GG > IL_44540.4 IL_1FJG_051 G 1274 C 1260 GAG*CC > IL_44540.4 IL_2AW7_050 U 1199 G 1058 UCAUC*GG > IL_44540.4 IL_1FJG_042 U 1199 G 1058 UCAGC*GG