| 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 3 I | 6 4 3 | 7 4 I | 8 5 4 | 9 5 I | 10 6 | 11 5 I | 12 5 5 | 13 4 I | 14 4 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_85033.2_Instance_1 IL_85033.2,IL_1D4R_001,G4_C25 | G | A | C | C | G | A | C | C | ||||||||||||||||
| IL_85033.2_Sequence_1 IL_85033.21D4R_G4_C25 | G | A | C | C | * | G | A | C | C | true | 91 | 0 | 0 | 0.86 | ||||||||||
| IL_85033.2_Instance_2 IL_85033.2,IL_1JID_002,G138_C159 | G | A | C | C | G | A | C | C | ||||||||||||||||
| IL_85033.2_Sequence_2 IL_85033.21JID_G138_C159 | G | A | C | C | * | G | A | C | C | true | 91 | 0 | 0 | 0.86 | ||||||||||
| IL_85033.2_Instance_3 IL_85033.2,IL_3WBM_003,G14_C13 | G | A | C | U | A | C | C | C | ||||||||||||||||
| IL_85033.2_Sequence_3 IL_85033.23WBM_G14_C13 | G | A | C | U | * | A | C | C | C | true | 79 | 0 | 0 | 1.99 | ||||||||||
| IL_85033.2_Instance_4 IL_85033.2,IL_3WBM_002,G14_C13 | G | A | C | U | A | C | C | C | ||||||||||||||||
| IL_85033.2_Sequence_4 IL_85033.23WBM_G14_C13 | G | A | C | U | * | A | C | C | C | true | 79 | 0 | 0 | 1.99 | ||||||||||
| IL_85033.2_Instance_5 IL_85033.2,IL_1D4R_003,G22_C7 | G | A | C | C | G | A | C | C | ||||||||||||||||
| IL_85033.2_Sequence_5 IL_85033.21D4R_G22_C7 | G | A | C | C | * | G | A | C | C | true | 91 | 0 | 0 | 0.86 | ||||||||||
| IL_85033.2_Instance_6 IL_85033.2,IL_1MFQ_004,G156_C141 | G | A | C | C | G | A | C | C | ||||||||||||||||
| IL_85033.2_Sequence_6 IL_85033.21MFQ_G156_C141 | G | A | C | C | * | G | A | C | C | true | 91 | 0 | 0 | 0.86 | ||||||||||
| IL_85033.2_Instance_7 IL_85033.2,IL_5EW4_002,C8_G17 | C | C | C | G | C | C | C | G | ||||||||||||||||
| IL_85033.2_Sequence_7 IL_85033.25EW4_C8_G17 | C | C | C | G | * | C | C | C | G | true | 57 | 0 | 0 | 4.04 | ||||||||||
| IL_85033.2_Instance_8 IL_85033.2,IL_1L9A_005,G138_C159 | G | A | C | C | G | A | C | C | ||||||||||||||||
| IL_85033.2_Sequence_8 IL_85033.21L9A_G138_C159 | G | A | C | C | * | G | A | C | C | true | 91 | 0 | 0 | 0.86 | ||||||||||
| IL_85033.2_Instance_9 IL_85033.2,IL_4K27_001,C4_G52 | C | C | U | G | C | C | U | G | ||||||||||||||||
| IL_85033.2_Sequence_9 IL_85033.24K27_C4_G52 | C | C | U | G | * | C | C | U | G | true | 68 | 0 | 0 | 3.00 | ||||||||||
| IL_85033.2_Instance_10 IL_85033.2,IL_8FER_001,G7_C10 | G | U | U | C | G | U | U | C | ||||||||||||||||
| IL_85033.2_Sequence_10 IL_85033.28FER_G7_C10 | G | U | U | C | * | G | U | U | C | true | 79 | 0 | 0 | 2.01 | ||||||||||
| IL_85033.2_Instance_11 IL_85033.2,IL_7VYX_002,C13_G53 | C | U | U | C | G | G | U | G | ||||||||||||||||
| IL_85033.2_Sequence_11 IL_85033.27VYX_C13_G53 | C | U | U | C | * | G | G | U | G | true | 79 | 0 | 0 | 1.96 | ||||||||||
| IL_85033.2_Instance_12 IL_85033.2,IL_8P9A_419,G953_C874 | G | G | A | C | G | G | U | C | ||||||||||||||||
| IL_85033.2_Sequence_12 IL_85033.28P9A_G953_C874 | G | G | A | C | * | G | G | U | C | true | 94 | 0 | 0 | 0.60 | ||||||||||
| IL_85033.2_Instance_13 IL_85033.2,IL_8CRE_433,G938_C859 | G | G | A | C | G | G | U | C | ||||||||||||||||
| IL_85033.2_Sequence_13 IL_85033.28CRE_G938_C859 | G | G | A | C | * | G | G | U | C | true | 94 | 0 | 0 | 0.60 | ||||||||||
| IL_85033.2_Instance_14 IL_85033.2,IL_6JDV_002,A63_U38 | A | C | C | G | C | C | U | U | ||||||||||||||||
| IL_85033.2_Sequence_14 IL_85033.26JDV_A63_U38 | A | C | C | G | * | C | C | U | U | true | 66 | 0 | 0 | 3.19 | ||||||||||
| IL_85033.2_Instance_15 IL_85033.2,IL_8CRE_018,A445_U484 | A | U | U | U | G | U | U | U | ||||||||||||||||
| IL_85033.2_Sequence_15 IL_85033.28CRE_A445_U484 | A | U | U | U | * | G | U | U | U | true | 63 | 0 | 0 | 3.49 | ||||||||||
| IL_85033.2_Instance_16 IL_85033.2,IL_5LQT_002,G4_C7 | G | G | A | C | G | G | A | C | ||||||||||||||||
| IL_85033.2_Sequence_16 IL_85033.25LQT_G4_C7 | G | G | A | C | * | G | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_85033.2_Instance_17 IL_85033.2,IL_333D_001,C3_G6 | C | A | G | G | C | A | G | G | ||||||||||||||||
| IL_85033.2_Sequence_17 IL_85033.2333D_C3_G6 | C | A | G | G | * | C | A | G | G | true | 92 | 0 | 0 | 0.75 | ||||||||||
| IL_85033.2_Instance_18 IL_85033.2,IL_7R9G_002,C5_G8 | C | G | G | G | C | G | G | G | ||||||||||||||||
| IL_85033.2_Sequence_18 IL_85033.27R9G_C5_G8 | C | G | G | G | * | C | G | G | G | true | 55 | 0 | 0 | 4.32 | ||||||||||
| IL_85033.2_Instance_19 IL_85033.2,IL_5J7L_283,G1038_C1117 | G | A | A | G | C | G | G | C | ||||||||||||||||
| IL_85033.2_Sequence_19 IL_85033.25J7L_G_1038_C_1117 | G | A | A | G | * | C | G | G | C | true | 95 | 0 | 0 | 0.46 | ||||||||||
| IL_85033.2_Instance_20 IL_85033.2,IL_5LQO_002,G4_C7 | G | G | A | C | G | G | A | C | ||||||||||||||||
| IL_85033.2_Sequence_20 IL_85033.25LQO_G4_C7 | G | G | A | C | * | G | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_85033.2_Instance_21 IL_85033.2,IL_8CRE_109,U2707_A2693 | U | A | C | A | U | U | G | A | ||||||||||||||||
| IL_85033.2_Sequence_21 IL_85033.28CRE_U_2707_A_2693 | U | A | C | A | * | U | U | G | A | true | 75 | 0 | 0 | 2.37 | ||||||||||
| IL_85033.2_Instance_22 IL_85033.2,IL_8CRE_440,G1059_U1029 | G | C | A | C | G | G | A | U | ||||||||||||||||
| IL_85033.2_Sequence_22 IL_85033.28CRE_G_1059_U_1029 | G | C | A | C | * | G | G | A | U | true | 72 | 0 | 0 | 2.66 | ||||||||||
| IL_85033.2_Instance_23 IL_85033.2,IL_3CJZ_001,G5_C21 | G | G | A | C | G | G | A | C | ||||||||||||||||
| IL_85033.2_Sequence_23 IL_85033.23CJZ_G5_C21 | G | G | A | C | * | G | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_85033.2_Instance_24 IL_85033.2,IL_8P9A_327,U2735_A2721 | U | A | C | A | U | U | G | A | ||||||||||||||||
| IL_85033.2_Sequence_24 IL_85033.28P9A_U_2735_A_2721 | U | A | C | A | * | U | U | G | A | true | 75 | 0 | 0 | 2.37 | ||||||||||
| IL_85033.2_Instance_25 IL_85033.2,IL_8P9A_426,G1074_U1044 | G | C | A | C | G | G | A | U | ||||||||||||||||
| IL_85033.2_Sequence_25 IL_85033.28P9A_G_1074_U_1044 | G | C | A | C | * | G | G | A | U | true | 72 | 0 | 0 | 2.66 | ||||||||||
| IL_85033.2_Instance_26 IL_85033.2,IL_8P9A_421,A924_U888 | A | G | A | C | G | U | A | U | ||||||||||||||||
| IL_85033.2_Sequence_26 IL_85033.28P9A_A924_U888 | A | G | A | C | * | G | U | A | U | true | 78 | 0 | 0 | 2.09 | ||||||||||
| IL_85033.2_Instance_27 IL_85033.2,IL_5UNE_005,G21_C24 | G | C | A | C | G | C | A | C | ||||||||||||||||
| IL_85033.2_Sequence_27 IL_85033.25UNE_G21_C24 | G | C | A | C | * | G | C | A | C | true | 70 | 0 | 0 | 2.83 | ||||||||||
| IL_85033.2_Instance_28 IL_85033.2,IL_8CRE_435,A909_U873 | A | G | A | C | G | U | A | U | ||||||||||||||||
| IL_85033.2_Sequence_28 IL_85033.28CRE_A909_U873 | A | G | A | C | * | G | U | A | U | true | 78 | 0 | 0 | 2.09 | ||||||||||
| IL_85033.2_Instance_29 IL_85033.2,IL_5J7L_033,U740_G666 | U | G | G | A | U | A | G | A | G | |||||||||||||||
| IL_85033.2_Sequence_29 IL_85033.25J7L_U740_G666 | U | G | G | A | * | U | A | G | A | G | true | 53 | 0 | 0 | 4.47 | |||||||||
| IL_85033.2_Instance_30 IL_85033.2,IL_4LFB_029,U740_G666 | U | G | G | U | G | A | G | A | G | |||||||||||||||
| IL_85033.2_Sequence_30 IL_85033.24LFB_U740_G666 | U | G | G | U | * | G | A | G | A | G | true | 47 | 0 | 0 | 5.01 | |||||||||
| IL_85033.2_Instance_31 IL_85033.2,IL_1G1X_006,U740_G666 | U | G | G | U | G | A | G | A | G | |||||||||||||||
| IL_85033.2_Sequence_31 IL_85033.21G1X_U740_G666 | U | G | G | U | * | G | A | G | A | G | true | 47 | 0 | 0 | 5.01 | |||||||||
| IL_85033.2_Instance_32 IL_85033.2,IL_1G1X_003,U740_G666 | U | G | G | U | G | A | G | A | G | |||||||||||||||
| IL_85033.2_Sequence_32 IL_85033.21G1X_U740_G666 | U | G | G | U | * | G | A | G | A | G | true | 47 | 0 | 0 | 5.01 | |||||||||
| IL_85033.2_Instance_33 IL_85033.2,IL_8CRE_434,C859_G938 | C | G | G | G | G | C | A | A | G | |||||||||||||||
| IL_85033.2_Sequence_33 IL_85033.28CRE_C859_G938 | C | G | G | G | G | * | C | A | A | G | true | 59 | 0 | 0 | 3.85 | |||||||||
| IL_85033.2_Instance_34 IL_85033.2,IL_8P9A_420,C874_G953 | C | G | G | G | G | C | A | A | G | |||||||||||||||
| IL_85033.2_Sequence_34 IL_85033.28P9A_C874_G953 | C | G | G | G | G | * | C | A | A | G | true | 59 | 0 | 0 | 3.85 | |||||||||
| IL_85033.2_Instance_35 IL_85033.2,IL_1KUQ_003,U39_G30 | U | G | G | U | G | A | G | A | G | |||||||||||||||
| IL_85033.2_Sequence_35 IL_85033.21KUQ_U39_G30 | U | G | G | U | * | G | A | G | A | G | true | 47 | 0 | 0 | 5.01 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 2 8 s55 3 4 s35 3 6 cWW 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for IL_85033.2:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000115088153469] | Pair Probability [[0.007682320,0.026133847,0.008689026,0.158634876,0.000000000],[0.044312126,0.009379228,0.180587492,0.010109338,0.000000000],[0.008687435,0.240631375,0.001753755,0.048208849,0.000000000],[0.146233858,0.010136286,0.089274448,0.009545740,0.000000000],[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 [0.855888435,0.143836523,0.000264855,0.000010187] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [8] // Basepair G4 - C25 cWW BasepairNode | Deletion Probability [0.0000181219558778] | Pair Probability [[0.013403974,0.155351779,0.139284205,0.020574552,0.000000000],[0.057164216,0.020980079,0.017081266,0.055720192,0.000000000],[0.162933689,0.017726201,0.065347822,0.089048633,0.000000000],[0.016843308,0.037444120,0.030589893,0.100506071,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.941449748,0.058397433,0.000148744,0.000004075] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | 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 [7] // Basepair A5 - C24 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014912692,0.035797027,0.212905716,0.040123374,0.000000000],[0.094914434,0.052460327,0.026156769,0.065107891,0.000000000],[0.210744066,0.025542656,0.012677954,0.015721826,0.000000000],[0.025811485,0.056005737,0.064779661,0.046338385,0.000000000],[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 [3] | Right Index [6] // Basepair C6 - A23 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007385870,0.013469154,0.008548634,0.155660799,0.000000000],[0.045134987,0.009274620,0.263329698,0.010233458,0.000000000],[0.008605882,0.195005778,0.001705025,0.019258968,0.000000000],[0.153860105,0.010003744,0.090390033,0.008133247,0.000000000],[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 [4] | Right Index [5] // Basepair C7 - G22 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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_85033.2:
> IL_85033.2 1D4R G 4 C 25 GACC*GACC > IL_85033.2 1JID G 138 C 159 GACC*GACC > IL_85033.2 3WBM G 14 C 13 GACU*ACCC > IL_85033.2 3WBM G 14 C 13 GACU*ACCC > IL_85033.2 1D4R G 22 C 7 GACC*GACC > IL_85033.2 1MFQ G 156 C 141 GACC*GACC > IL_85033.2 5EW4 C 8 G 17 CCCG*CCCG > IL_85033.2 1L9A G 138 C 159 GACC*GACC > IL_85033.2 4K27 C 4 G 52 CCUG*CCUG > IL_85033.2 8FER G 7 C 10 GUUC*GUUC > IL_85033.2 7VYX C 13 G 53 CUUC*GGUG > IL_85033.2 8P9A G 953 C 874 GGAC*GGUC > IL_85033.2 8CRE G 938 C 859 GGAC*GGUC > IL_85033.2 6JDV A 63 U 38 ACCG*CCUU > IL_85033.2 8CRE A 445 U 484 AUUU*GUUU > IL_85033.2 5LQT G 4 C 7 GGAC*GGAC > IL_85033.2 333D C 3 G 6 CAGG*CAGG > IL_85033.2 7R9G C 5 G 8 CGGG*CGGG > IL_85033.2 5J7L G 1038 C 1117 GAAG*CGGC > IL_85033.2 5LQO G 4 C 7 GGAC*GGAC > IL_85033.2 8CRE U 2707 A 2693 UACA*UUGA > IL_85033.2 8CRE G 1059 U 1029 GCAC*GGAU > IL_85033.2 3CJZ G 5 C 21 GGAC*GGAC > IL_85033.2 8P9A U 2735 A 2721 UACA*UUGA > IL_85033.2 8P9A G 1074 U 1044 GCAC*GGAU > IL_85033.2 8P9A A 924 U 888 AGAC*GUAU > IL_85033.2 5UNE G 21 C 24 GCAC*GCAC > IL_85033.2 8CRE A 909 U 873 AGAC*GUAU > IL_85033.2 5J7L U 740 G 666 UGGA*UAGAG > IL_85033.2 4LFB U 740 G 666 UGGU*GAGAG > IL_85033.2 1G1X U 740 G 666 UGGU*GAGAG > IL_85033.2 1G1X U 740 G 666 UGGU*GAGAG > IL_85033.2 8CRE C 859 G 938 CGGGG*CAAG > IL_85033.2 8P9A C 874 G 953 CGGGG*CAAG > IL_85033.2 1KUQ U 39 G 30 UGGU*GAGAG