| 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 | 13 3 I | 14 2 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_73276.5_Instance_1 IL_73276.5_IL_3V2F_100_C2680_G2727 | C | C | U | C | U | A | U | G | ||||||||||||||
| IL_73276.5_Sequence_1 IL_73276.5_IL_3V2F_100_C_2680_G_2727 | C | C | U | C | U | * | A | U | G | true | 75 | 0 | 0 | 2.37 | ||||||||
| IL_73276.5_Instance_2 IL_73276.5_IL_4IOA_097_C2659_G2707 | C | C | G | C | U | A | U | G | ||||||||||||||
| IL_73276.5_Sequence_2 IL_73276.5_IL_4IOA_097_C_2659_G_2707 | C | C | G | C | U | * | A | U | G | true | 67 | 0 | 0 | 3.22 | ||||||||
| IL_73276.5_Instance_3 IL_73276.5_IL_4JRC_003_C29_G75 | C | C | U | C | U | A | C | G | ||||||||||||||
| IL_73276.5_Sequence_3 IL_73276.5_IL_4JRC_003_C29_G75 | C | C | U | C | U | * | A | C | G | true | 82 | 0 | 0 | 1.76 | ||||||||
| IL_73276.5_Instance_4 IL_73276.5_IL_2QBG_102_U2680_A2727 | U | C | A | C | U | A | A | A | ||||||||||||||
| IL_73276.5_Sequence_4 IL_73276.5_IL_2QBG_102_U_2680_A_2727 | U | C | A | C | U | * | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_73276.5_Instance_5 IL_73276.5_IL_1KOG_002_C96_G76 | C | C | A | C | U | A | U | G | ||||||||||||||
| IL_73276.5_Sequence_5 IL_73276.5_IL_1KOG_002_C96_G76 | C | C | A | C | U | * | A | U | G | true | 91 | 0 | 0 | 0.82 | ||||||||
| IL_73276.5_Instance_6 IL_73276.5_IL_3U5F_060_U1617_A1160 | U | C | C | C | U | A | CC | A | ||||||||||||||
| IL_73276.5_Sequence_6 IL_73276.5_IL_3U5F_060_U_1617_A_1160 | U | C | C | C | U | * | A | CC | A | true | 53 | 0 | 0 | 4.53 | ||||||||
| IL_73276.5_Instance_7 IL_73276.5_IL_1S72_091_C2717_G2763 | C | C | A | C | U | A | C | G | ||||||||||||||
| IL_73276.5_Sequence_7 IL_73276.5_IL_1S72_091_C_2717_G_2763 | C | C | A | C | U | * | A | C | G | true | 98 | 0 | 0 | 0.20 | ||||||||
| IL_73276.5_Instance_8 IL_73276.5_IL_4BPP_057_U1589_A1132 | U | C | C | C | U | A | C | A | ||||||||||||||
| IL_73276.5_Sequence_8 IL_73276.5_IL_4BPP_057_U_1589_A_1132 | U | C | C | C | U | * | A | C | A | true | 74 | 0 | 0 | 2.46 | ||||||||
| IL_73276.5_Instance_9 IL_73276.5_IL_3V2F_048_G1319_C1333 | G | C | A | A | U | A | G | C | ||||||||||||||
| IL_73276.5_Sequence_9 IL_73276.5_IL_3V2F_048_G_1319_C_1333 | G | C | A | A | U | * | A | G | C | true | 87 | 0 | 0 | 1.24 | ||||||||
| IL_73276.5_Instance_10 IL_73276.5_IL_1S72_051_G1425_C1439 | G | C | A | C | U | A | G | C | ||||||||||||||
| IL_73276.5_Sequence_10 IL_73276.5_IL_1S72_051_G_1425_C_1439 | G | C | A | C | U | * | A | G | C | true | 93 | 0 | 0 | 0.65 | ||||||||
| IL_73276.5_Instance_11 IL_73276.5_IL_2QBG_033_G864_C912 | G | C | A | C | U | A | AA | C | ||||||||||||||
| IL_73276.5_Sequence_11 IL_73276.5_IL_2QBG_033_G864_C912 | G | C | A | C | U | * | A | AA | C | true | 87 | 0 | 0 | 1.22 | ||||||||
| IL_73276.5_Instance_12 IL_73276.5_IL_2QBG_050_C1319_G1333 | C | C | A | A | C | G | G | G | ||||||||||||||
| IL_73276.5_Sequence_12 IL_73276.5_IL_2QBG_050_C_1319_G_1333 | C | C | A | A | C | * | G | G | G | true | 70 | 0 | 0 | 2.89 | ||||||||
| IL_73276.5_Instance_13 IL_73276.5_IL_4MGN_003_C29_G75 | C | C | U | C | U | A | C | G | ||||||||||||||
| IL_73276.5_Sequence_13 IL_73276.5_IL_4MGN_003_C29_G75 | C | C | U | C | U | * | A | C | G | true | 82 | 0 | 0 | 1.76 | ||||||||
| IL_73276.5_Instance_14 IL_73276.5_IL_4IOA_028_G877_C924 | G | C | A | C | U | A | AA | C | ||||||||||||||
| IL_73276.5_Sequence_14 IL_73276.5_IL_4IOA_028_G877_C924 | G | C | A | C | U | * | A | AA | C | true | 87 | 0 | 0 | 1.22 | ||||||||
| IL_73276.5_Instance_15 IL_73276.5_IL_3V2F_029_G864_C912 | G | C | A | C | U | A | AA | C | ||||||||||||||
| IL_73276.5_Sequence_15 IL_73276.5_IL_3V2F_029_G864_C912 | G | C | A | C | U | * | A | AA | C | true | 87 | 0 | 0 | 1.22 | ||||||||
| IL_73276.5_Instance_16 IL_73276.5_IL_4IOA_049_G1332_C1346 | G | G | A | A | G | C | G | C | ||||||||||||||
| IL_73276.5_Sequence_16 IL_73276.5_IL_4IOA_049_G_1332_C_1346 | G | G | A | A | G | * | C | G | C | true | 35 | 0 | 0 | 6.29 | ||||||||
| IL_73276.5_Instance_17 IL_73276.5_IL_1FJG_015_G371_C390 | G | C | A | A | U | A | C | |||||||||||||||
| IL_73276.5_Sequence_17 IL_73276.5_IL_1FJG_015_G371_C390 | G | C | A | A | U | * | A | C | true | 94 | 0 | 0 | 0.58 | |||||||||
| IL_73276.5_Instance_18 IL_73276.5_IL_3U5H_042_G999_C1049 | G | C | G | A | A | U | A | AA | C | |||||||||||||
| IL_73276.5_Sequence_18 IL_73276.5_IL_3U5H_042_G999_C_1049 | G | C | G | A | A | U | * | A | AA | C | true | 53 | 0 | 0 | 4.56 | |||||||
| IL_73276.5_Instance_19 IL_73276.5_IL_4A1B_046_G1025_C1075 | G | C | G | A | A | U | A | AA | C | |||||||||||||
| IL_73276.5_Sequence_19 IL_73276.5_IL_4A1B_046_G_1025_C_1075 | G | C | G | A | A | U | * | A | AA | C | true | 53 | 0 | 0 | 4.56 | |||||||
| IL_73276.5_Instance_20 IL_73276.5_IL_2AW7_018_A371_U390 | A | C | A | A | U | A | U | |||||||||||||||
| IL_73276.5_Sequence_20 IL_73276.5_IL_2AW7_018_A371_U390 | A | C | A | A | U | * | A | U | true | 86 | 0 | 0 | 1.31 | |||||||||
| IL_73276.5_Instance_21 IL_73276.5_IL_4A1C_005_U52_A27 | U | U | A | A | G | C | A | |||||||||||||||
| IL_73276.5_Sequence_21 IL_73276.5_IL_4A1C_005_U52_A27 | U | U | A | A | G | * | C | A | true | 27 | 0 | 0 | 7.00 | |||||||||
| IL_73276.5_Instance_22 IL_73276.5_IL_1FJG_047_C1128_G1143 | C | C | A | G | C | G | G | |||||||||||||||
| IL_73276.5_Sequence_22 IL_73276.5_IL_1FJG_047_C_1128_G_1143 | C | C | A | G | C | * | G | G | true | 50 | 0 | 0 | 4.78 |
1 2 s35 1 7 cWW 2 4 cSH 2 6 tWH 2 7 s55 3 4 s35 4 5 s35 4 7 cWS 5 6 cWW 6 7 s35JAR3D SCFG/MRF model for IL_73276.5:
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 [7] // Initial node C2680 - G2727 from junction ClusterNode | Deletion Probability [0.000000000000000000146283685379421310000000000000000000000000] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.008888954407175] // Cluster node C2680:U2684 and A2725:G2727 Interaction | Interacting Bases [2,6] | Pair Probability [[0.016212895,0.002088714,0.111481584,0.002088714,0.000000000],[0.355482037,0.009855145,0.215225219,0.002088714,0.000000000],[0.002088714,0.014532442,0.014015048,0.021263925,0.000000000],[0.020326329,0.014532442,0.009960906,0.188757171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - A2725 tWH Interaction | Interacting Bases [5,6] | Pair Probability [[0.007773162,0.016660361,0.008500029,0.171131704,0.000000000],[0.019645867,0.007811276,0.181182794,0.009165013,0.000000000],[0.008511496,0.180416929,0.001800083,0.020080857,0.000000000],[0.324199513,0.009115154,0.022960409,0.011045352,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2684 - A2725 cWW Interaction | Interacting Bases [1,7] | Pair Probability [[0.008273910,0.016324110,0.009447193,0.172538687,0.000000000],[0.016686769,0.007282678,0.238983699,0.010738157,0.000000000],[0.009443468,0.247301898,0.001797856,0.021312961,0.000000000],[0.198008406,0.010754857,0.021649574,0.009455779,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2680 - G2727 cWW Interaction | Interacting Bases [4,7] | Pair Probability [[0.069820510,0.113337012,0.066293327,0.077837807,0.000000000],[0.136330573,0.145599904,0.162841133,0.111769004,0.000000000],[0.010416831,0.009184966,0.054902910,0.007662833,0.000000000],[0.009188309,0.009573906,0.007480149,0.007760825,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2683 - G2727 cWS Interaction | Interacting Bases [2,4] | Pair Probability [[0.088151994,0.087434743,0.005896706,0.004967894,0.000000000],[0.146654711,0.205693479,0.013917998,0.094278770,0.000000000],[0.041390756,0.005358183,0.009542222,0.094186828,0.000000000],[0.021244251,0.084343406,0.001266537,0.095671523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - C2683 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.104166667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.145833333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U2682 Insertion | Location [2] | Length Distribution [0.906945833,0.092734748,0.000309116,0.000010304] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node Insertion | Location [6] | Length Distribution [0.182283898,0.544177099,0.272829207,0.000678936,0.000030861] | Letter Distribution [0.442307692,0.250000000,0.173076923,0.134615385,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node 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 [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_73276.5:
> IL_73276.5 IL_3V2F_100 C 2680 G 2727 CCUCU*AUG > IL_73276.5 IL_4IOA_097 C 2659 G 2707 CCGCU*AUG > IL_73276.5 IL_4JRC_003 C 29 G 75 CCUCU*ACG > IL_73276.5 IL_2QBG_102 U 2680 A 2727 UCACU*AAA > IL_73276.5 IL_1KOG_002 C 96 G 76 CCACU*AUG > IL_73276.5 IL_3U5F_060 U 1617 A 1160 UCCCU*ACCA > IL_73276.5 IL_1S72_091 C 2717 G 2763 CCACU*ACG > IL_73276.5 IL_4BPP_057 U 1589 A 1132 UCCCU*ACA > IL_73276.5 IL_3V2F_048 G 1319 C 1333 GCAAU*AGC > IL_73276.5 IL_1S72_051 G 1425 C 1439 GCACU*AGC > IL_73276.5 IL_2QBG_033 G 864 C 912 GCACU*AAAC > IL_73276.5 IL_2QBG_050 C 1319 G 1333 CCAAC*GGG > IL_73276.5 IL_4MGN_003 C 29 G 75 CCUCU*ACG > IL_73276.5 IL_4IOA_028 G 877 C 924 GCACU*AAAC > IL_73276.5 IL_3V2F_029 G 864 C 912 GCACU*AAAC > IL_73276.5 IL_4IOA_049 G 1332 C 1346 GGAAG*CGC > IL_73276.5 IL_1FJG_015 G 371 C 390 GCAAU*AC > IL_73276.5 IL_3U5H_042 G 999 C 1049 GCGAAU*AAAC > IL_73276.5 IL_4A1B_046 G 1025 C 1075 GCGAAU*AAAC > IL_73276.5 IL_2AW7_018 A 371 U 390 ACAAU*AU > IL_73276.5 IL_4A1C_005 U 52 A 27 UUAAG*CA > IL_73276.5 IL_1FJG_047 C 1128 G 1143 CCAGC*GG