| 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 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 5 I | 16 6 | 17 5 I | 18 4 8 | 19 4 I | 20 4 9 | 21 4 I | 22 4 10 | 23 4 I | 24 4 11 | 25 3 I | 26 3 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_17069.5_Instance_1 IL_17069.5,IL_5J7L_313,G1813_C1804 | G | G | A | C | G | U | A | U | A | U | G | C | A | A | A | C | ||||||||||||||||||
| IL_17069.5_Sequence_1 IL_17069.55J7L_G_1813_C_1804 | G | G | A | C | G | U | A | U | A | * | U | G | C | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_17069.5_Instance_2 IL_17069.5,IL_9DFE_070,G1813_C1804 | G | G | A | G | G | U | A | U | A | U | G | C | G | A | A | C | ||||||||||||||||||
| IL_17069.5_Sequence_2 IL_17069.59DFE_G_1813_C_1804 | G | G | A | G | G | U | A | U | A | * | U | G | C | G | A | A | C | true | 94 | 0 | 0 | 1.36 | ||||||||||||
| IL_17069.5_Instance_3 IL_17069.5,IL_7A0S_065,G1805_C1795 | G | G | A | C | G | U | A | U | A | U | G | C | C | A | A | C | ||||||||||||||||||
| IL_17069.5_Sequence_3 IL_17069.57A0S_G_1805_C_1795 | G | G | A | C | G | U | A | U | A | * | U | G | C | C | A | A | C | true | 98 | 0 | 0 | 0.51 | ||||||||||||
| IL_17069.5_Instance_4 IL_17069.5,IL_4WF9_069,U1840_A1831 | U | G | A | U | G | U | A | U | A | U | G | C | U | A | A | A | ||||||||||||||||||
| IL_17069.5_Sequence_4 IL_17069.54WF9_U_1840_A_1831 | U | G | A | U | G | U | A | U | A | * | U | G | C | U | A | A | A | true | 94 | 0 | 0 | 1.47 | ||||||||||||
| IL_17069.5_Instance_5 IL_17069.5,IL_4V9F_065,A1869_U1860 | A | C | U | C | G | U | A | C | G | C | G | C | A | A | A | U | ||||||||||||||||||
| IL_17069.5_Sequence_5 IL_17069.54V9F_A_1869_U_1860 | A | C | U | C | G | U | A | C | G | * | C | G | C | A | A | A | U | true | 78 | 0 | 0 | 4.91 |
1 2 s35 1 13 cWW 2 3 s33 2 12 tSH 2 13 s55 3 4 s55 3 11 tHH 4 5 s35 4 10 tWW 4 11 s55 5 9 tSS 6 7 s55 6 8 s53 6 9 s35 6 10 tHH 7 8 cWW 8 11 cSS 9 10 s53 10 11 s55 11 12 s35 12 13 s35 9 6 6BPh 6 9 6BPh 2 11 6BPh 3 11 6BPh 12 2 6BR 9 5 6BR 5 10 6BRJAR3D SCFG/MRF model for IL_17069.5:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009232134,0.019500591,0.010312042,0.204664107,0.000000000],[0.017651752,0.009334753,0.194329928,0.011901116,0.000000000],[0.010240301,0.226340278,0.002011487,0.030416758,0.000000000],[0.203164750,0.012194392,0.028499733,0.010205878,0.000000000],[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 [1] | Right Index [13] // Basepair G1813 - C1804 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041414128,0.043842436,0.000497149,0.002343065,0.000000000],[0.074474418,0.043740915,0.000497149,0.000497149,0.000000000],[0.386099537,0.003480043,0.017012825,0.295372891,0.000000000],[0.046229227,0.043504771,0.000497149,0.000497149,0.000000000],[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 [2] | Right Index [12] // Basepair G1814 - A1803 tSH ClusterNode | Deletion Probability [0.000000000000000000000000000240367436980883820394848611736768] | Num Left Bases [5] | Num Right Bases [4] | Left Index [3] | Right Index [11] | Norm Constant [0.031026615646034] // Cluster node 5J7L|1|DA|A|1815:5J7L|1|DA|A|1821 and 5J7L|1|DA|U|1798:5J7L|1|DA|A|1802 Interaction | Interacting Bases [5,6] | Pair Probability [[0.009105277,0.021043857,0.009858357,0.235835630,0.000000000],[0.016935920,0.009299660,0.190339875,0.010631190,0.000000000],[0.009819443,0.202966438,0.001992184,0.046554799,0.000000000],[0.190951522,0.011249173,0.022442202,0.010974474,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1821 - 5J7L|1|DA|U|1798 cWW Interaction | Interacting Bases [3,7] | Pair Probability [[0.011160714,0.011160714,0.078125000,0.011160714,0.000000000],[0.011160714,0.011160714,0.078125000,0.011160714,0.000000000],[0.011160714,0.011160714,0.078125000,0.011160714,0.000000000],[0.055803571,0.055803571,0.497767857,0.055803571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1818 - 5J7L|1|DA|G|1799 tSS Interaction | Interacting Bases [2,8] | Pair Probability [[0.018515490,0.024203011,0.006208099,0.030772721,0.000000000],[0.018215723,0.030035564,0.025413059,0.030862733,0.000000000],[0.006208099,0.668428937,0.018549235,0.026158791,0.000000000],[0.025853716,0.029415056,0.020166229,0.020993538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1817 - 5J7L|1|DA|C|1800 tWW Interaction | Interacting Bases [4,8] | Pair Probability [[0.323851019,0.450736645,0.022227255,0.041234139,0.000000000],[0.007046732,0.000575882,0.046681129,0.048873301,0.000000000],[0.002627765,0.047799269,0.000612259,0.000575882,0.000000000],[0.002675502,0.003331455,0.000575882,0.000575882,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1819 - 5J7L|1|DA|C|1800 tHH Interaction | Interacting Bases [1,9] | Pair Probability [[0.362562332,0.260179242,0.018243535,0.018360954,0.000000000],[0.046406917,0.001058030,0.041827002,0.006998226,0.000000000],[0.052997536,0.041282869,0.002245833,0.001058030,0.000000000],[0.072665564,0.071997872,0.001058030,0.001058030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1815 - 5J7L|1|DA|A|1802 tHH Interaction | Interacting Bases [6,9] | Pair Probability [[0.074293378,0.072180216,0.074029185,0.067008074,0.000000000],[0.086657268,0.077155077,0.003156774,0.057385713,0.000000000],[0.076242225,0.003225335,0.008452370,0.065558422,0.000000000],[0.117730893,0.070666533,0.073270499,0.072988039,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1798 - 5J7L|1|DA|A|1802 cSS Insertion | Location [1] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.500000000,0.214285714,0.214285714,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node Insertion | Location [4] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000]// Insertion after nucleotide 6, position 4 in cluster node Insertion | Location [8] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.357142857,0.214285714,0.214285714,0.214285714,0.000000000]// Insertion after nucleotide 10, position 8 in cluster node InitialNode | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [7] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_17069.5:
> IL_17069.5 5J7L G 1813 C 1804 GGACGUAUA*UGCAAAC > IL_17069.5 9DFE G 1813 C 1804 GGAGGUAUA*UGCGAAC > IL_17069.5 7A0S G 1805 C 1795 GGACGUAUA*UGCCAAC > IL_17069.5 4WF9 U 1840 A 1831 UGAUGUAUA*UGCUAAA > IL_17069.5 4V9F A 1869 U 1860 ACUCGUACG*CGCAAAU