| 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 5 5 | 11 5 I | 12 5 6 | 13 6 I | 14 7 | 15 6 I | 16 5 7 | 17 5 I | 18 5 8 | 19 5 I | 20 5 9 | 21 4 I | 22 4 10 | 23 3 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_37053.1_Instance_1 IL_37053.1_IL_4A1B_077_U1735_A1757 | U | G | A | A | A | U | U | A | G | A | G | A | U | A | ||||||||||||||||||
| IL_37053.1_Sequence_1 IL_37053.1_IL_4A1B_077_U_1735_A_1757 | U | G | A | A | A | U | U | * | A | G | A | G | A | U | A | true | 97 | 0 | 0 | 0.40 | ||||||||||||
| IL_37053.1_Instance_2 IL_37053.1_IL_3U5H_081_C1711_G1733 | C | G | G | A | A | U | U | G | G | A | G | A | U | G | ||||||||||||||||||
| IL_37053.1_Sequence_2 IL_37053.1_IL_3U5H_081_C_1711_G_1733 | C | G | G | A | A | U | U | * | G | G | A | G | A | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_37053.1_Instance_3 IL_37053.1_IL_1S72_058_U1587_G1608 | U | G | G | A | A | G | C | A | G | G | A | A | G | |||||||||||||||||||
| IL_37053.1_Sequence_3 IL_37053.1_IL_1S72_058_U_1587_G_1608 | U | G | G | A | A | G | * | C | A | G | G | A | A | G | true | 92 | 0 | 0 | 1.30 |
1 2 s35 1 12 cWW 2 3 s35 2 11 tSH 2 12 s55 3 4 s35 3 9 s33 3 10 tSH 4 7 tSS 4 8 s33 4 9 tHS 4 10 s55 6 7 cWW 10 11 s35 11 12 s35 2 10 6BPh 3 10 6BPh 4 7 6BR 3 9 6BR 4 9 6BRJAR3D SCFG/MRF model for IL_37053.1:
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 [12] // Initial node U1735 - A1757 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010617565,0.017207514,0.012224139,0.144725988,0.000000000],[0.119578446,0.011276938,0.159608290,0.013787516,0.000000000],[0.012394940,0.145308958,0.002585264,0.020771623,0.000000000],[0.159746803,0.012984375,0.144469588,0.012712053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair U1735 - A1757 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.019680511,0.052135779,0.000598716,0.003321980,0.000000000],[0.019508401,0.020008761,0.000598716,0.000598716,0.000000000],[0.378788100,0.004191009,0.025571885,0.418046764,0.000000000],[0.035351914,0.020401319,0.000598716,0.000598716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1736 - U1756 tSH BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.168008325,0.137401149,0.001642125,0.011900428,0.000000000],[0.047047609,0.037864462,0.000532653,0.000532653,0.000000000],[0.278182915,0.002619096,0.013399396,0.204760253,0.000000000],[0.048415624,0.046628008,0.000532653,0.000532653,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A1737 - A1755 tSH ClusterNode | Deletion Probability [0.000000000000000002141016935993338200000000000000000000000000] | Num Left Bases [3] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.203059297941871] // Cluster node A1738:U1741 and A1751:G1754 Interaction | Interacting Bases [1,4] | Pair Probability [[0.246133399,0.253695198,0.246453931,0.224620956,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.002474039,0.002668836,0.003464906,0.016323442,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - A1751 tSS Interaction | Interacting Bases [3,4] | Pair Probability [[0.010671796,0.018383968,0.012272411,0.145081933,0.000000000],[0.118399456,0.011223837,0.147716963,0.013568949,0.000000000],[0.012345101,0.157172007,0.002585120,0.022020461,0.000000000],[0.159365085,0.013201127,0.143217320,0.012774467,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1741 - A1751 cWW Interaction | Interacting Bases [1,6] | Pair Probability [[0.186964122,0.188627543,0.254394136,0.203223383,0.000000000],[0.043586124,0.039541834,0.000450536,0.039155962,0.000000000],[0.000450536,0.000450536,0.002182752,0.000450536,0.000000000],[0.002145394,0.000450536,0.037475536,0.000450536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - G1754 tHS Interaction | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1739 Interaction | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1752 Insertion | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node Insertion | Location [5] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 5 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 [7] | Right Index [6] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_37053.1:
> IL_37053.1 IL_4A1B_077 U 1735 A 1757 UGAAAUU*AGAGAUA > IL_37053.1 IL_3U5H_081 C 1711 G 1733 CGGAAUU*GGAGAUG > IL_37053.1 IL_1S72_058 U 1587 G 1608 UGGAAG*CAGGAAG