Alignment of IL_44540.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_44540.4
The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
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_A957UCCGA
IL_44540.4_Sequence_1 IL_44540.4_IL_1S72_035_U_1009_A957UCC*GAtrue100000.00
IL_44540.4_Instance_2 IL_44540.4_IL_3V2F_028_U913_A863UCCGA
IL_44540.4_Sequence_2 IL_44540.4_IL_3V2F_028_U913_A863UCC*GAtrue100000.00
IL_44540.4_Instance_3 IL_44540.4_IL_4IOA_027_U925_A876UCCGA
IL_44540.4_Sequence_3 IL_44540.4_IL_4IOA_027_U925_A876UCC*GAtrue100000.00
IL_44540.4_Instance_4 IL_44540.4_IL_2QBG_008_U434_A44UCCGA
IL_44540.4_Sequence_4 IL_44540.4_IL_2QBG_008_U434_A44UCC*GAtrue100000.00
IL_44540.4_Instance_5 IL_44540.4_IL_1Y0Q_003_A120_U193ACGCU
IL_44540.4_Sequence_5 IL_44540.4_IL_1Y0Q_003_A120_U193ACG*CUtrue80001.94
IL_44540.4_Instance_6 IL_44540.4_IL_3V2F_078_U2438_A2071UACCGA
IL_44540.4_Sequence_6 IL_44540.4_IL_3V2F_078_U_2438_A_2071UACC*GAtrue84001.53
IL_44540.4_Instance_7 IL_44540.4_IL_1S72_075_U2473_A2112UACCGA
IL_44540.4_Sequence_7 IL_44540.4_IL_1S72_075_U_2473_A_2112UACC*GAtrue84001.53
IL_44540.4_Instance_8 IL_44540.4_IL_2QBG_081_U2438_A2071UACUAA
IL_44540.4_Sequence_8 IL_44540.4_IL_2QBG_081_U_2438_A_2071UACU*AAtrue82001.69
IL_44540.4_Instance_9 IL_44540.4_IL_3U5F_029_A518_U533ACAUU
IL_44540.4_Sequence_9 IL_44540.4_IL_3U5F_029_A518_U533ACA*UUtrue75002.35
IL_44540.4_Instance_10 IL_44540.4_IL_4IOA_076_U2417_A2054UACCGA
IL_44540.4_Sequence_10 IL_44540.4_IL_4IOA_076_U_2417_A_2054UACC*GAtrue84001.53
IL_44540.4_Instance_11 IL_44540.4_IL_3U5H_041_U1050_A998UUUAA
IL_44540.4_Sequence_11 IL_44540.4_IL_3U5H_041_U_1050_A998UUU*AAtrue71002.75
IL_44540.4_Instance_12 IL_44540.4_IL_4A1B_096_U2795_A2408UACCGA
IL_44540.4_Sequence_12 IL_44540.4_IL_4A1B_096_U_2795_A_2408UACC*GAtrue84001.53
IL_44540.4_Instance_13 IL_44540.4_IL_1FJG_038_C1226_G954CACGG
IL_44540.4_Sequence_13 IL_44540.4_IL_1FJG_038_C_1226_G954CAC*GGtrue98000.16
IL_44540.4_Instance_14 IL_44540.4_IL_3U5H_099_U2807_A2413UACCGA
IL_44540.4_Sequence_14 IL_44540.4_IL_3U5H_099_U_2807_A_2413UACC*GAtrue84001.53
IL_44540.4_Instance_15 IL_44540.4_IL_1U6B_007_G128_C178GAGCC
IL_44540.4_Sequence_15 IL_44540.4_IL_1U6B_007_G128_C178GAG*CCtrue79002.01
IL_44540.4_Instance_16 IL_44540.4_IL_4BPP_069_C1278_G1290CUGCG
IL_44540.4_Sequence_16 IL_44540.4_IL_4BPP_069_C_1278_G_1290CUG*CGtrue82001.66
IL_44540.4_Instance_17 IL_44540.4_IL_2AW7_045_C1226_G954CACGG
IL_44540.4_Sequence_17 IL_44540.4_IL_2AW7_045_C_1226_G954CAC*GGtrue98000.16
IL_44540.4_Instance_18 IL_44540.4_IL_4BPP_059_C1430_G1151CACGG
IL_44540.4_Sequence_18 IL_44540.4_IL_4BPP_059_C_1430_G_1151CAC*GGtrue98000.16
IL_44540.4_Instance_19 IL_44540.4_IL_4IOA_003_U447_A43UCCGA
IL_44540.4_Sequence_19 IL_44540.4_IL_4IOA_003_U447_A43UCC*GAtrue100000.00
IL_44540.4_Instance_20 IL_44540.4_IL_2GDI_003_C23_G36CCUAG
IL_44540.4_Sequence_20 IL_44540.4_IL_2GDI_003_C23_G36CCU*AGtrue66003.22
IL_44540.4_Instance_21 IL_44540.4_IL_4A1B_128_U3338_A3282UCUAA
IL_44540.4_Sequence_21 IL_44540.4_IL_4A1B_128_U_3338_A_3282UCU*AAtrue98000.16
IL_44540.4_Instance_22 IL_44540.4_IL_4A1B_020_C470_G507CACGG
IL_44540.4_Sequence_22 IL_44540.4_IL_4A1B_020_C470_G507CAC*GGtrue98000.16
IL_44540.4_Instance_23 IL_44540.4_IL_2QWY_006_U40_A24UAGCA
IL_44540.4_Sequence_23 IL_44540.4_IL_2QWY_006_U40_A24UAG*CAtrue85001.43
IL_44540.4_Instance_24 IL_44540.4_IL_2QWY_003_U40_A24UAGCA
IL_44540.4_Sequence_24 IL_44540.4_IL_2QWY_003_U40_A24UAG*CAtrue85001.43
IL_44540.4_Instance_25 IL_44540.4_IL_2GDI_007_C23_G36CCUAG
IL_44540.4_Sequence_25 IL_44540.4_IL_2GDI_007_C23_G36CCU*AGtrue66003.22
IL_44540.4_Instance_26 IL_44540.4_IL_2AW7_035_A746_U659AAGCU
IL_44540.4_Sequence_26 IL_44540.4_IL_2AW7_035_A746_U659AAG*CUtrue77002.21
IL_44540.4_Instance_27 IL_44540.4_IL_3U5F_071_C1306_G1318CUGCG
IL_44540.4_Sequence_27 IL_44540.4_IL_3U5F_071_C_1306_G_1318CUG*CGtrue82001.66
IL_44540.4_Instance_28 IL_44540.4_IL_2AW7_067_U1440_G1461UAGCG
IL_44540.4_Sequence_28 IL_44540.4_IL_2AW7_067_U_1440_G_1461UAG*CGtrue78002.09
IL_44540.4_Instance_29 IL_44540.4_IL_4A1B_049_G1039_C1063GACUAC
IL_44540.4_Sequence_29 IL_44540.4_IL_4A1B_049_G_1039_C_1063GACU*ACtrue55004.30
IL_44540.4_Instance_30 IL_44540.4_IL_3V2F_070_G1846_C1894GAAGCC
IL_44540.4_Sequence_30 IL_44540.4_IL_3V2F_070_G_1846_C_1894GAAG*CCtrue63003.54
IL_44540.4_Instance_31 IL_44540.4_IL_3IWN_001_G89_C3GAUAC
IL_44540.4_Sequence_31 IL_44540.4_IL_3IWN_001_G89_C3GAU*ACtrue79001.97
IL_44540.4_Instance_32 IL_44540.4_IL_1X8W_004_G129_C193GUUAC
IL_44540.4_Sequence_32 IL_44540.4_IL_1X8W_004_G129_C193GUU*ACtrue56004.22
IL_44540.4_Instance_33 IL_44540.4_IL_3RW6_001_U53_A8UAAUAA
IL_44540.4_Sequence_33 IL_44540.4_IL_3RW6_001_U53_A8UAAU*AAtrue69002.92
IL_44540.4_Instance_34 IL_44540.4_IL_4BPP_005_C49_G421CAUAG
IL_44540.4_Sequence_34 IL_44540.4_IL_4BPP_005_C49_G421CAU*AGtrue97000.32
IL_44540.4_Instance_35 IL_44540.4_IL_3U5F_005_C50_G429CAUAG
IL_44540.4_Sequence_35 IL_44540.4_IL_3U5F_005_C50_G429CAU*AGtrue97000.32
IL_44540.4_Instance_36 IL_44540.4_IL_3U5F_062_C1459_G1179CACGG
IL_44540.4_Sequence_36 IL_44540.4_IL_3U5F_062_C_1459_G_1179CAC*GGtrue98000.16
IL_44540.4_Instance_37 IL_44540.4_IL_1S72_033_U942_G1024UAGCG
IL_44540.4_Sequence_37 IL_44540.4_IL_1S72_033_U942_G_1024UAG*CGtrue78002.09
IL_44540.4_Instance_38 IL_44540.4_IL_1FJG_004_C54_G357CAUAG
IL_44540.4_Sequence_38 IL_44540.4_IL_1FJG_004_C54_G357CAU*AGtrue97000.32
IL_44540.4_Instance_39 IL_44540.4_IL_2AW7_004_C54_G357CAUAG
IL_44540.4_Sequence_39 IL_44540.4_IL_2AW7_004_C54_G357CAU*AGtrue97000.32
IL_44540.4_Instance_40 IL_44540.4_IL_1FJG_052_C1260_G1274CACGG
IL_44540.4_Sequence_40 IL_44540.4_IL_1FJG_052_C_1260_G_1274CAC*GGtrue98000.16
IL_44540.4_Instance_41 IL_44540.4_IL_1FJG_051_G1274_C1260GAGCC
IL_44540.4_Sequence_41 IL_44540.4_IL_1FJG_051_G_1274_C_1260GAG*CCtrue79002.01
IL_44540.4_Instance_42 IL_44540.4_IL_2AW7_050_U1199_G1058UCAUCGG
IL_44540.4_Sequence_42 IL_44540.4_IL_2AW7_050_U_1199_G_1058UCAUC*GGtrue21007.50
IL_44540.4_Instance_43 IL_44540.4_IL_1FJG_042_U1199_G1058UCAGCGG
IL_44540.4_Sequence_43 IL_44540.4_IL_1FJG_042_U_1199_G_1058UCAGC*GGtrue-120010.68

Conserved interactions between motif group positions in IL_44540.4:
1 2 cSH 
1 3 s35 
1 5 cWW 
2 3 s35 
2 5 tHS 
3 4 cWW 
3 5 s55 
4 5 s35 
JAR3D 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 truncation
Sequences 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