Alignment of IL_56465.4 sequences from 3D to the JAR3D model

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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
3

2
5
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_56465.4_Instance_1 IL_56465.4_IL_4IOA_005_A189_U161AAGCU
IL_56465.4_Sequence_1 IL_56465.4_IL_4IOA_005_A189_U161AAG*CUtrue95000.47
IL_56465.4_Instance_2 IL_56465.4_IL_4A1B_001_G54_C26GAGCC
IL_56465.4_Sequence_2 IL_56465.4_IL_4A1B_001_G54_C26GAG*CCtrue100000.00
IL_56465.4_Instance_3 IL_56465.4_IL_3V2F_005_G212_C184GAGCC
IL_56465.4_Sequence_3 IL_56465.4_IL_3V2F_005_G212_C184GAG*CCtrue100000.00
IL_56465.4_Instance_4 IL_56465.4_IL_3V2F_024_G940_C838GAGCC
IL_56465.4_Sequence_4 IL_56465.4_IL_3V2F_024_G940_C838GAG*CCtrue100000.00
IL_56465.4_Instance_5 IL_56465.4_IL_3U5H_004_G56_C28GAGCC
IL_56465.4_Sequence_5 IL_56465.4_IL_3U5H_004_G56_C28GAG*CCtrue100000.00
IL_56465.4_Instance_6 IL_56465.4_IL_4IOA_021_G951_C851GAGCC
IL_56465.4_Sequence_6 IL_56465.4_IL_4IOA_021_G951_C851GAG*CCtrue100000.00
IL_56465.4_Instance_7 IL_56465.4_IL_2QBG_010_G212_C184GAGCC
IL_56465.4_Sequence_7 IL_56465.4_IL_2QBG_010_G212_C184GAG*CCtrue100000.00
IL_56465.4_Instance_8 IL_56465.4_IL_1S72_005_G182_C154GAGCC
IL_56465.4_Sequence_8 IL_56465.4_IL_1S72_005_G182_C154GAG*CCtrue100000.00
IL_56465.4_Instance_9 IL_56465.4_IL_2QBG_027_G940_C838GAGCC
IL_56465.4_Sequence_9 IL_56465.4_IL_2QBG_027_G940_C838GAG*CCtrue100000.00
IL_56465.4_Instance_10 IL_56465.4_IL_1S72_079_U2436_A2455UAGCA
IL_56465.4_Sequence_10 IL_56465.4_IL_1S72_079_U_2436_A_2455UAG*CAtrue96000.33
IL_56465.4_Instance_11 IL_56465.4_IL_2QBG_090_C2498_G2454CCUAG
IL_56465.4_Sequence_11 IL_56465.4_IL_2QBG_090_C_2498_G_2454CCU*AGtrue73002.61
IL_56465.4_Instance_12 IL_56465.4_IL_4IOA_056_A1463_U1478AAGCU
IL_56465.4_Sequence_12 IL_56465.4_IL_4IOA_056_A_1463_U_1478AAG*CUtrue95000.47
IL_56465.4_Instance_13 IL_56465.4_IL_2AW7_047_G1041_C999GAGCC
IL_56465.4_Sequence_13 IL_56465.4_IL_2AW7_047_G_1041_C999GAG*CCtrue100000.00
IL_56465.4_Instance_14 IL_56465.4_IL_3U5H_009_C163_G258CAAUG
IL_56465.4_Sequence_14 IL_56465.4_IL_3U5H_009_C163_G258CAA*UGtrue99000.14
IL_56465.4_Instance_15 IL_56465.4_IL_3U5H_146_C47_G30CUGCG
IL_56465.4_Sequence_15 IL_56465.4_IL_3U5H_146_C47_G30CUG*CGtrue87001.20
IL_56465.4_Instance_16 IL_56465.4_IL_2O3X_001_G42_C7GUCGUC
IL_56465.4_Sequence_16 IL_56465.4_IL_2O3X_001_G42_C7GUC*GUCtrue39005.84
IL_56465.4_Instance_17 IL_56465.4_IL_1O9M_001_G1494_C1407GUCGUC
IL_56465.4_Sequence_17 IL_56465.4_IL_1O9M_001_G_1494_C_1407GUC*GUCtrue39005.84
IL_56465.4_Instance_18 IL_56465.4_IL_4M30_001_U25_A2UUAUA
IL_56465.4_Sequence_18 IL_56465.4_IL_4M30_001_U25_A2UUA*UAtrue80001.95
IL_56465.4_Instance_19 IL_56465.4_IL_4A1B_073_U1802_A1695UUGCA
IL_56465.4_Sequence_19 IL_56465.4_IL_4A1B_073_U_1802_A_1695UUG*CAtrue82001.68
IL_56465.4_Instance_20 IL_56465.4_IL_2QBG_029_G926_C851GAAUC
IL_56465.4_Sequence_20 IL_56465.4_IL_2QBG_029_G926_C851GAA*UCtrue97000.27
IL_56465.4_Instance_21 IL_56465.4_IL_4A1B_042_U1138_A995UAGCA
IL_56465.4_Sequence_21 IL_56465.4_IL_4A1B_042_U_1138_A995UAG*CAtrue96000.33
IL_56465.4_Instance_22 IL_56465.4_IL_1FJG_046_G1143_C1128GGCGC
IL_56465.4_Sequence_22 IL_56465.4_IL_1FJG_046_G_1143_C_1128GGC*GCtrue79002.03
IL_56465.4_Instance_23 IL_56465.4_IL_4IOA_085_C2477_G2433CCUAG
IL_56465.4_Sequence_23 IL_56465.4_IL_4IOA_085_C_2477_G_2433CCU*AGtrue73002.61
IL_56465.4_Instance_24 IL_56465.4_IL_2AW7_024_C477_G455CAUGG
IL_56465.4_Sequence_24 IL_56465.4_IL_2AW7_024_C477_G455CAU*GGtrue79002.03
IL_56465.4_Instance_25 IL_56465.4_IL_3U5H_037_U1111_A970UAGCA
IL_56465.4_Sequence_25 IL_56465.4_IL_3U5H_037_U_1111_A970UAG*CAtrue96000.33
IL_56465.4_Instance_26 IL_56465.4_IL_3V2F_088_C2498_G2454CCUAG
IL_56465.4_Sequence_26 IL_56465.4_IL_3V2F_088_C_2498_G_2454CCU*AGtrue73002.61
IL_56465.4_Instance_27 IL_56465.4_IL_1ZX7_001_C26_G10CACGAAG
IL_56465.4_Sequence_27 IL_56465.4_IL_1ZX7_001_C26_G10CAC*GAAGtrue84001.48
IL_56465.4_Instance_28 IL_56465.4_IL_4IOA_046_G1241_C1234GAGUAC
IL_56465.4_Sequence_28 IL_56465.4_IL_4IOA_046_G_1241_C_1234GAG*UACtrue59003.86
IL_56465.4_Instance_29 IL_56465.4_IL_3MOJ_004_C2540_G2523CAAUG
IL_56465.4_Sequence_29 IL_56465.4_IL_3MOJ_004_C_2540_G_2523CAA*UGtrue99000.14
IL_56465.4_Instance_30 IL_56465.4_IL_3T4B_001_U287_G137UACGAG
IL_56465.4_Sequence_30 IL_56465.4_IL_3T4B_001_U287_G137UAC*GAGtrue62003.61
IL_56465.4_Instance_31 IL_56465.4_IL_4A1B_009_U173_G246UAAUG
IL_56465.4_Sequence_31 IL_56465.4_IL_4A1B_009_U173_G246UAA*UGtrue81001.78
IL_56465.4_Instance_32 IL_56465.4_IL_4A1B_018_U466_G512UAAUG
IL_56465.4_Sequence_32 IL_56465.4_IL_4A1B_018_U466_G512UAA*UGtrue81001.78
IL_56465.4_Instance_33 IL_56465.4_IL_1ZX7_007_C26_G10CACGAAG
IL_56465.4_Sequence_33 IL_56465.4_IL_1ZX7_007_C26_G10CAC*GAAGtrue84001.48
IL_56465.4_Instance_34 IL_56465.4_IL_2O3X_003_C30_G19CACGAAG
IL_56465.4_Sequence_34 IL_56465.4_IL_2O3X_003_C30_G19CAC*GAAGtrue84001.48
IL_56465.4_Instance_35 IL_56465.4_IL_2AW7_025_U472_A459UUGUA
IL_56465.4_Sequence_35 IL_56465.4_IL_2AW7_025_U472_A459UUG*UAtrue63003.49
IL_56465.4_Instance_36 IL_56465.4_IL_2QBG_084_A2184_U2105AUGCCU
IL_56465.4_Sequence_36 IL_56465.4_IL_2QBG_084_A_2184_U_2105AUG*CCUtrue42005.46
IL_56465.4_Instance_37 IL_56465.4_IL_2QWY_002_C43_G22CUAUG
IL_56465.4_Sequence_37 IL_56465.4_IL_2QWY_002_C43_G22CUA*UGtrue84001.48
IL_56465.4_Instance_38 IL_56465.4_IL_1T0E_001_C16_G10CACGAAG
IL_56465.4_Sequence_38 IL_56465.4_IL_1T0E_001_C16_G10CAC*GAAGtrue84001.48
IL_56465.4_Instance_39 IL_56465.4_IL_1MWL_003_C28_G18CACGAAG
IL_56465.4_Sequence_39 IL_56465.4_IL_1MWL_003_C28_G18CAC*GAAGtrue84001.48
IL_56465.4_Instance_40 IL_56465.4_IL_1MWL_002_C6_G40CACGAAG
IL_56465.4_Sequence_40 IL_56465.4_IL_1MWL_002_C6_G40CAC*GAAGtrue84001.48
IL_56465.4_Instance_41 IL_56465.4_IL_2O3X_002_C7_G42CACGAAG
IL_56465.4_Sequence_41 IL_56465.4_IL_2O3X_002_C7_G42CAC*GAAGtrue84001.48
IL_56465.4_Instance_42 IL_56465.4_IL_1O9M_002_C1407_G1494CACGAAG
IL_56465.4_Sequence_42 IL_56465.4_IL_1O9M_002_C_1407_G_1494CAC*GAAGtrue84001.48
IL_56465.4_Instance_43 IL_56465.4_IL_4IOA_102_G2818_C2849GGCGGAC
IL_56465.4_Sequence_43 IL_56465.4_IL_4IOA_102_G_2818_C_2849GGC*GGACtrue32006.51
IL_56465.4_Instance_44 IL_56465.4_IL_1DUH_001_C66_G43CAAUACCAG
IL_56465.4_Sequence_44 IL_56465.4_IL_1DUH_001_C66_G43CAA*UACCAGtrue24007.21
IL_56465.4_Instance_45 IL_56465.4_IL_1DUH_005_C66_G43CAAUACCAG
IL_56465.4_Sequence_45 IL_56465.4_IL_1DUH_005_C66_G43CAA*UACCAGtrue24007.21
IL_56465.4_Instance_46 IL_56465.4_IL_3TD1_002_C7_G42CGCGAAG
IL_56465.4_Sequence_46 IL_56465.4_IL_3TD1_002_C7_G42CGC*GAAGtrue64003.46
IL_56465.4_Instance_47 IL_56465.4_IL_3TD1_005_C30_G19CGCGAAG
IL_56465.4_Sequence_47 IL_56465.4_IL_3TD1_005_C30_G19CGC*GAAGtrue64003.46

Conserved interactions between motif group positions in IL_56465.4:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
3 4 cWW 
4 5 s35 
JAR3D SCFG/MRF model for IL_56465.4:
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 A189 - U161 from junction 
BasepairNode | Deletion Probability [0.0000004752076360] | Pair Probability [[0.007013269,0.013200437,0.008049529,0.149653816,0.000000000],[0.027041859,0.006359192,0.273371709,0.009196872,0.000000000],[0.008076843,0.238547761,0.001552997,0.017140816,0.000000000],[0.170808705,0.009069603,0.052955769,0.007960824,0.000000000],[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 [0.616195094,0.107125059,0.233832083,0.000299453,0.042500850,0.000045200,0.000002260] | Right Letter Distribution [0.743243243,0.148648649,0.040540541,0.067567568,0.000000000] | Left Index [1] | Right Index [5] // Basepair A189 - U161 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.663265306,0.071428571,0.091836735,0.173469388,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007092369,0.022541509,0.007972059,0.192002477,0.000000000],[0.017778225,0.006243616,0.237874688,0.008951255,0.000000000],[0.007961221,0.251860467,0.001550452,0.040958339,0.000000000],[0.150342859,0.009001170,0.028902739,0.008966555,0.000000000],[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 G191 - C160 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_56465.4:
> IL_56465.4 IL_4IOA_005 A  189 U  161
AAG*CU
> IL_56465.4 IL_4A1B_001 G   54 C   26
GAG*CC
> IL_56465.4 IL_3V2F_005 G  212 C  184
GAG*CC
> IL_56465.4 IL_3V2F_024 G  940 C  838
GAG*CC
> IL_56465.4 IL_3U5H_004 G   56 C   28
GAG*CC
> IL_56465.4 IL_4IOA_021 G  951 C  851
GAG*CC
> IL_56465.4 IL_2QBG_010 G  212 C  184
GAG*CC
> IL_56465.4 IL_1S72_005 G  182 C  154
GAG*CC
> IL_56465.4 IL_2QBG_027 G  940 C  838
GAG*CC
> IL_56465.4 IL_1S72_079 U 2436 A 2455
UAG*CA
> IL_56465.4 IL_2QBG_090 C 2498 G 2454
CCU*AG
> IL_56465.4 IL_4IOA_056 A 1463 U 1478
AAG*CU
> IL_56465.4 IL_2AW7_047 G 1041 C  999
GAG*CC
> IL_56465.4 IL_3U5H_009 C  163 G  258
CAA*UG
> IL_56465.4 IL_3U5H_146 C   47 G   30
CUG*CG
> IL_56465.4 IL_2O3X_001 G   42 C    7
GUC*GUC
> IL_56465.4 IL_1O9M_001 G 1494 C 1407
GUC*GUC
> IL_56465.4 IL_4M30_001 U   25 A    2
UUA*UA
> IL_56465.4 IL_4A1B_073 U 1802 A 1695
UUG*CA
> IL_56465.4 IL_2QBG_029 G  926 C  851
GAA*UC
> IL_56465.4 IL_4A1B_042 U 1138 A  995
UAG*CA
> IL_56465.4 IL_1FJG_046 G 1143 C 1128
GGC*GC
> IL_56465.4 IL_4IOA_085 C 2477 G 2433
CCU*AG
> IL_56465.4 IL_2AW7_024 C  477 G  455
CAU*GG
> IL_56465.4 IL_3U5H_037 U 1111 A  970
UAG*CA
> IL_56465.4 IL_3V2F_088 C 2498 G 2454
CCU*AG
> IL_56465.4 IL_1ZX7_001 C   26 G   10
CAC*GAAG
> IL_56465.4 IL_4IOA_046 G 1241 C 1234
GAG*UAC
> IL_56465.4 IL_3MOJ_004 C 2540 G 2523
CAA*UG
> IL_56465.4 IL_3T4B_001 U  287 G  137
UAC*GAG
> IL_56465.4 IL_4A1B_009 U  173 G  246
UAA*UG
> IL_56465.4 IL_4A1B_018 U  466 G  512
UAA*UG
> IL_56465.4 IL_1ZX7_007 C   26 G   10
CAC*GAAG
> IL_56465.4 IL_2O3X_003 C   30 G   19
CAC*GAAG
> IL_56465.4 IL_2AW7_025 U  472 A  459
UUG*UA
> IL_56465.4 IL_2QBG_084 A 2184 U 2105
AUG*CCU
> IL_56465.4 IL_2QWY_002 C   43 G   22
CUA*UG
> IL_56465.4 IL_1T0E_001 C   16 G   10
CAC*GAAG
> IL_56465.4 IL_1MWL_003 C   28 G   18
CAC*GAAG
> IL_56465.4 IL_1MWL_002 C    6 G   40
CAC*GAAG
> IL_56465.4 IL_2O3X_002 C    7 G   42
CAC*GAAG
> IL_56465.4 IL_1O9M_002 C 1407 G 1494
CAC*GAAG
> IL_56465.4 IL_4IOA_102 G 2818 C 2849
GGC*GGAC
> IL_56465.4 IL_1DUH_001 C   66 G   43
CAA*UACCAG
> IL_56465.4 IL_1DUH_005 C   66 G   43
CAA*UACCAG
> IL_56465.4 IL_3TD1_002 C    7 G   42
CGC*GAAG
> IL_56465.4 IL_3TD1_005 C   30 G   19
CGC*GAAG