Query 50dd0926e2cec run time not recorded
Unaligned nucleotides are translucent. Right click to view Jmol menu. More HelpQuery summary
- Molecule 1
- PDB id: 2ZJR, Chains: Y, Nucleotides: all
- Molecule 2
- PDB id: 3V2F, Chains: B, Nucleotides: all
- Iteration 1
- d = 0.5, p = 2, β = 60
- Iteration 2
- d = 0.5, p = 8, β = 20
Local geometric similarity
Blue (low geometric discrepancy) indicates high 3D similarity.
Red (high geometric discrepancy) indicates low 3D similarity.
Bar Diagram Help
The arcs indicate basepairing interactions and are colored by type.
Bar Diagram Help
Basepair interactions are annotated according to the
Leontis-Westhof nomenclature and are colored by type.
Basepair Table Help
<0.1 | <0.2 | <0.3 | <0.4 | <0.5 | <0.6 | <0.7 | <0.8 | <0.9 | <1.0 | >=1.0 |
2ZJR | 3V2F | Disc | ||||
---|---|---|---|---|---|---|
Y:C2 | --- | --- | --- | |||
Y:A3 | cWW | Y:U122 | B:U1 | ncWW | B:A120 | |
Y:C4 | cWW | Y:G121 | B:C2 | cWW | B:G119 | |
Y:C5 | cWW | Y:G120 | B:C3 | cWW | B:G118 | |
Y:C6 | cWW | Y:G119 | B:C4 | cWW | B:G117 | |
Y:C7 | cWW | Y:G118 | B:C5 | cWW | B:G116 | |
Y:C8 | cWW | Y:G117 | B:C6 | cWW | B:G115 | |
Y:G9 | cWW | Y:C116 | B:G7 | cWW | B:C114 | |
Y:U10 | cWW | Y:G115 | B:U8 | cWW | B:G113 | |
Y:G11 | cWW | Y:C114 | B:G9 | cWW | B:U112 | |
Y:C12 | cWW | Y:G113 | B:C10 | cWW | B:G111 | |
--- | Y:A112 | B:C11 | cWW | B:G110 | ||
--- | --- | B:C12 | --- | |||
Y:C13 | --- | --- | --- | |||
Y:C14 | --- | --- | --- | |||
Y:A15 | tSS | Y:G71 | B:A13 | ntSS | B:G69 | |
Y:U16 | --- | B:U14 | --- | |||
--- | --- | B:A15 | --- | |||
Y:A17 | --- | --- | --- | |||
Y:G18 | cWW | Y:C70 | B:G16 | cWW | B:C68 | |
Y:C19 | cWW | Y:G69 | B:C17 | cWW | B:G67 | |
Y:C19 | cHS | Y:C111 | B:C17 | ncHW | B:C109 | |
Y:A20 | cWW | Y:C67 | B:G18 | cWW | B:C65 | |
Y:C21 | cWW | Y:G66 | B:G19 | cWW | B:C64 | |
Y:U22 | cWW | Y:A65 | B:C20 | cWW | B:G63 | |
Y:G23 | cWW | Y:C64 | B:G21 | cWW | B:C62 | |
Y:U24 | cWW | Y:A63 | B:U22 | cWW | B:G61 | |
Y:G25 | cWW | Y:C62 | B:G23 | cWW | B:C60 | |
Y:G26 | ntSW | Y:C29 | B:G24 | tSW | B:C27 | |
--- | --- | B:A25 | --- | |||
Y:A27 | --- | --- | --- | |||
Y:A28 | --- | B:A26 | --- | |||
Y:C29 | ntWS | Y:G26 | B:C27 | tWS | B:G24 | |
Y:C30 | cWW | Y:G58 | B:C28 | cWW | B:G56 | |
Y:A31 | cWW | Y:U57 | B:A29 | cWW | B:U55 | |
Y:C32 | cWW | Y:G56 | B:C30 | cWW | B:G54 | |
Y:C33 | cWW | Y:G53 | B:C31 | ncWW | B:G51 | |
Y:C34 | cWW | Y:G52 | B:C32 | cWW | B:G50 | |
Y:C35 | cWW | Y:G51 | B:G33 | cWW | B:C49 | |
Y:A36 | ncSH | Y:C38 | B:U34 | cSH | B:C36 | |
Y:A36 | ncWW | Y:U50 | B:U34 | cWW | B:A48 | |
--- | --- | B:U35 | --- | |||
Y:C37 | --- | --- | --- | |||
Y:C38 | ncHS | Y:A36 | B:C36 | cHS | B:U34 | |
Y:C38 | ---- | Y:G51 | B:C36 | cWS | B:C49 | |
Y:C39 | ---- | Y:U50 | B:C37 | cWS | B:A48 | |
Y:C40 | ncWW | Y:G46 | B:C38 | cWW | B:G44 | |
Y:A41 | ncSW | Y:A48 | B:A39 | cSW | B:A46 | |
Y:U42 | tSH | Y:A47 | B:U40 | ntSH | B:A45 | |
Y:G43 | --- | B:U41 | --- | |||
Y:C44 | --- | B:C42 | --- | |||
Y:C45 | --- | B:C43 | --- | |||
Y:G46 | ncWW | Y:C40 | B:G44 | cWW | B:C38 | |
Y:G46 | Y:C49 | B:G44 | tSW | B:C47 | ||
Y:A47 | tHS | Y:U42 | B:A45 | ntHS | B:U40 | |
Y:A48 | ncWS | Y:A41 | B:A46 | cWS | B:A39 | |
Y:C49 | Y:G46 | B:C47 | tWS | B:G44 | ||
Y:U50 | ncWW | Y:A36 | B:A48 | cWW | B:U34 | |
Y:U50 | ---- | Y:C39 | B:A48 | cSW | B:C37 | |
Y:G51 | cWW | Y:C35 | B:C49 | cWW | B:G33 | |
Y:G51 | ---- | Y:C38 | B:C49 | cSW | B:C36 | |
Y:G52 | cWW | Y:C34 | B:G50 | cWW | B:C32 | |
Y:G53 | cWW | Y:C33 | B:G51 | ncWW | B:C31 | |
--- | --- | B:A52 | --- | |||
--- | --- | B:A53 | --- | |||
Y:U54 | --- | --- | --- | |||
Y:C55 | --- | --- | --- | |||
Y:G56 | cWW | Y:C32 | B:G54 | cWW | B:C30 | |
Y:U57 | cWW | Y:A31 | B:U55 | cWW | B:A29 | |
Y:G58 | cWW | Y:C30 | B:G56 | cWW | B:C28 | |
Y:A59 | --- | B:A57 | --- | |||
Y:A60 | --- | B:A58 | --- | |||
Y:A61 | --- | B:A59 | --- | |||
Y:C62 | cWW | Y:G25 | B:C60 | cWW | B:G23 | |
Y:A63 | cWW | Y:U24 | B:G61 | cWW | B:U22 | |
Y:C64 | cWW | Y:G23 | B:C62 | cWW | B:G21 | |
Y:A65 | cWW | Y:U22 | B:G63 | cWW | B:C20 | |
Y:G66 | cWW | Y:C21 | B:C64 | cWW | B:G19 | |
Y:C67 | cWW | Y:A20 | B:C65 | cWW | B:G18 | |
Y:A68 | --- | B:A66 | --- | |||
Y:G69 | cWW | Y:C19 | B:G67 | cWW | B:C17 | |
Y:C70 | cWW | Y:G18 | B:C68 | cWW | B:G16 | |
Y:G71 | tSS | Y:A15 | B:G69 | ntSS | B:A13 | |
Y:G71 | ncWW | Y:U110 | B:G69 | cWW | B:U108 | |
Y:C72 | cWW | Y:G109 | B:C70 | cWW | B:G107 | |
Y:C73 | cWW | Y:G108 | B:C71 | cWW | B:G106 | |
Y:A74 | tSH | Y:C107 | B:G72 | tSH | B:A105 | |
Y:A75 | tHW | Y:U106 | B:A73 | tHW | B:U104 | |
Y:U76 | tHW | Y:G105 | B:U74 | nbif | B:G103 | |
Y:G77 | --- | B:G75 | --- | |||
Y:A78 | bif | Y:A103 | B:G76 | bif | B:G101 | |
Y:U79 | tWH | Y:A102 | B:U77 | tWH | B:A100 | |
Y:A80 | tHS | Y:A101 | B:A78 | tHS | B:G99 | |
Y:C81 | cWW | Y:G100 | B:C79 | cWW | B:G98 | |
Y:U82 | cWW | Y:G99 | B:U80 | cWW | B:G97 | |
Y:C83 | bif | Y:C98 | B:G81 | cWW | B:U96 | |
Y:G84 | cWW | Y:C97 | B:G82 | cWW | B:C95 | |
Y:G85 | cWW | Y:C96 | B:G83 | cWW | B:C94 | |
Y:A86 | cWW | Y:U95 | B:C84 | cWW | B:G93 | |
Y:C87 | cWW | Y:G94 | B:G85 | cWW | B:C92 | |
Y:C88 | cWW | Y:G93 | B:G86 | cWW | B:C91 | |
Y:G89 | --- | B:G87 | --- | |||
Y:C90 | --- | B:C88 | --- | |||
Y:A91 | --- | B:G89 | --- | |||
Y:G92 | --- | B:A90 | --- | |||
Y:G93 | cWW | Y:C88 | B:C91 | cWW | B:G86 | |
Y:G94 | cWW | Y:C87 | B:C92 | cWW | B:G85 | |
Y:U95 | cWW | Y:A86 | B:G93 | cWW | B:C84 | |
Y:C96 | cWW | Y:G85 | B:C94 | cWW | B:G83 | |
Y:C97 | cWW | Y:G84 | B:C95 | cWW | B:G82 | |
Y:C98 | bif | Y:C83 | B:U96 | cWW | B:G81 | |
Y:G99 | cWW | Y:U82 | B:G97 | cWW | B:U80 | |
Y:G100 | cWW | Y:C81 | B:G98 | cWW | B:C79 | |
Y:A101 | tSH | Y:A80 | B:G99 | tSH | B:A78 | |
Y:A102 | tHW | Y:U79 | B:A100 | tHW | B:U77 | |
Y:A103 | bif | Y:A78 | B:G101 | bif | B:G76 | |
Y:A104 | --- | B:A102 | --- | |||
Y:G105 | tWH | Y:U76 | B:G103 | nbif | B:U74 | |
Y:U106 | tWH | Y:A75 | B:U104 | tWH | B:A73 | |
Y:C107 | tHS | Y:A74 | B:A105 | tHS | B:G72 | |
Y:G108 | cWW | Y:C73 | B:G106 | cWW | B:C71 | |
Y:G109 | cWW | Y:C72 | B:G107 | cWW | B:C70 | |
Y:U110 | ncWW | Y:G71 | B:U108 | cWW | B:G69 | |
Y:C111 | cSH | Y:C19 | B:C109 | ncWH | B:C17 | |
Y:A112 | --- | B:G110 | cWW | B:C11 | ||
Y:G113 | cWW | Y:C12 | B:G111 | cWW | B:C10 | |
Y:C114 | cWW | Y:G11 | B:U112 | cWW | B:G9 | |
Y:G115 | cWW | Y:U10 | B:G113 | cWW | B:U8 | |
Y:C116 | cWW | Y:G9 | B:C114 | cWW | B:G7 | |
Y:G117 | cWW | Y:C8 | B:G115 | cWW | B:C6 | |
Y:G118 | cWW | Y:C7 | B:G116 | cWW | B:C5 | |
Y:G119 | cWW | Y:C6 | B:G117 | cWW | B:C4 | |
Y:G120 | cWW | Y:C5 | B:G118 | cWW | B:C3 | |
Y:G121 | cWW | Y:C4 | B:G119 | cWW | B:C2 | |
Y:U122 | cWW | Y:A3 | B:A120 | ncWW | B:U1 | |
Y:U123 | --- | --- | --- |
CACCCCCGUGC--CCAU-AGCACUGUGG-AACCACCCCA-CCCCAUGCCGAACUGGG--UCGUGAAACACAGCAGCGCCA -UCCCCCGUGCCC--AUA-GCGGCGUGGA-ACCACCCGUU-CCCAUUCCGAACACGGAA--GUGAAACGCGCCAGCGCCG AUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUU- AUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA--
Summary statistics
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