Locus 4898

Sequence ID 2R_DroMel_CAF1
Location 16,008,779 – 16,008,895
Length 116
Max. P 0.838229
window7849 window7850

overview

Window 9

Location 16,008,779 – 16,008,869
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -28.22
Consensus MFE -18.77
Energy contribution -18.83
Covariance contribution 0.06
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.67
SVM decision value 0.74
SVM RNA-class probability 0.838229
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16008779 90 + 20766785
-------CGUUGUUUGAG----UGUAUAUUGGCGACUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCUUGUUUUGUUCGAGACCAAC
-------.((((((((((----((((....(....)...)))))))(((((((((((...((((.-.....))))..)))))))))))......))).)))) ( -30.80)
>DroSec_CAF1 63950 89 + 1
-------CGUUGUUUGAG----UGUAUAUUGGCGACUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCU-GCAUUGUUUGAGACCAAC
-------...((((((((----((((....(....)...))))))))))))((((((...((((.-.....))))..))))))-.................. ( -28.90)
>DroSim_CAF1 64955 89 + 1
-------CCUUGUUUGAG----UGUAUAUUGGCGAAUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCU-CCAUUGUUUGAGACCAAC
-------..(((((((((----((((((((....)))).)))))))))))))(((((...((((.-.....))))..))))).-.................. ( -27.90)
>DroEre_CAF1 70410 89 + 1
-------CGUUGUUUGAG----UGUAUAUUGGUGACUGUUGCGCUCGAGCAAGCAGCACAAACUU-UUCGCAGUUAAGCUGCU-CCAUUGUUUGGGACCAAC
-------..(((((((((----((((....(....)...)))))))))))))(((((...((((.-.....))))..)))))(-(((.....))))...... ( -31.10)
>DroYak_CAF1 73183 96 + 1
CUUCUUUUUUUGUUCGAG----UGUAUAUUGGUGACUGUUGCGCUCGAGCAAGCAGCACAAACUU-UUCGCAGUUAAGCUGCU-CCAUUGUUUGAGACCAAC
..((((...(((((((((----((((....(....)...)))))))))))))(((((...((((.-.....))))..))))).-.........))))..... ( -31.60)
>DroAna_CAF1 72794 95 + 1
------UGUUUGUGCAACUGCUUCUGUAUUGGCGACUGUUGCACUUGAGUAAGCAGCGACAACUUUUUUCCAGUUAAGCUCGU-CUUUUGUCCAAAAUAAAC
------.....(((((((((((........))))...)))))))(((..((((..((((.((((.......))))....))))-..))))..)))....... ( -19.00)
>consensus
_______CGUUGUUUGAG____UGUAUAUUGGCGACUGUUGCGCUCGAGCAAGCAGCCCGAACUU_UUCGCAGUUAAGCUGCU_CCAUUGUUUGAGACCAAC
.....................................((((..((((((((((((((...((((.......))))..)))))).....))))))))..)))) (-18.77 = -18.83 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,008,801 – 16,008,895
Length 94
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 80.49
Mean single sequence MFE -23.38
Consensus MFE -19.98
Energy contribution -20.03
Covariance contribution 0.06
Combinations/Pair 1.18
Mean z-score -1.59
Structure conservation index 0.85
SVM decision value 0.70
SVM RNA-class probability 0.827229
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16008801 94 + 20766785
GACUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCUUGUUUUGUUCGAGACCAACUUAAAUAAGAAGACGCAAGAU--AUAGC
...(.(((((.(((((((((((((...((((.-.....))))..)))))))))))((((..((.....))..))))....))))))).).--..... ( -28.50)
>DroSec_CAF1 63972 93 + 1
GACUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCU-GCAUUGUUUGAGACCAACUUAAAGAACAAGAUACAAGAU--AUAGC
....((((.(((((((((((((((...((((.-.....)))).....)))-)).))))))))).))))).....................--..... ( -25.80)
>DroSim_CAF1 64977 93 + 1
GAAUGUUGCGCUCGAGCAAGCAGCCCGAACUU-UUCGUAGUUAAGCUGCU-CCAUUGUUUGAGACCAACUUAAAUAACAAGAUACAAGAU--AUAGC
....((((.(((((((((((((((...((((.-.....))))..))))))-....)))))))).))))).....................--..... ( -25.10)
>DroEre_CAF1 70432 95 + 1
GACUGUUGCGCUCGAGCAAGCAGCACAAACUU-UUCGCAGUUAAGCUGCU-CCAUUGUUUGGGACCAACUUAAACAACAAGAUACAAAAUGCAUAGC
....((((.(((((((((((((((...((((.-.....))))..))))))-....)))))))).)))))............................ ( -22.40)
>DroYak_CAF1 73212 93 + 1
GACUGUUGCGCUCGAGCAAGCAGCACAAACUU-UUCGCAGUUAAGCUGCU-CCAUUGUUUGAGACCAACUUGAAUAGCAAGAUACAAAAU--AUAGC
....((((.(((((((((((((((...((((.-.....))))..))))))-....)))))))).))))).....................--..... ( -23.30)
>DroAna_CAF1 72821 87 + 1
GACUGUUGCACUUGAGUAAGCAGCGACAACUUUUUUCCAGUUAAGCUCGU-CUUUUGUCCAAAAUAAACUCGAAUUCCGAGGCAUCAA---------
...((.(((..(((..((((..((((.((((.......))))....))))-..))))..)))......((((.....))))))).)).--------- ( -15.20)
>consensus
GACUGUUGCGCUCGAGCAAGCAGCCCGAACUU_UUCGCAGUUAAGCUGCU_CCAUUGUUUGAGACCAACUUAAAUAACAAGAUACAAAAU__AUAGC
....((((..((((((((((((((...((((.......))))..)))))).....))))))))..))))............................ (-19.98 = -20.03 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:43 2006