Locus 4716

Sequence ID 2R_DroMel_CAF1
Location 15,451,565 – 15,451,689
Length 124
Max. P 0.603355
window7588 window7589

overview

Window 8

Location 15,451,565 – 15,451,661
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 75.54
Mean single sequence MFE -36.31
Consensus MFE -13.24
Energy contribution -13.33
Covariance contribution 0.09
Combinations/Pair 1.35
Mean z-score -2.17
Structure conservation index 0.36
SVM decision value 0.10
SVM RNA-class probability 0.582136
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15451565 96 + 20766785
GACCAGCUACCAGG--------CAGCCAUCUCCAUCUC-CAGCUC--GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGACUGCAUCCUGCUGCUUUUGCUGUCGG
(((.(((....(((--------((((........((((-(((...--.)))--))))(((((((.((......---)).))))))).........)))))))..)))))).. ( -39.60)
>DroSec_CAF1 249454 85 + 1
GGCCGGCUACCAGG--------C-------UCCAGCUC-CA------GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGGCUGCAUCCUGCUGCUUUUGCUGUUGG
..(((((.....((--------(-------.(((((((-((------((((--(((.........))))))))---.)))))))))))(((......))).......))))) ( -38.30)
>DroSim_CAF1 228376 85 + 1
GGCCGGCUACCAGG--------C-------UCCAGCUC-CA------GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGGCUGCAUCCUGCUGCUUUUGCUGUCGG
..(((((.....((--------(-------.(((((((-((------((((--(((.........))))))))---.)))))))))))(((......))).......))))) ( -40.30)
>DroEre_CAF1 236662 106 + 1
GGCCAGCUACCAGGCUGCCAGGCUGCCAUCUCCGUCUC-CAGCUCCAGCUG--GAUAUCCAGCUGCUCCGACU---AGGAGCUGGACUGCAUCCUGCUGGUUUUGCUGUCGG
(((.(((.(((((.....((((.(((....((((.(((-(((.((((((((--(....)))))))....))))---.)))).))))..))).)))))))))...)))))).. ( -44.40)
>DroYak_CAF1 244875 94 + 1
GGCCAGCUACCAGA--------CUGCCAUCUCCAGCUC-CAGUUCCA------GAGAUCCAGCUGCUCCGACU---AGGAGCUAGACUGCAUCCUGCUGGUUUUGCUGUCGG
(((.(((.....).--------)))))..(..((((.(-(((...((------(.(((.((((((((((....---.))))).)).))).))))))))))....))))..). ( -33.80)
>DroAna_CAF1 230111 102 + 1
GCAUAGCUACCAGG--------CUGCCAUCUCCGUCUCUCAGCUU--UCCGACCAAGUCCAGCUCCUUCUCCUUCCCCAGUCCCAACUGCAUCCUGCUGGUUUUGCUGUCGG
....((((...(((--------(..........))))...)))).--.(((((((((.(((((..............((((....))))......))))).))))..))))) ( -21.45)
>consensus
GGCCAGCUACCAGG________CUGCCAUCUCCAGCUC_CAGCUC__GUUG__GAGAUCCAGCUGCUCCGACU___AGGAGCUGGACUGCAUCCUGCUGCUUUUGCUGUCGG
((.((((.....((.................))..........................((((.(((((........))))).(((.....))).)))).....)))))).. (-13.24 = -13.33 +   0.09)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,451,596 – 15,451,689
Length 93
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 82.15
Mean single sequence MFE -32.81
Consensus MFE -21.37
Energy contribution -21.65
Covariance contribution 0.28
Combinations/Pair 1.24
Mean z-score -1.79
Structure conservation index 0.65
SVM decision value 0.14
SVM RNA-class probability 0.603355
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15451596 93 + 20766785
AGCUC--GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGACUGCAUCCUGCUGCUUUUGCUGUCGGCUGGGGCACCCAAUGCUGUCGAAACAAA
(((..--((((--(...((((((((((((....---.)))))..(((.(((............))).))))))))))....))))))))........... ( -33.00)
>DroSec_CAF1 249478 89 + 1
A------GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGGCUGCAUCCUGCUGCUUUUGCUGUUGGCUGUGGCAGCCAAUGCUGUCGAAACAAA
(------((((--(....))))))(((((....---.)))))..(((.((((...((((((...((.....))...))))))..)))).)))........ ( -36.60)
>DroSim_CAF1 228400 89 + 1
A------GUUG--GAGAUCCAGCUGCUCCGACU---AGGAGCUGGGCUGCAUCCUGCUGCUUUUGCUGUCGGCUGUGGCACCCAAUGCUGUCGAAACAAA
.------(((.--..((..((((.(((((....---.))))).((((..((.((.((.((....)).)).)).))..)).))....))))))..)))... ( -33.00)
>DroEre_CAF1 236701 95 + 1
AGCUCCAGCUG--GAUAUCCAGCUGCUCCGACU---AGGAGCUGGACUGCAUCCUGCUGGUUUUGCUGUCGGCUGGAGCACCCAGUGCUGUCGAAACAAA
.((((((((((--(....(((((.(((((....---.))))).(((.....))).)))))........)))))))))))..................... ( -40.00)
>DroYak_CAF1 244906 91 + 1
AGUUCCA------GAGAUCCAGCUGCUCCGACU---AGGAGCUAGACUGCAUCCUGCUGGUUUUGCUGUCGGCUGGGGCACCCAAUGCUGUCGAAACAAA
.(((...------((...(((((((((((....---.)))))..(((.(((.((....))...))).)))))))))((((.....)))).))..)))... ( -32.70)
>DroAna_CAF1 230143 97 + 1
AGCUU--UCCGACCAAGUCCAGCUCCUUCUCCUUCCCCAGUCCCAACUGCAUCCUGCUGGUUUUGCUGUCGGCUAGGGCAC-AAAUGCUGUCGAAACAAA
.((((--((((((((((.(((((..............((((....))))......))))).))))..)))))..)))))..-.................. ( -21.55)
>consensus
AGCUC__GUUG__GAGAUCCAGCUGCUCCGACU___AGGAGCUGGACUGCAUCCUGCUGCUUUUGCUGUCGGCUGGGGCACCCAAUGCUGUCGAAACAAA
..................(((((((((((........)))))..(((.(((............))).)))))))))((((.....))))........... (-21.37 = -21.65 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:32 2006