Locus 4266

Sequence ID 2L_DroMel_CAF1
Location 12,192,682 – 12,192,813
Length 131
Max. P 0.938402
window6731 window6732

overview

Window 1

Location 12,192,682 – 12,192,793
Length 111
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 81.89
Mean single sequence MFE -23.17
Consensus MFE -12.42
Energy contribution -13.42
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.54
SVM decision value 0.40
SVM RNA-class probability 0.720256
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12192682 111 + 22407834
CCCCCGUUCGAACUCAAUCCCC-CCC--UCCCCCGAAUAUCCUGCCAACCGACCAACUAUGGCACUUCAUUUGCUCCACUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG-CA
.....(((((............-...--.....))))).....(((((((((.(((..((((((.......)))(((((....)))))........)))))).))).)))))-). ( -23.05)
>DroSec_CAF1 21528 106 + 1
UCCCCGUUCGAACACCUU------CC--CCCUCCGAAUAUCCUGCCAACCGACCAACUAUGGCACUUCAUUUGCUCCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG-CA
.....(((((........------..--.....))))).....((((((.(.(((....))))..............((.((((((((......))))))))...)))))))-). ( -23.66)
>DroSim_CAF1 19459 112 + 1
CCCCUUUUCGAACUCCUUACCUACCC--CCCUCCGAAUAUCCUGCCAACCGACCAACUAUGGCACUUCAUUUGCUCCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG-CA
......((((................--.....))))......((((((.(.(((....))))..............((.((((((((......))))))))...)))))))-). ( -21.70)
>DroEre_CAF1 19620 100 + 1
CCCCCGCUUGAACUGCUU------C----CCCCCGCAUAUCCUGCCAAC----CAACUAUGGCACUUCAUUUGCAGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCCUUGG-CA
...((((((((..((((.------.----.....(((.....(((((..----......))))).......))))))).)))))))).................(((....)-)) ( -23.41)
>DroYak_CAF1 20215 100 + 1
CCCCCGCUUCAACUCCUU------C----CCCCCGCAUAUCCUGCCAAC----CAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCCUUUG-CA
.....((...........------.----.....(((.....(((((..----......))))).......))).(((..((((((((......))))))))..)))....)-). ( -20.60)
>DroPer_CAF1 39495 109 + 1
--CC-UCUCCAGCAACCCCCCCACCCCACCGCCCCAACCUGCUGCCCAC---CCAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGGGCA
--..-....(((((.........................)))))....(---(((((...((((.......))))(((..((((((((......))))))))..))))))))).. ( -26.61)
>consensus
CCCCCGCUCGAACUCCUU______CC__CCCCCCGAAUAUCCUGCCAAC___CCAACUAUGGCACUUCAUUUGCUCCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG_CA
...........................................((((((...........((((.......))))..((.((((((((......))))))))...))))))).). (-12.42 = -13.42 +   1.00)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 12,192,717 – 12,192,813
Length 96
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 77.94
Mean single sequence MFE -24.35
Consensus MFE -11.44
Energy contribution -12.13
Covariance contribution 0.69
Combinations/Pair 1.07
Mean z-score -2.64
Structure conservation index 0.47
SVM decision value 1.29
SVM RNA-class probability 0.938402
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12192717 96 + 22407834
--AUCCUGCCAACCGACCAACUAUGGCACUUCAUUUGCUCCACUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG-CA-AAAA----------AAA-AAAAGAA----GAG-UAA
--....((((((((((.(((..((((((.......)))(((((....)))))........)))))).))).)))))-))-....----------...-.......----...-... ( -22.00)
>DroGri_CAF1 24614 105 + 1
--CUCCAGC--AC-CAGCUCCUCUGGCACUUCAUUUGCAGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGCACUGCAACAAAACGACACAA-AAAAGAAAGAA----AAA-AAA
--....((.--.(-(((.....))))..))....(((((((((.((((((((......))))))))...))))..))))).............-...........----...-... ( -22.30)
>DroSim_CAF1 19495 96 + 1
--AUCCUGCCAACCGACCAACUAUGGCACUUCAUUUGCUCCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG-CA-AAAA----------AAA-AAGAGUA----GAG-UAA
--....(((((............)))))......((((((..((((((((....)))))...(((.(((((....)-))-)).)----------)).-..)))..----)))-))) ( -25.40)
>DroYak_CAF1 20243 94 + 1
--AUCCUGCCAAC----CAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCCUUUG-CA-AAAA----------AA---AGAGUAAAAUAAG-UAA
--.....((((..----......))))((((..(((((((((..((((((((......))))))))..)))((((.-..-....----------))---))))))))..)))-).. ( -22.40)
>DroAna_CAF1 20172 100 + 1
UCCUCCUGCCAAC----CAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCUCUGGGCA-AAAA------CAAAAAA-AAAUGUA----GAGGAAA
(((((.(((((..----......))))).....(((((((((..((((((((......))))))))..)))....))))-))..------.......-.......----))))).. ( -28.10)
>DroPer_CAF1 39530 89 + 1
--CUGCUGCCCAC---CCAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGGGCA-ACAA----------AAA-AAAAGA----------AA
--.((.((((((.---........((((.......))))((((.((((((((......))))))))...))))))))))-.)).----------...-......----------.. ( -25.90)
>consensus
__AUCCUGCCAAC___CCAACUAUGGCACUUCAUUUGCUGCGCUCAAGUGGAUCCACUUUCAUUUGUUUGCGUUGG_CA_AAAA__________AAA_AAAAGAA____GAG_UAA
.......((((............))))............(((..((((((((......))))))))..)))............................................. (-11.44 = -12.13 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:47 2006