Locus 633

Sequence ID 3R_DroMel_CAF1
Location 2,331,041 – 2,331,218
Length 177
Max. P 0.864886
window1004 window1005 window1006

overview

Window 4

Location 2,331,041 – 2,331,149
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.58
Mean single sequence MFE -32.67
Consensus MFE -20.20
Energy contribution -20.23
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -2.26
Structure conservation index 0.62
SVM decision value 0.23
SVM RNA-class probability 0.644469
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2331041 108 + 27905053
GCUUUGUGAGAGGGCUU------GUCAGUUGGCUUGUAGAUUGAAAGCA------AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
....((((.....((((------.((((((........)))))))))).------..((((..((((((.....))))))..)))))))).((((((((((......))))))))))... ( -32.80)
>DroPse_CAF1 40345 120 + 1
GCUUUGUCAGUGGGCAUGGGCAUGUACAUAUGUAUGUAGAUCGAAAGCAGAGGCAGACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
((((((((....)))).))))((((.(((((((.(((....(....).....))).........(((((.....)))))))))))).))))((((((((((......))))))))))... ( -36.30)
>DroEre_CAF1 42136 106 + 1
GCUUUGUGCU--GGCUU------GUCAGUUGGCUUGUAGAUUGAAAGCA------AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
....(((((.--.((((------.((((((........)))))))))).------...(((..((((((.....))))))..)))))))).((((((((((......))))))))))... ( -34.30)
>DroYak_CAF1 36606 106 + 1
ACGUUGUGUG--AGCUU------CUCAGUUGGCUUGUAGAUUGAAAGCA------AAUGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
....(((((.--.((((------.((((((........)))))))))).------...(((..((((((.....))))))..)))))))).((((((((((......))))))))))... ( -32.70)
>DroAna_CAF1 37916 106 + 1
UCAUUGUUCG--AGCUU------GUUAGCUGGCUUGUAGAUUGAAACCA------AACGCAAAUUGAAGAACAACUUCAGAGUGUGCACAUGCAAAGCUUAAUGAGAUGAGUUCUGCCAA
(((.....((--((((.------(....).)))))).....))).....------..((((..((((((.....))))))..)))).....(((.((((((......)))))).)))... ( -24.80)
>DroPer_CAF1 40197 116 + 1
GCUUUGUCAGUGGGCAUGGGCAUGUACAUAU----GUAGAUAGAAAGCAGAGGCAGACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
((((((((....)))).))))((((.(((((----((.........((....))..........(((((.....)))))))))))).))))((((((((((......))))))))))... ( -35.10)
>consensus
GCUUUGUGAG__GGCUU______GUCAGUUGGCUUGUAGAUUGAAAGCA______AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAA
.........................................................((((..((((((.....))))))..)))).....((((((((((......))))))))))... (-20.20 = -20.23 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,331,075 – 2,331,188
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.46
Mean single sequence MFE -33.77
Consensus MFE -27.55
Energy contribution -27.67
Covariance contribution 0.11
Combinations/Pair 1.11
Mean z-score -2.22
Structure conservation index 0.82
SVM decision value 0.54
SVM RNA-class probability 0.775104
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2331075 113 + 27905053
UUGAAAGCA------AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG-GCGUGGGGUGCACAGG
......(((------.((((....(((((.....)))))(((..(((.(((((((((((((......))))))))))...))))))..)))............-))))....)))..... ( -37.20)
>DroPse_CAF1 40385 117 + 1
UCGAAAGCAGAGGCAGACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGGCAGGGGGCAUGGG---CAUGAU
......((....((....))....(((((.....)))))))..((((.(((((((((((((......)))))))).((..((.((((.....)))).))..)).))))).)---)))... ( -35.70)
>DroEre_CAF1 42168 110 + 1
UUGAAAGCA------AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGUGUGUGUAAUGUGACAGGG-ACGUGGG---CGCAGU
(((...((.------.((((....(((((.....)))))(((((..(((((((((((((((......))))))))))......)))))..).))))......)-.)))..)---).))). ( -32.70)
>DroYak_CAF1 36638 110 + 1
UUGAAAGCA------AAUGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGGGUGUGUAAUGUGACAGGG-GCGUGGG---UGCAGU
......(((------.((((....(((((.....)))))((((.(((((((((((((((((......))))))))))........))))))))))).......-))))...---)))... ( -34.10)
>DroAna_CAF1 37948 100 + 1
UUGAAACCA------AACGCAAAUUGAAGAACAACUUCAGAGUGUGCACAUGCAAAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACGGGG--CGC------------
......((.------..((((..((((((.....))))))....(((((((((...((((....(((.....)))...)))).))))))))).))))...)).--...------------ ( -27.20)
>DroPer_CAF1 40233 117 + 1
UAGAAAGCAGAGGCAGACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGGCAGGGGGCAUGGG---CAUGAU
......((....((....))....(((((.....)))))))..((((.(((((((((((((......)))))))).((..((.((((.....)))).))..)).))))).)---)))... ( -35.70)
>consensus
UUGAAAGCA______AACGCAAAUUGAAGAACAACUUCAGCAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG_GCGUGGG___CACAGU
.................((((...(((((.....)))))(((..(((.(((((((((((((......))))))))))...))))))..)))..))))....................... (-27.55 = -27.67 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,331,109 – 2,331,218
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.46
Mean single sequence MFE -39.18
Consensus MFE -22.71
Energy contribution -22.35
Covariance contribution -0.36
Combinations/Pair 1.18
Mean z-score -2.44
Structure conservation index 0.58
SVM decision value 0.84
SVM RNA-class probability 0.864886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2331109 109 + 27905053
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG-GCGUGGGGUGCACAGGGGCGGUACUGAUGGUA---------CUGAUG-GUACUGAA
(((((.(....((((((((((......))))))))))...((.((((.....)))).))..).-))))).(((((.((....((((((.....)))---------))).))-)))))... ( -39.20)
>DroSec_CAF1 36790 118 + 1
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG-GCGUGGGGUGCGCCGGGGCGGUACUGAUGGUACUGAUGGUACUGAUG-GUACUGAA
((..(((.(((((((((((((......))))))))))...))))))..))............(-((((.....)))))....((((((((.((((((.....)))))).))-)))))).. ( -44.00)
>DroSim_CAF1 37040 118 + 1
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG-GCGUGGGGUGCGCCGGGGCGGUACUGAUGGUACUGAUGGUACUGAUG-GUACUGAA
((..(((.(((((((((((((......))))))))))...))))))..))............(-((((.....)))))....((((((((.((((((.....)))))).))-)))))).. ( -44.00)
>DroEre_CAF1 42202 106 + 1
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGUGUGUGUAAUGUGACAGGG-ACGUGGG---CGCAGUGGCGCUACUGACGGUA---------CUGAUG-GUACUGAU
(((((.(....((((((((((......))))))))))...((.(..(.....)..).))..).-)))))((---(((....))))).....(((((---------(.....-)))))).. ( -36.80)
>DroYak_CAF1 36672 100 + 1
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGGGUGUGUAAUGUGACAGGG-GCGUGGG---UGCAGU------ACCGCCGGUA---------CUGAUG-CUACUAAA
(((((((((((((((((((((......))))))))))........)))))).)))))..((..-((((.((---(((.(.------.....).)))---------)).)))-)..))... ( -34.20)
>DroPer_CAF1 40273 104 + 1
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGGCAGGGGGCAUGGG---CAUGAU------GCUG------C-GAUGGCAAUGGCAUCCAGUCAA
(((((.(....((((((((((......))))))))))...((.((((.....)))).))...).)))))((---(..(((------((((------(-....))...))))))..))).. ( -36.90)
>consensus
CAUGUGCACAUGCAGAGCUUAAUGAGAUGAGUUCUGCCAAGUGGCGUGUGUAAUGUGACAGGG_GCGUGGG___CGCAGGGGCGGUACUGAUGGUA_________CUGAUG_GUACUGAA
(((((.(....((((((((((......))))))))))...((.((((.....)))).))...).)))))................................................... (-22.71 = -22.35 +  -0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:58 2006