Locus 4167

Sequence ID 2L_DroMel_CAF1
Location 11,965,405 – 11,965,556
Length 151
Max. P 0.761998
window6582 window6583

overview

Window 2

Location 11,965,405 – 11,965,518
Length 113
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 79.23
Mean single sequence MFE -21.10
Consensus MFE -14.61
Energy contribution -15.05
Covariance contribution 0.44
Combinations/Pair 1.18
Mean z-score -1.58
Structure conservation index 0.69
SVM decision value 0.06
SVM RNA-class probability 0.565710
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11965405 113 - 22407834
AAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCUUGCGUUUUU---UAAAGUGUUUUUU-UUUGUUAUUUUUUGGUUUUUGUGGCAGUGUCCGCCUC
.((((((((.....))))))))(((..(((((.(((((((.(((........))).)))))))---.((((((......-.....))))))...........))))).)))...... ( -20.20)
>DroSec_CAF1 184790 103 - 1
AAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUUUCGUGCAUUUUU---UUAAGUGUUAUUU-----------UUUUUUUUUUGUGUCAGUGCCCGCCUC
..........((((((((....(((((((((......))))))))).........((((((..---..)))))).....-----------............))))))))....... ( -18.80)
>DroSim_CAF1 151157 99 - 1
AAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCAUACAUUUUU---UUAAGUGUU---------------UUUCUUUUUUGUGGCAGUGCCCGCCUC
..((((..((((((.((.....(((((((((......))))))))).....))))))))..))---)).......---------------............(((.......))).. ( -20.40)
>DroEre_CAF1 159572 106 - 1
AAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCCUGCAUUUUUUUUUGUAGUGCUGUUUUCUUGCUG-----------CUGCUGCAGUGCCCGCCCC
((((((..(((((..((.....(((((((((......)))))))))...))...)))))..))))))...(..((((......((..-----------..)).))))..)....... ( -25.00)
>consensus
AAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCAUGCAUUUUU___UUAAGUGUU_UUU___________UUU_UUUUUUGUGGCAGUGCCCGCCUC
.((((((((.....))))))))(((((((((......))))))))).........(((((((.....)))))))..........................((((......))))... (-14.61 = -15.05 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,965,442 – 11,965,556
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.88
Mean single sequence MFE -29.38
Consensus MFE -19.56
Energy contribution -20.42
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -2.54
Structure conservation index 0.67
SVM decision value 0.50
SVM RNA-class probability 0.761998
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11965442 114 - 22407834
UGCUG--GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCUUGCGUUUUU---UAAAGUGUUUUU-U
(((..--(((((((.........)))))))..)))........(((..(((((..((.....(((((((((......)))))))))...))...)))))..))---)...........-. ( -29.20)
>DroVir_CAF1 168773 95 - 1
UGCUGCUGUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUG--G-C-AUCGUGGAUAUAUUUGG-CGA-CGAUC-------------------
...(((....)))(((((...((.((((((.(.((.(((((..((((((.....))))))))))).))--.-)-)))))).)).....)))-)).-.....------------------- ( -22.70)
>DroSec_CAF1 184817 114 - 1
UGCUG--GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUUUCGUGCAUUUUU---UUAAGUGUUAUU-U
(((..--(((((((.........)))))))..))).......((((..((((((.((.....(((((((((......))))))))).....))))))))..))---))..........-. ( -31.60)
>DroSim_CAF1 151184 110 - 1
UGCUG--GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCAUACAUUUUU---UUAAGUGUU-----
(((..--(((((((.........)))))))..))).......((((..((((((.((.....(((((((((......))))))))).....))))))))..))---)).......----- ( -31.30)
>DroEre_CAF1 159599 117 - 1
UGCUG--GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCCUGCAUUUUUUUUUGUAGUGCUGUU-U
(((..--(((((((.........)))))))..)))...((((((((..(((((..((.....(((((((((......)))))))))...))...))))).))))))))..........-. ( -32.60)
>DroYak_CAF1 155948 117 - 1
UGCUG--GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUUAAAGCGGAAGUUUCUUCUCUU-CUUAUUUUUUUUUAGUGUUGAUUU
(((..--(((((((.........)))))))..))).(((((((((((((.....))))))))(((((((((......))))))))).........-.................))))).. ( -28.90)
>consensus
UGCUG__GUUGCAUGCCACAAAUGUGCGAUUGGCAUGUCAAAAGAAUUAUGUAUUGAUUUUUGAUUUCUGCCUAAAAGCGGAAGUUUCUUCUCGUGCAUUUUU___UUAAGUGUU_UU_U
........((((((((((............))))))).)))((((((((.....))))))))(((((((((......))))))))).................................. (-19.56 = -20.42 +   0.86)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:23 2006