Locus 7703

Sequence ID X_DroMel_CAF1
Location 19,200,526 – 19,200,662
Length 136
Max. P 0.745490
window12633 window12634

overview

Window 3

Location 19,200,526 – 19,200,627
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.85
Mean single sequence MFE -21.72
Consensus MFE -11.79
Energy contribution -12.35
Covariance contribution 0.56
Combinations/Pair 1.20
Mean z-score -1.70
Structure conservation index 0.54
SVM decision value 0.20
SVM RNA-class probability 0.633077
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19200526 101 + 22224390
UUU----UUUCCAUUUAC-------A-------GCAAAGGUAUUUGCAUUCAUUUUUC-UUAUAUGUGAAAGAUUGAUUUCGAUAUUUGUGGUGGUUUCGUUGCACACUAUGCAUAGUGG
...----...(((((...-------.-------((..(((((((.(.(((.(((((((-........))))))).))).).)))))))((((((((......)).))))))))..))))) ( -19.20)
>DroSec_CAF1 22079 107 + 1
UUU-----UUCCAUUUAC-------AUACCUCUGAAAAGGUAUUUGCUUUCUUUUCCU-UUAUAUCUGAAAGAUUGAUUUCGAUAUUUGUGGUGGGUUCGUUGCCCACUAUGCAUAGUUG
...-----..........-------((((((......)))))).(((...........-..(((((.((((......)))))))))..(((((((((.....))))))))))))...... ( -24.80)
>DroEre_CAF1 19592 94 + 1
-------------------------AUAACUCUGAACAACUUUUUGCUUACCUUUUCUUUUGUAUCUAAAAGAUUAAUUUCGAUAUUUGCAGUGGGAUU-UUGCCCACUAUGCAUAGUUG
-------------------------...........(((((...(((........(((((((....))))))).................((((((...-...))))))..))).))))) ( -19.80)
>DroYak_CAF1 19544 118 + 1
UUUCAUUUUCCCAUUUGCAGCGCACAUAACUCUGAAAAACUAUUUGCUUUCGUUUUCU-UUGUGUCUAAAAGAUUAAUAUCGAUAUUUGUAGUGGGUUU-UUGCCCACUAUGCAUAGUUG
(((((..........(((...)))........)))))(((((..(((..(((...(((-((.......))))).......))).....(((((((((..-..))))))))))))))))). ( -23.07)
>consensus
UUU_____UUCCAUUUAC_______AUAACUCUGAAAAACUAUUUGCUUUCAUUUUCU_UUAUAUCUAAAAGAUUAAUUUCGAUAUUUGUAGUGGGUUC_UUGCCCACUAUGCAUAGUUG
............................................(((..............(((((.(((.......))).)))))..(((((((((.....))))))))))))...... (-11.79 = -12.35 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,200,548 – 19,200,662
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.36
Mean single sequence MFE -21.42
Consensus MFE -10.11
Energy contribution -12.43
Covariance contribution 2.31
Combinations/Pair 1.20
Mean z-score -2.48
Structure conservation index 0.47
SVM decision value 0.46
SVM RNA-class probability 0.745490
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19200548 114 - 22224390
CAUA-AUAUACUGU----AGUUGAGUUGAUAAAGUUAAUUCCACUAUGCAUAGUGUGCAACGAAACCACCACAAAUAUCGAAAUCAAUCUUUCACAUAUAA-GAAAAAUGAAUGCAAAUA
....-.......((----(((.((((((((...)))))))).)))))((((.(((((.........)).)))...........(((...((((........-))))..)))))))..... ( -15.80)
>DroSec_CAF1 22107 108 - 1
CACA-------UAU----AGUUGAGUUGAUAAAGUUAAUUCAACUAUGCAUAGUGGGCAACGAACCCACCACAAAUAUCGAAAUCAAUCUUUCAGAUAUAA-AGGAAAAGAAAGCAAAUA
....-------.((----((((((((((((...))))))))))))))((...(((((.......))))).....(((((((((......)))).)))))..-...........))..... ( -26.50)
>DroEre_CAF1 19607 119 - 1
CACAUAUAUAAUUUAAUCAGCUUUGCUAGUGAACUUGAUUCAACUAUGCAUAGUGGGCAA-AAUCCCACUGCAAAUAUCGAAAUUAAUCUUUUAGAUACAAAAGAAAAGGUAAGCAAAAA
...................((((((((((((((.....))).)))).)))(((((((...-...)))))))................((((((......))))))......))))..... ( -21.00)
>DroYak_CAF1 19584 118 - 1
CAAAUAUAUAAUUUAAUCAGCUUUGCUAGUUAAGUUGAUUCAACUAUGCAUAGUGGGCAA-AAACCCACUACAAAUAUCGAUAUUAAUCUUUUAGACACAA-AGAAAACGAAAGCAAAUA
..............(((((((((........)))))))))......(((.(((((((...-...)))))))................(((((.......))-)))........))).... ( -22.40)
>consensus
CACA_AUAUAAUUU____AGCUGAGCUAAUAAAGUUAAUUCAACUAUGCAUAGUGGGCAA_AAACCCACCACAAAUAUCGAAAUCAAUCUUUCAGAUACAA_AGAAAAAGAAAGCAAAUA
..................(((((((((((.....))))))))))).(((.(((((((.......)))))))........((((......))))....................))).... (-10.11 = -12.43 +   2.31)

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 12:45:27 2006