Locus 999

Sequence ID 3L_DroMel_CAF1
Location 2,975,152 – 2,975,282
Length 130
Max. P 0.999483
window1546 window1547 window1548 window1549

overview

Window 6

Location 2,975,152 – 2,975,254
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 94.25
Mean single sequence MFE -21.76
Consensus MFE -18.46
Energy contribution -18.74
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.81
Structure conservation index 0.85
SVM decision value 1.46
SVM RNA-class probability 0.956285
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2975152 102 + 23771897
AUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUUGUGCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCA
..(((.((((....)))).....(((((.......)))))(((((((...(((((.(((((.............))))).)))))..)))))))...))).. ( -23.92)
>DroSec_CAF1 9418 100 + 1
AUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU--UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCA
..(((((((....(((((......)))))(((....--..)))))))((((((...(((((.............)))))......))))))......))).. ( -21.62)
>DroSim_CAF1 9361 100 + 1
AUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU--UGUGUAUGGACGAGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCA
..(((........(((((......)))))......(--(((((((((...(((((.(((((.............))))).)))))..))))))))))))).. ( -24.72)
>DroEre_CAF1 11690 100 + 1
AUGGGCCAUAAAAAUAUAAAAACGCAUAUACAAAUU--UCUGUAUGGAUGGGUUUACAGCUGAAGUGUUUCAAAAGCUGAAAACUACCCGUAUAUAAGCUCA
.(((((.......((((........)))).......--..(((((((...(((((.(((((.............))))).)))))..)))))))...))))) ( -21.42)
>DroYak_CAF1 9570 100 + 1
AUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU--UCUGUAUGAAUGGGUUUACAGCUGAAAUGUUUCAAAGGCUGCAAACUAUCCGUAUAUAAGCUCG
..(((........(((((......))))).......--..((((((....(((((.((((((((....)))...))))).)))))...))))))...))).. ( -17.10)
>consensus
AUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU__UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCA
..(((........(((((......)))))...........(((((((...(((((.(((((.............))))).)))))..)))))))...))).. (-18.46 = -18.74 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,975,152 – 2,975,254
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -24.66
Consensus MFE -22.00
Energy contribution -22.24
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -2.26
Structure conservation index 0.89
SVM decision value 3.22
SVM RNA-class probability 0.998780
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2975152 102 - 23771897
UGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGCACAAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAU
((.(((((((.((((((...((((((((...(((....)))))))))))))))))..((((((......)))))).................))))))))). ( -27.00)
>DroSec_CAF1 9418 100 - 1
UGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA--AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAU
((.(((((((.((((((...((((((((...(((....)))))))))))))))))..((((((.--...)))))).................))))))))). ( -26.90)
>DroSim_CAF1 9361 100 - 1
UGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACUCGUCCAUACACA--AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAU
.((((.((((((((((((((((((((((...(((....)))))))))))))).((......)).--.))))))))))).))))(((((....)))))..... ( -25.30)
>DroEre_CAF1 11690 100 - 1
UGAGCUUAUAUACGGGUAGUUUUCAGCUUUUGAAACACUUCAGCUGUAAACCCAUCCAUACAGA--AAUUUGUAUAUGCGUUUUUAUAUUUUUAUGGCCCAU
.((((.(((((((((((.((((.(((((...(((....)))))))).))))..))))....(..--..)..))))))).))))................... ( -18.40)
>DroYak_CAF1 9570 100 - 1
CGAGCUUAUAUACGGAUAGUUUGCAGCCUUUGAAACAUUUCAGCUGUAAACCCAUUCAUACAGA--AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAU
.((((.(((((((((((.(((((((((...((((....)))))))))))))...(((.....))--)))))))))))).))))(((((....)))))..... ( -25.70)
>consensus
UGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA__AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAU
.(.(((((((...((((.(((((((((...((((....)))))))))))))..))))(((((((....))))))).................)))))))).. (-22.00 = -22.24 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,975,182 – 2,975,282
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 93.72
Mean single sequence MFE -27.78
Consensus MFE -26.92
Energy contribution -27.04
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.97
SVM decision value 3.64
SVM RNA-class probability 0.999483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2975182 100 + 23771897
CAAAUUGUGCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAAUGGAUUCUGCCGAUUGGCUUAAAGGCU
........(((((((((...(((((.(((((.............))))).)))))..)))))).(((((.((((((......)).)))))))))..))). ( -28.62)
>DroSec_CAF1 9448 98 + 1
CAAAUU--UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCGAUUGGCUUAAAGGCU
......--..(((((((...(((((.(((((.............))))).)))))..)))))))((((((.(((((......))))).))))))...... ( -29.12)
>DroSim_CAF1 9391 98 + 1
CAAAUU--UGUGUAUGGACGAGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCGAUUGGCUUAAAGGCU
.....(--(((((((((...(((((.(((((.............))))).)))))..))))))))))(((.(((((......))))).)))......... ( -29.22)
>DroEre_CAF1 11720 98 + 1
CAAAUU--UCUGUAUGGAUGGGUUUACAGCUGAAGUGUUUCAAAAGCUGAAAACUACCCGUAUAUAAGCUCAUUCGAUUCUGCCGAUUGGCUUAAAGGCU
......--..(((((((...(((((.(((((.............))))).)))))..)))))))(((((.((.(((.......))).)))))))...... ( -26.52)
>DroYak_CAF1 9600 98 + 1
CAAAUU--UCUGUAUGAAUGGGUUUACAGCUGAAAUGUUUCAAAGGCUGCAAACUAUCCGUAUAUAAGCUCGUUGGAUGCUGCCGAUUGGCUUAAAGGCU
......--..((((((....(((((.((((((((....)))...))))).)))))...))))))((((((.(((((......))))).))))))...... ( -25.40)
>consensus
CAAAUU__UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCGAUUGGCUUAAAGGCU
..........(((((((...(((((.(((((.............))))).)))))..)))))))((((((.(((((......))))).))))))...... (-26.92 = -27.04 +   0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,975,182 – 2,975,282
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -23.34
Consensus MFE -18.98
Energy contribution -18.62
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.70
Structure conservation index 0.81
SVM decision value 0.74
SVM RNA-class probability 0.837486
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2975182 100 - 23771897
AGCCUUUAAGCCAAUCGGCAGAAUCCAUUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGCACAAUUUG
.........(((....))).......((((.((((((..((((((...((((((((...(((....)))))))))))))))))..))).))).))))... ( -28.40)
>DroSec_CAF1 9448 98 - 1
AGCCUUUAAGCCAAUCGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA--AAUUUG
.........(((....)))......(((....(((((..((((((...((((((((...(((....)))))))))))))))))..))).)).--...))) ( -23.50)
>DroSim_CAF1 9391 98 - 1
AGCCUUUAAGCCAAUCGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACUCGUCCAUACACA--AAUUUG
.((((.(((((..((.((......)).))..))))).....))))(((((((((((...(((....))))))))))))))............--...... ( -22.50)
>DroEre_CAF1 11720 98 - 1
AGCCUUUAAGCCAAUCGGCAGAAUCGAAUGAGCUUAUAUACGGGUAGUUUUCAGCUUUUGAAACACUUCAGCUGUAAACCCAUCCAUACAGA--AAUUUG
......(((((((.((((.....)))).)).))))).....((((.((((.(((((...(((....)))))))).))))..)))).......--...... ( -21.50)
>DroYak_CAF1 9600 98 - 1
AGCCUUUAAGCCAAUCGGCAGCAUCCAACGAGCUUAUAUACGGAUAGUUUGCAGCCUUUGAAACAUUUCAGCUGUAAACCCAUUCAUACAGA--AAUUUG
.........(((....)))(((.((....))))).......((((.(((((((((...((((....)))))))))))))..)))).......--...... ( -20.80)
>consensus
AGCCUUUAAGCCAAUCGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA__AAUUUG
.........(((....)))......................((((.(((((((((...((((....)))))))))))))..))))............... (-18.98 = -18.62 +  -0.36)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:34 2006