Locus 365

Sequence ID X_DroMel_CAF1
Location 1,115,310 – 1,115,445
Length 135
Max. P 0.999958
window547 window548 window549

overview

Window 7

Location 1,115,310 – 1,115,418
Length 108
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 94.06
Mean single sequence MFE -33.44
Consensus MFE -34.90
Energy contribution -35.18
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -2.25
Structure conservation index 1.04
SVM decision value 4.88
SVM RNA-class probability 0.999958
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1115310 108 + 22224390
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------UGAGGACGUUGCCGGGA-UCUCU
..(((((.....(((....)))..)))))................(((((((((......((((((((...)))))))).((((..-------...))))))))))))).-..... ( -37.20)
>DroSec_CAF1 11922 108 + 1
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGCCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGACGUUGCCGGGA-UCUCU
..(((((.....(((....)))..)))))................((((.((((......((((((((...)))))))).((((..-------...)))))))).)))).-..... ( -30.10)
>DroSim_CAF1 12529 108 + 1
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGACGUUGCCGGGA-UCUCU
..(((((.....(((....)))..)))))................(((((((((......((((((((...)))))))).((((..-------...))))))))))))).-..... ( -37.20)
>DroEre_CAF1 13095 116 + 1
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUUUGUCCUACGAGGACGUCGUCGGGAAUCUUU
..(((((.....(((....)))..)))))................((((((.((...(((((((((((...)))))).)))))....((((.....)))))).))))))....... ( -32.90)
>DroYak_CAF1 12100 107 + 1
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGGCGUCGUCGGGA-UCUU-
..(((((.....(((....)))..)))))................((((((.((......((((((((...)))))))).((((..-------...)))))).)))))).-....- ( -29.80)
>consensus
GCUGUAAUAUAAUCCUAAUGGAAUUUACACUCAAACUUUACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU_______CGAGGACGUUGCCGGGA_UCUCU
..(((((.....(((....)))..)))))................(((((((((......((((((((...)))))))).((((((........)))))))))))))))....... (-34.90 = -35.18 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,115,310 – 1,115,418
Length 108
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 94.06
Mean single sequence MFE -30.76
Consensus MFE -25.76
Energy contribution -26.36
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.84
SVM decision value 0.13
SVM RNA-class probability 0.598438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1115310 108 - 22224390
AGAGA-UCCCGGCAACGUCCUCA-------AAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGCCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
...((-(((.((((((((((...-------..))))..(((((((...))))))).......)))))).)).))).......((((((((((..(((....)))))))))).))). ( -33.80)
>DroSec_CAF1 11922 108 - 1
AGAGA-UCCCGGCAACGUCCUCG-------AAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGGCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
.....-(((.(....)((((...-------..))))...)))...((((((.(((.((((....))))))))))))).....((((((((((..(((....)))))))))).))). ( -32.40)
>DroSim_CAF1 12529 108 - 1
AGAGA-UCCCGGCAACGUCCUCG-------AAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGCCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
...((-(((.((((((((((...-------..))))..(((((((...))))))).......)))))).)).))).......((((((((((..(((....)))))))))).))). ( -33.80)
>DroEre_CAF1 13095 116 - 1
AAAGAUUCCCGACGACGUCCUCGUAGGACAAAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGCCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
...(((.((.(.((((((((.....))))...((....(((((((...)))))))..))...)))).).)).))).......((((((((((..(((....)))))))))).))). ( -29.40)
>DroYak_CAF1 12100 107 - 1
-AAGA-UCCCGACGACGCCCUCG-------AAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGCCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
-..((-(((..(.((.((.((((-------((..(((((((((((...))))))).(((..........))).))))....)))))).))....))..)..))))).......... ( -24.40)
>consensus
AGAGA_UCCCGGCAACGUCCUCG_______AAGGACAAAGGACACGCAGUGUCCUCGCCAUUGUUGCCAGGCAUUGUAAAGUUUGAGUGUAAAUUCCAUUAGGAUUAUAUUACAGC
..........(((...(((((..........)))))..(((((((...))))))).)))...((((.(((((........)))))(((((((..(((....)))))))))).)))) (-25.76 = -26.36 +   0.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,115,348 – 1,115,445
Length 97
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 83.44
Mean single sequence MFE -38.08
Consensus MFE -32.30
Energy contribution -32.58
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.85
SVM decision value 0.91
SVM RNA-class probability 0.878783
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1115348 97 + 22224390
UACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------UGAGGACGUUGCCGGGA-UCUCUCUGC-UGGCGAAAGGAAGCAAUAGCGCC------------
.......(((((((((......((((((((...)))))))).((((..-------...))))))))))))).-......(((-(..(....)..))))........------------ ( -39.80)
>DroSec_CAF1 11960 97 + 1
UACAAUGCCUGCCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGACGUUGCCGGGA-UCUCUCUUC-UGGCGAAAGGAAGCAAAAGCGCC------------
.....(((((((((....)))).))).)).(((...((((((((((..-------...))))..((((((((-......)))-))))))))))).)))........------------ ( -35.00)
>DroSim_CAF1 12567 97 + 1
UACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGACGUUGCCGGGA-UCUCUCUUC-UGGCGAAAGGAAGCAAUAGCGCC------------
.......(((((((((......((((((((...)))))))).((((..-------...))))))))))))).-.........-.((((...(....).....))))------------ ( -37.10)
>DroEre_CAF1 13133 118 + 1
UACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUUUGUCCUACGAGGACGUCGUCGGGAAUCUUUCUGCUGUGCGAAAGGAAGCAAUAUAGGCAGCAAUGGAGAG
.......((((((.((...(((((((((((...)))))).)))))....((((.....)))))).))))))..((((((((((.(((........))).....)))))....))))). ( -40.00)
>DroYak_CAF1 12138 100 + 1
UACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU-------CGAGGGCGUCGUCGGGA-UCUU--CGCCUGGCGAAAGGAAGCAAUUGAGGCAACC--------
.....((((((....)...((((((((..((((((((((((.......-------.))))))).)).)))..-))))--))))..((........)).....)))))...-------- ( -38.50)
>consensus
UACAAUGCCUGGCAACAAUGGCGAGGACACUGCGUGUCCUUUGUCCUU_______CGAGGACGUUGCCGGGA_UCUCUCUGC_UGGCGAAAGGAAGCAAUAGCGCC____________
.......(((((((((......((((((((...)))))))).((((((........)))))))))))))))..............((........))..................... (-32.30 = -32.58 +   0.28)

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 09:42:40 2006