Locus 5614

Sequence ID X_DroMel_CAF1
Location 14,477,283 – 14,477,431
Length 148
Max. P 0.998720
window9118 window9119 window9120

overview

Window 8

Location 14,477,283 – 14,477,391
Length 108
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 87.64
Mean single sequence MFE -28.75
Consensus MFE -22.52
Energy contribution -23.36
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.46
Structure conservation index 0.78
SVM decision value -0.01
SVM RNA-class probability 0.526289
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14477283 108 - 22224390
UGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUACACUCGGAAAAC-----UCAAAGUUCGCCCUAAAAUUUAUAUUUAAA--CCA
(((((.(((((((........))))))).(..(.((((....)))).)..).........)))))...((..(((-----.....)))..))..................--... ( -26.00)
>DroSec_CAF1 2499 107 - 1
UGUGGAUGACGCCUCCCAGUAGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAA-ACCUGCACUCGGAAAAC-----UCAAAGUUCGCCCUAAAAUUUAUAUUUACA--AUA
((((((((((((((......)))))))..........((((.((((((((((.....-...)))))...((....-----))....)))))))))........)))))))--... ( -31.40)
>DroSim_CAF1 8997 108 - 1
UGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC-----UCAAAGUUCGCCCUAAAAUUUAUAUUUACA--AUA
(((((((((((((........))))))..........((((.((((((((((.........)))))...((....-----))....)))))))))........)))))))--... ( -29.70)
>DroEre_CAF1 130 113 - 1
UGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAAGCUACACUCAGAAAACUUCACUCGAACUUCUCCCCAAAAGUUAUAGCUUGG--GCA
((((..(((((((........)))))))..))))......(.(((((((........................))))))).).........((((..(((....))))))--).. ( -28.26)
>DroYak_CAF1 5145 110 - 1
CGUGAAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC-----UCGAACUUCUCCCUGCAAGUUAUAUUUAAAAAAAA
.(((..(((((((........)))))))..)))....((((.(.((((((((.........)))..((((.....-----))))))))).))))).................... ( -28.40)
>consensus
UGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC_____UCAAAGUUCGCCCUAAAAUUUAUAUUUAAA__ACA
.(((..(((((((........)))))))..)))....((((.((((((((((.........)))))...((.........))....))))))))).................... (-22.52 = -23.36 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,477,316 – 14,477,431
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 94.11
Mean single sequence MFE -27.82
Consensus MFE -26.58
Energy contribution -26.02
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.32
Structure conservation index 0.96
SVM decision value 1.17
SVM RNA-class probability 0.924928
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14477316 115 + 22224390
GUUUUCCGAGUGUAGGUUUUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCGACUGAGAGGCGUCAUCCACAUCGUUUUCUUCUUUUUUUUUGCCACUUUGCGCAACUUCUU
.......((((((((.......)))))))).......((((((....(((((((........)))))))....))))))..............(((((.....).))))...... ( -26.60)
>DroSec_CAF1 2532 109 + 1
GUUUUCCGAGUGCAGGU-UUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCUACUGGGAGGCGUCAUCCACAUCAUUUUCU-----UUUUUGGCCACUUUGCGCAACUUCUU
.........((((((((-.(((.......))).))))((((((....((((((((......))))))))....)))))).....-----..............))))........ ( -31.10)
>DroSim_CAF1 9030 110 + 1
GUUUUCCGAGUGCAGGUUUUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCGACUGAGAGGCGUCAUCCACAUCGUUUUCU-----UUUUUGGCCACUUUGCGCAACUUCUU
.........((((((((..(((.......))).))))((((((....(((((((........)))))))....)))))).....-----..............))))........ ( -28.00)
>DroEre_CAF1 168 109 + 1
GUUUUCUGAGUGUAGCUUUUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCGACUGAGAGGCGUCAUCCACAUCGUUUUCU-----U-UUUGGCCACUUUGCGCAACUUCUU
.......(((((((((....).)))))))).......((((((....(((((((........)))))))....)))))).....-----.-.(((((......)).)))...... ( -25.80)
>DroYak_CAF1 5180 110 + 1
GUUUUCCGAGUGCAGGUUUUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCGACUGAGAGGCGUCAUUCACGUCGUUUUCU-----UUUUUGGCCACUUUGCGCAACUUCUU
.........((((((((..(((.......))).))))((((((....(((((((........)))))))....)))))).....-----..............))))........ ( -27.60)
>consensus
GUUUUCCGAGUGCAGGUUUUGAUUGCACUUCACACCUAUGAUGCACCUGACGCCGACUGAGAGGCGUCAUCCACAUCGUUUUCU_____UUUUUGGCCACUUUGCGCAACUUCUU
.......((((((((.......)))))))).......((((((....(((((((........)))))))....))))))................(((.....).))........ (-26.58 = -26.02 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,477,316 – 14,477,431
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 94.11
Mean single sequence MFE -31.12
Consensus MFE -28.64
Energy contribution -29.08
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.92
SVM decision value 3.20
SVM RNA-class probability 0.998720
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14477316 115 - 22224390
AAGAAGUUGCGCAAAGUGGCAAAAAAAAAGAAGAAAACGAUGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUACACUCGGAAAAC
.....((..(.....)..)).................((((((((.(((((((........))))))).(..(.((((....)))).)..).........))))).)))...... ( -31.50)
>DroSec_CAF1 2532 109 - 1
AAGAAGUUGCGCAAAGUGGCCAAAAA-----AGAAAAUGAUGUGGAUGACGCCUCCCAGUAGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAA-ACCUGCACUCGGAAAAC
.....((..(.....)..))......-----.....((((((((..((((((((......))))))))..))))))))...(.(((.(((((.....-...)))))))).).... ( -34.90)
>DroSim_CAF1 9030 110 - 1
AAGAAGUUGCGCAAAGUGGCCAAAAA-----AGAAAACGAUGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC
.....((..(.....)..))......-----.......((((((..(((((((........)))))))..)))))).....(.(((.(((((.........)))))))).).... ( -31.50)
>DroEre_CAF1 168 109 - 1
AAGAAGUUGCGCAAAGUGGCCAAA-A-----AGAAAACGAUGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAAGCUACACUCAGAAAAC
.....((..(.....)..))....-.-----.......((((((..(((((((........)))))))..))))))...((((((....((........))))))))........ ( -29.30)
>DroYak_CAF1 5180 110 - 1
AAGAAGUUGCGCAAAGUGGCCAAAAA-----AGAAAACGACGUGAAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC
.....((..(.....)..))......-----......(((.(((..(((((((........))))))).(..(.((((....)))).)..)............))))))...... ( -28.40)
>consensus
AAGAAGUUGCGCAAAGUGGCCAAAAA_____AGAAAACGAUGUGGAUGACGCCUCUCAGUCGGCGUCAGGUGCAUCAUAGGUGUGAAGUGCAAUCAAAACCUGCACUCGGAAAAC
.....((..(.....)..))..................((((((..(((((((........)))))))..)))))).....(.(((.(((((.........)))))))).).... (-28.64 = -29.08 +   0.44)

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 11:52:20 2006