Locus 6986

Sequence ID X_DroMel_CAF1
Location 17,486,048 – 17,486,179
Length 131
Max. P 0.999966
window11411 window11412 window11413 window11414

overview

Window 1

Location 17,486,048 – 17,486,147
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 96.36
Mean single sequence MFE -25.18
Consensus MFE -24.34
Energy contribution -24.38
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.88
Structure conservation index 0.97
SVM decision value 4.98
SVM RNA-class probability 0.999966
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17486048 99 + 22224390
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUGUU
((((((.......((....))(((..........(((((....))))).(((((.....))))))))))))))..((((((.((....))))))))... ( -25.80)
>DroSec_CAF1 3937 99 + 1
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACUAAAUACUAAGCAAUUGUAUUUCUU
((((((.......((....))(((..........(((((....))))).(((((.....))))))))))))))..((((((.((....))))))))... ( -25.10)
>DroSim_CAF1 3719 99 + 1
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUCUU
((((((.......((....))(((..........(((((....))))).(((((.....))))))))))))))..((((((.((....))))))))... ( -25.20)
>DroEre_CAF1 4008 99 + 1
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUCGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAAUGUAUUUGUU
((((((.......((....))(((..........(((((....))))).(((((.....))))))))))))))..((((((.........))))))... ( -25.50)
>DroYak_CAF1 4081 98 + 1
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUUGAAGCCCGUGCUUCUUGGCUU-UCUUGCCGGUCACUUGACAAAAUACUAAGCAAAUGUAUUUGUU
((((((.......((....))(((..........(((((....))))).((((..-....)))))))))))))..((((((.........))))))... ( -24.30)
>consensus
UCAAGUUUAAUCCGCCUCGGCGACACUUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUGUU
((((((.......((....))(((..........(((((....))))).(((((.....))))))))))))))..((((((.........))))))... (-24.34 = -24.38 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,486,048 – 17,486,147
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 96.36
Mean single sequence MFE -26.00
Consensus MFE -24.34
Energy contribution -24.54
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.94
SVM decision value 2.97
SVM RNA-class probability 0.997940
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17486048 99 - 22224390
AACAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
...((((((.........))))))..((((((((((((((.....))))).(((((....)))))..........)))((....)).......)))))) ( -25.90)
>DroSec_CAF1 3937 99 - 1
AAGAAAUACAAUUGCUUAGUAUUUAGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
...((((((.........))))))..((((((((((((((.....))))).(((((....)))))..........)))((....)).......)))))) ( -26.60)
>DroSim_CAF1 3719 99 - 1
AAGAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
..(((((((.........))))))).((((((((((((((.....))))).(((((....)))))..........)))((....)).......)))))) ( -27.80)
>DroEre_CAF1 4008 99 - 1
AACAAAUACAUUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCGAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
...((((((.........))))))..((((((((((((((.....))))).(((((....)))))..........)))((....)).......)))))) ( -25.90)
>DroYak_CAF1 4081 98 - 1
AACAAAUACAUUUGCUUAGUAUUUUGUCAAGUGACCGGCAAGA-AAGCCAAGAAGCACGGGCUUCAAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
...((((((.........))))))..(((((((((((((....-..)))..(((((....)))))........).)))((....)).......)))))) ( -23.80)
>consensus
AACAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAAGUGUCGCCGAGGCGGAUUAAACUUGA
...((((((.........))))))..(((((((((.((((.....))))..(((((....)))))..........)))((....)).......)))))) (-24.34 = -24.54 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,486,074 – 17,486,179
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 95.43
Mean single sequence MFE -20.06
Consensus MFE -18.58
Energy contribution -18.50
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.14
Structure conservation index 0.93
SVM decision value 3.35
SVM RNA-class probability 0.999066
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17486074 105 + 22224390
UUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUGUUGUAUUUGCUUUAAUAAUUAUUUUCCCACCAUG
......(((((((..((((....(((((.....)))))(((....))).((((((.((....))))))))...))))..)))))))................... ( -20.50)
>DroSec_CAF1 3963 105 + 1
UUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACUAAAUACUAAGCAAUUGUAUUUCUUGUAUUUGCUUUAAUAAUUAUUUUCCCACCACG
......(((((((..((((.....((((.....))))((((....))))((((((.((....))))))))...))))..)))))))................... ( -19.60)
>DroSim_CAF1 3745 105 + 1
UUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUCUUGUAUUUGCUUUAAUAAUUAUUUUCCCACCACG
......(((((((..((((....(((((.....)))))(((....))).((((((.((....))))))))...))))..)))))))................... ( -19.90)
>DroEre_CAF1 4034 105 + 1
UUUUUCUCGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAAUGUAUUUGUUGUAUUUGCUUUAAUAAUUAUUUUCCCACCACG
........(((((....))))).(((((.....)))))(((....)))........(((((((((((.....)))))))))))...................... ( -21.50)
>DroYak_CAF1 4107 104 + 1
UUUUUCUUGAAGCCCGUGCUUCUUGGCUU-UCUUGCCGGUCACUUGACAAAAUACUAAGCAAAUGUAUUUGUUGUAUUUGUUUCAAUAAUUAUUUUCCCACCACG
......(((((((..((((....((((..-....))))(((....))).((((((.........))))))...))))..)))))))................... ( -18.80)
>consensus
UUUUUCUUGAAGCCCGUGCUUCUUGGCUUUUCCAGCCAGUCACUUGACAAAAUACUAAGCAAUUGUAUUUGUUGUAUUUGCUUUAAUAAUUAUUUUCCCACCACG
......(((((((..((((....(((((.....)))))(((....))).((((((.........))))))...))))..)))))))................... (-18.58 = -18.50 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,486,074 – 17,486,179
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 95.43
Mean single sequence MFE -21.40
Consensus MFE -17.24
Energy contribution -17.84
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.81
SVM decision value 0.43
SVM RNA-class probability 0.735189
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17486074 105 - 22224390
CAUGGUGGGAAAAUAAUUAUUAAAGCAAAUACAACAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAA
(((..(((.((((((.......((((((...............))))))..)))))).))).)))..(((((.....))))).(((((....)))))........ ( -22.96)
>DroSec_CAF1 3963 105 - 1
CGUGGUGGGAAAAUAAUUAUUAAAGCAAAUACAAGAAAUACAAUUGCUUAGUAUUUAGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAA
.((..(..((...(((.((((((.((((...............)))))))))).))).))..)..))(((((.....))))).(((((....)))))........ ( -21.66)
>DroSim_CAF1 3745 105 - 1
CGUGGUGGGAAAAUAAUUAUUAAAGCAAAUACAAGAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAA
.....(((.((((((.......((((((...............))))))..)))))).)))......(((((.....))))).(((((....)))))........ ( -20.76)
>DroEre_CAF1 4034 105 - 1
CGUGGUGGGAAAAUAAUUAUUAAAGCAAAUACAACAAAUACAUUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCGAGAAAAA
.................((((((.((((((...........))))))))))))((((.((.......(((((.....))))).(((((....))))))).)))). ( -23.30)
>DroYak_CAF1 4107 104 - 1
CGUGGUGGGAAAAUAAUUAUUGAAACAAAUACAACAAAUACAUUUGCUUAGUAUUUUGUCAAGUGACCGGCAAGA-AAGCCAAGAAGCACGGGCUUCAAGAAAAA
...(((.(...........((((...((((((((((((....)))).)).))))))..)))).).)))(((....-..)))..(((((....)))))........ ( -18.30)
>consensus
CGUGGUGGGAAAAUAAUUAUUAAAGCAAAUACAACAAAUACAAUUGCUUAGUAUUUUGUCAAGUGACUGGCUGGAAAAGCCAAGAAGCACGGGCUUCAAGAAAAA
.....(((.((((((.......((((((...............))))))..)))))).))).......((((.....))))..(((((....)))))........ (-17.24 = -17.84 +   0.60)

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 12:27:25 2006