Locus 5329

Sequence ID X_DroMel_CAF1
Location 13,915,773 – 13,915,923
Length 150
Max. P 0.982159
window8626 window8627 window8628

overview

Window 6

Location 13,915,773 – 13,915,888
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.26
Mean single sequence MFE -30.56
Consensus MFE -22.46
Energy contribution -21.86
Covariance contribution -0.60
Combinations/Pair 1.18
Mean z-score -2.70
Structure conservation index 0.73
SVM decision value 1.24
SVM RNA-class probability 0.934274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13915773 115 - 22224390
-----AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUCCGUGGAUGUUGCAUCCAUUGCUGCGGCGGGGGGAAAAUAUGCAUGAAAGCGAAUAAAAUAAAUAAAUUAUGGAAAAAUCGA
-----...((.((((((.((((((.((((.....))))...((((((...)))))))))))).)))))).))......(((......))).............................. ( -31.70)
>DroSec_CAF1 16085 115 - 1
-----AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUUCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUCCAUGAAAGCGACUAAAAUAAAUAAAUUAUAGAUAAAUCGA
-----...((((.(((....)))..............((((((((((((...(((.((((....)))))))...)))))))))))).))))(((.(((......))).)))......... ( -33.80)
>DroSim_CAF1 38053 113 - 1
-----AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUUCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUCCAUGAAAGCGACUAAAAUAAAUAAAUUAUGGAU--AUCGA
-----...((((.(((....)))..............((((((((((((...(((.((((....)))))))...)))))))))))).))))(((.(((......))).)))..--..... ( -33.50)
>DroEre_CAF1 12000 120 - 1
UCGAAAAAUCGCCUGCCAUCGCAAAAUUGUACAACAGUCCGUAAAUGUUGCAUCCAUCGCUUCGGUGGGGGAAAAAUGUGCAUGAAAGCGACCAAAAUAAAUAAAUUAUGGAUAAAUCGA
((((....((((.(((....)))....((((((....((((((.....))).(((((((...))))))))))....)))))).....))))(((.(((......))).))).....)))) ( -28.90)
>DroYak_CAF1 26743 114 - 1
-----AAAUCGCCUGCCACAGCAAAAUUGCACAACAGUCCGUGGAUGUUGCAUCCAGCGCUUCGGUGGGGGAA-AAUAUGCAUGAAAGCGACUAAAAUAAAUAAAUUAUGGAUAAAUCGA
-----...(((((((.....(((....)))....)))..((((.(((((...(((..(((....)))..))).-))))).))))...))))(((.(((......))).)))......... ( -24.90)
>consensus
_____AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUCCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUGCAUGAAAGCGACUAAAAUAAAUAAAUUAUGGAUAAAUCGA
........((((.(((....)))................((((.(((((...(((..(((....)))..)))..))))).))))...))))............................. (-22.46 = -21.86 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,915,813 – 13,915,923
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.37
Mean single sequence MFE -36.89
Consensus MFE -23.70
Energy contribution -23.74
Covariance contribution 0.04
Combinations/Pair 1.18
Mean z-score -2.14
Structure conservation index 0.64
SVM decision value 0.12
SVM RNA-class probability 0.593845
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13915813 110 + 22224390
CAUAUUUUCCCCCCGCCGCAGCAAUGGAUGCAACAUCCACGGACUGUUUUACAAUUUUGCUGUGGCAGGCGAUUU-------U-CCGAUU-UUCCACCGGCCUUCC-AUUCGCUGGGGGA
.........(((((((((((((((((((((...)))))).....((.....))...)))))))))).(((((...-------.-(((...-......)))......-..)))))))))). ( -41.90)
>DroSec_CAF1 16125 110 + 1
GAUAUUUUCCCCCCGCCGAAGCGAUGGAUGCAACAUCCACGAACUGUUUUACAAUUUUGCUGUGGCAGGCGAUUU-------U-CCGAUUUUUCCACCGGCCUUCC-AUCCGCCGGGG-C
..........((((((((.(((((((((((...)))))).....((.....))...))))).)))).((((....-------.-..((....))....((....))-...))))))))-. ( -31.70)
>DroSim_CAF1 38091 109 + 1
GAUAUUUUCCCCCCGCCGAAGCGAUGGAUGCAACAUCCACGAACUGUUUUACAAUUUUGCUGUGGCAGGCGAUUU-------U-CCGAUU-UUCCACCGGCCUUCC-AUCCGGCGGGG-C
..........((((((((.(((((((((((...)))))).....((.....))...)))))((((.((((.....-------.-......-........)))).))-)).))))))))-. ( -36.35)
>DroEre_CAF1 12040 117 + 1
CACAUUUUUCCCCCACCGAAGCGAUGGAUGCAACAUUUACGGACUGUUGUACAAUUUUGCGAUGGCAGGCGAUUUUUCGAUUUUUCGAUU-UUCCACCGGCCUUCC-AUCCGCCGGGG-G
.........(((((..((..((((..(.(((((((.........))))))))....))))(((((.((((((....((((....))))..-.)).....)))).))-)))))..))))-) ( -36.30)
>DroYak_CAF1 26783 110 + 1
CAUAUU-UUCCCCCACCGAAGCGCUGGAUGCAACAUCCACGGACUGUUGUGCAAUUUUGCUGUGGCAGGCGAUUU-------UGUCGAUU-UUUCACCGGCCUUUCAAUUCGCUGGGG-G
......-..((((((.((((..(((((..((((((((....)).))))))((((..(((((......)))))..)-------))).....-.....))))).......)))).)))))-) ( -38.20)
>consensus
CAUAUUUUCCCCCCGCCGAAGCGAUGGAUGCAACAUCCACGGACUGUUUUACAAUUUUGCUGUGGCAGGCGAUUU_______U_CCGAUU_UUCCACCGGCCUUCC_AUCCGCCGGGG_C
..........((((((((.(((((((((((...)))))).....((.....))...))))).)))).((((.............(((..........)))..........)))))))).. (-23.70 = -23.74 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,915,813 – 13,915,923
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.37
Mean single sequence MFE -41.46
Consensus MFE -30.08
Energy contribution -30.28
Covariance contribution 0.20
Combinations/Pair 1.17
Mean z-score -3.03
Structure conservation index 0.73
SVM decision value 1.91
SVM RNA-class probability 0.982159
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13915813 110 - 22224390
UCCCCCAGCGAAU-GGAAGGCCGGUGGAA-AAUCGG-A-------AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUCCGUGGAUGUUGCAUCCAUUGCUGCGGCGGGGGGAAAAUAUG
((((((.((((..-......(((((....-.)))))-.-------...)))).((((.((((((.((((.....))))...((((((...)))))))))))).))))))))))....... ( -43.70)
>DroSec_CAF1 16125 110 - 1
G-CCCCGGCGGAU-GGAAGGCCGGUGGAAAAAUCGG-A-------AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUUCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUC
.-(((((((((.(-((....(((((......)))))-.-------...))).))))).......(((((.....))))).(((((((...)))))))(((....)))))))......... ( -38.60)
>DroSim_CAF1 38091 109 - 1
G-CCCCGCCGGAU-GGAAGGCCGGUGGAA-AAUCGG-A-------AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUUCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUC
.-(((((((((((-((.((((((((....-.))))(-.-------....))))).)))..((..(((((.....))))).(((((((...))))))).)))))))))))).......... ( -42.10)
>DroEre_CAF1 12040 117 - 1
C-CCCCGGCGGAU-GGAAGGCCGGUGGAA-AAUCGAAAAAUCGAAAAAUCGCCUGCCAUCGCAAAAUUGUACAACAGUCCGUAAAUGUUGCAUCCAUCGCUUCGGUGGGGGAAAAAUGUG
(-(((((.(((((-(((.(((.(((((..-..((((....))))....))))).)))...((((.....(((........)))....)))).))))))....)).))))))......... ( -43.60)
>DroYak_CAF1 26783 110 - 1
C-CCCCAGCGAAUUGAAAGGCCGGUGAAA-AAUCGACA-------AAAUCGCCUGCCACAGCAAAAUUGCACAACAGUCCGUGGAUGUUGCAUCCAGCGCUUCGGUGGGGGAA-AAUAUG
(-(((((.(((((((...(((.(((((..-........-------...))))).)))...(((....)))....)))).((((((((...)))))).))..))).))))))..-...... ( -39.32)
>consensus
C_CCCCGGCGGAU_GGAAGGCCGGUGGAA_AAUCGG_A_______AAAUCGCCUGCCACAGCAAAAUUGUAAAACAGUCCGUGGAUGUUGCAUCCAUCGCUUCGGCGGGGGGAAAAUAUG
..((((.((((((.(...(((.(((((.....................))))).)))...(((....)))....).))))))(((((...)))))..(((....)))))))......... (-30.08 = -30.28 +   0.20)

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 11:45:04 2006