Locus 5161

Sequence ID 3R_DroMel_CAF1
Location 13,545,054 – 13,545,360
Length 306
Max. P 0.994210
window8432 window8433 window8434

overview

Window 2

Location 13,545,054 – 13,545,172
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.73
Mean single sequence MFE -29.98
Consensus MFE -21.42
Energy contribution -22.73
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -2.85
Structure conservation index 0.71
SVM decision value 2.46
SVM RNA-class probability 0.994210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13545054 118 - 27905053
UAUCACAGCAAGUCGAAAGCAGUGUACUGUAAUUCUC-GUAC-GUGUGCUGUUAAUGUCAGUAACAUUUUACUGUUAAGCGCAACUUCUCUUAUUAGCAAAUUGUGCAAGCAGUUCAAAA
....((((((.(((((..((((....)))).....))-).))-...)))))).(((((.....)))))..((((((..((((((.((((......)).)).)))))).))))))...... ( -25.70)
>DroSec_CAF1 19829 119 - 1
UAGCACACCUAGUUGAAAGCAGUGUACUGUAAAUAUC-GUACAGUGUGCUGUAAAUAUCAGUAACAUUUUACUGUUAAGCGCAACUUCUCUUAUUAGUAAAUUGUGCAAGCAGUGUACUA
(((.((((..........((((..(((((((......-.)))))))..))))........(((.((.(((((((.((((.(......).)))).))))))).))))).....)))).))) ( -31.50)
>DroSim_CAF1 16851 119 - 1
UAUCACAGCUAGUCGAAAGCAGUGUACUGUAAAUAUC-GUACAGUGUGCUGUAAAUAUCAGUAACAUUUUACUGUUAAGCGCAACUUCUCUUAUUAGUAAAUUGUGCAAGCAGUGCACUA
.......(((.......)))((((((((((.......-(((.(((((((((.......)))).))))).)))......((((((.((..((....))..))))))))..)))))))))). ( -33.30)
>DroYak_CAF1 24727 99 - 1
UAUCAAAAC-------AAGCAGUGUACUGUAAGUACCAGUACAUUGUGCUGUAAAUGUUACUAACAUUUUACUGUUAAACGCAACUUCU--------------GCGCAAGCAGUGCACUA
.......((-------(.(((((((((((.......)))))))))))..)))....(((..(((((......))))))))(((....((--------------((....))))))).... ( -29.40)
>consensus
UAUCACAGCUAGUCGAAAGCAGUGUACUGUAAAUAUC_GUACAGUGUGCUGUAAAUAUCAGUAACAUUUUACUGUUAAGCGCAACUUCUCUUAUUAGUAAAUUGUGCAAGCAGUGCACUA
..................((((..(((((((........)))))))..)))).................(((((((..((((((.................)))))).)))))))..... (-21.42 = -22.73 +   1.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,545,133 – 13,545,252
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.75
Mean single sequence MFE -32.02
Consensus MFE -22.10
Energy contribution -22.29
Covariance contribution 0.19
Combinations/Pair 1.16
Mean z-score -1.69
Structure conservation index 0.69
SVM decision value 0.19
SVM RNA-class probability 0.627145
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13545133 119 + 27905053
AC-GAGAAUUACAGUACACUGCUUUCGACUUGCUGUGAUAUCGAGCAUUCCUGGUAUCGAGUGCAAAAUGGCGGCAUUUUAAGUUCAAUUUAACACGAUUAGGUUGAGCUUGUCGAUUCU
..-.((((...(((....)))...(((((.((((((.((.....((((((........))))))...)).))))))....(((((((((((((.....)))))))))))))))))))))) ( -34.40)
>DroSec_CAF1 19909 119 + 1
AC-GAUAUUUACAGUACACUGCUUUCAACUAGGUGUGCUAUCGAGCAUUCAUGGUAUCGAAUGCAAAAUGGCGGCAUUUUAAGUUCAAUUUAUCACGAUUAGGUUGAGCUUGUCGGUUCU
.(-(((......((((((((...........)))))))))))).((((((........)))))).......(((((.....(((((((((((.......))))))))))))))))..... ( -32.80)
>DroSim_CAF1 16931 119 + 1
AC-GAUAUUUACAGUACACUGCUUUCGACUAGCUGUGAUAUCGAGCAUUCCUGGUAUCGAGUGCAAAAUGGCGGCAUUUUAAGUUCAAUUUAACACGAUUAGGUUGAGCUUGUCGGUUCU
.(-((((((.(((((................)))))))))))).((((((........)))))).......(((((.....((((((((((((.....)))))))))))))))))..... ( -32.69)
>DroYak_CAF1 24793 113 + 1
ACUGGUACUUACAGUACACUGCUU-------GUUUUGAUAUCGAGUAUUCCUGGUAUCGAGCAGAAAAUGGCGGCAUUUCUAGAUCAAUUUAACACGAUUAGAUUGAGCUUGCCAGUUUU
(((((((...........(((((.-------.(((((...((((.(((.....))))))).)))))...))))).......((.(((((((((.....))))))))).)))))))))... ( -28.20)
>consensus
AC_GAUAUUUACAGUACACUGCUUUCGACUAGCUGUGAUAUCGAGCAUUCCUGGUAUCGAGUGCAAAAUGGCGGCAUUUUAAGUUCAAUUUAACACGAUUAGGUUGAGCUUGUCGGUUCU
...((.............(((((........(((.((((((((........))))))))))).......))))).....((((((((((((((.....))))))))))))))))...... (-22.10 = -22.29 +   0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,545,252 – 13,545,360
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 91.20
Mean single sequence MFE -23.82
Consensus MFE -18.14
Energy contribution -19.08
Covariance contribution 0.94
Combinations/Pair 1.13
Mean z-score -1.53
Structure conservation index 0.76
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13545252 108 - 27905053
GCUGCCGCCUGCAACUCGCUCAGUUGCGUCACAAUAAGUAGCAACAAAAUAAAUAAAAUGCGACUCAUUAUGCGUUUAAUGAAACAUUUGUUGGCUUAUACUUAAAAA
..........((((((.....))))))......((((((..(((((((....((.(((((((........))))))).))......)))))))))))))......... ( -20.30)
>DroSec_CAF1 20028 108 - 1
GCUGCAGCCUGCAACUCGCCCAGUUGCGUUACAAUAAGUAGCAACGAAAUAAAUAAAAUGCGACUCAUUUUGCGUUUAAGGAAACAUUUGUUGGCUUAUACUUAAAAA
.....((((.((((((.....))))))(((((.....)))))((((((.......((((((((......))))))))..(....).))))))))))............ ( -27.20)
>DroSim_CAF1 17050 108 - 1
GCUGCAGCCUGCAACUCGCCCAGUUGCGUCACAAUAAGUAGCAACGAAAUAAAUAAAAUGCGACUCAUUUUGCGUUUAAUGAAACAUUUGUUGGCUUAUACUUAUAAA
(.((((((..((.....))...)))))).)...(((((((.(((((((....((.((((((((......)))))))).))......))))))).....)))))))... ( -23.30)
>DroYak_CAF1 24906 108 - 1
GCUGCCGCCUGCAACUCGCCGAGUUGUGUCACAAGUAGCAGCAACAAAAUAAAUAAAGUGCGACACAUUAUGCCUUUAAUGAAACAUUUGUUGGCGUAUACUAAAAAU
(((((..(.((((((((...)))))).....)).)..)))))...............(((...)))..((((((..(((........)))..)))))).......... ( -24.50)
>consensus
GCUGCAGCCUGCAACUCGCCCAGUUGCGUCACAAUAAGUAGCAACAAAAUAAAUAAAAUGCGACUCAUUAUGCGUUUAAUGAAACAUUUGUUGGCUUAUACUUAAAAA
((....))..((((((.....))))))......((((((..(((((((....((.((((((((......)))))))).))......)))))))))))))......... (-18.14 = -19.08 +   0.94)

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 11:48:03 2006