Locus 1648

Sequence ID X_DroMel_CAF1
Location 4,664,612 – 4,664,765
Length 153
Max. P 0.988247
window2707 window2708 window2709 window2710

overview

Window 7

Location 4,664,612 – 4,664,732
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -26.45
Consensus MFE -23.64
Energy contribution -23.20
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.89
SVM decision value 1.08
SVM RNA-class probability 0.912548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4664612 120 + 22224390
AAACUAGGCUAAGCAAAAAGUGCUCGUUUAUUUGCACUCCGCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACACAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCA
...(((((..(((((...(((((..........)))))..(((..((....))))).........)))))..)))))............(((((((((...........))))))))).. ( -23.90)
>DroSec_CAF1 25945 120 + 1
AAACUGGGCUAAGCAAAAAGUGCUCGUUUAUUUGCACUCCGCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACACAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCA
...(..((..(((((...(((((..........)))))..(((..((....))))).........)))))..))..)............(((((((((...........))))))))).. ( -23.70)
>DroEre_CAF1 26700 120 + 1
AAACCAGGCUAUGCAAAAAGUGCACGUUUAUUUGCACUCCGCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCA
.......((.(((((...((((((........))))))..(((.......))))))))......(((((((........))))))))).(((((((((...........))))))))).. ( -25.80)
>DroYak_CAF1 23110 120 + 1
AAACUAGGCUGUGCAAAAAGUGCACGUUUAUUUGCAUUCCGCAGCGCACAUGCUGCAUCAUCAAAUGUUUUAUUUCGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCA
....(((((.(((((.....))))))))))(((((.....((((((....))))))........(((((((........))))))))))))(((((((...........))))))).... ( -32.40)
>consensus
AAACUAGGCUAAGCAAAAAGUGCACGUUUAUUUGCACUCCGCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCA
......(((((((((.....)))).....(((((((....(((..((....))))).........(((((.....))))).....))))))))))))......(((....)))....... (-23.64 = -23.20 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,664,612 – 4,664,732
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -36.93
Consensus MFE -33.47
Energy contribution -34.48
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.14
Structure conservation index 0.91
SVM decision value 1.80
SVM RNA-class probability 0.977901
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4664612 120 - 22224390
UGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGCGGAGUGCAAAUAAACGAGCACUUUUUGCUUAGCCUAGUUU
.((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))((...(((((((((..........))))))..)))...))....... ( -38.70)
>DroSec_CAF1 25945 120 - 1
UGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGCGGAGUGCAAAUAAACGAGCACUUUUUGCUUAGCCCAGUUU
.((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))((...(((((((((..........))))))..)))...))....... ( -38.70)
>DroEre_CAF1 26700 120 - 1
UGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUUUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGCGGAGUGCAAAUAAACGUGCACUUUUUGCAUAGCCUGGUUU
.((((((((((...........))))))))))(((((((.(((((((((.....)))))..)))).)))))))((..(((((((((((........)))))))..))))..))....... ( -34.70)
>DroYak_CAF1 23110 120 - 1
UGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUUUGUCGAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGCUGCGGAAUGCAAAUAAACGUGCACUUUUUGCACAGCCUAGUUU
.((((((((((...........))))))))))((..(((((((....)))))))(((((((..((((((......))))))..)).)))))....(((((.....))))).))....... ( -35.60)
>consensus
UGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGCGGAGUGCAAAUAAACGAGCACUUUUUGCAUAGCCUAGUUU
.((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))((...(((((((((..........))))))..)))...))....... (-33.47 = -34.48 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,664,652 – 4,664,765
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.56
Mean single sequence MFE -22.24
Consensus MFE -17.45
Energy contribution -17.70
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.54
Structure conservation index 0.78
SVM decision value 0.88
SVM RNA-class probability 0.874135
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4664652 113 + 22224390
GCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACACAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCAAUUAAAUUUCC-AUGGCGAA------UAAUAGAACUUAAA
....(((.((((.(((((.......(((((.....)))))....)))))(((((((((...........)))))))))............)-))))))..------.............. ( -21.90)
>DroSec_CAF1 25985 114 + 1
GCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACACAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCAAUUAAAUUUCCAAUGGCGAA------UAAUAAAACUUAAA
....(((.(((..(((((.......(((((.....)))))....)))))(((((((((...........)))))))))..............))))))..------.............. ( -19.60)
>DroEre_CAF1 26740 113 + 1
GCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCAAUUAAAUUUCU-AUGGCGAA------UAAUAAAACUUAGA
....(((.((((.(((((.......(((((.....)))))....)))))(((((((((...........)))))))))............)-))))))..------.............. ( -20.20)
>DroYak_CAF1 23150 119 + 1
GCAGCGCACAUGCUGCAUCAUCAAAUGUUUUAUUUCGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCAAUUAAAUUUCC-AUUGCGAGUUUCCACAAUGAAACUUAAA
((((((....))))))........(((((((........)))))))((((((((((((...........))))))))..............-.))))(((((((......)))))))... ( -27.26)
>consensus
GCAACGCACAUGCUGCAUCAUCAAAUGUUUUAUUUGGACAAAACAUGCAAAUUAGCCAAAAACGCUAAAUGGCUAAUUCAAUUAAAUUUCC_AUGGCGAA______UAAUAAAACUUAAA
....(((......(((((.......(((((.....)))))....)))))(((((((((...........))))))))).................)))...................... (-17.45 = -17.70 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,664,652 – 4,664,765
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.56
Mean single sequence MFE -30.30
Consensus MFE -26.77
Energy contribution -27.52
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.88
SVM decision value 2.11
SVM RNA-class probability 0.988247
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4664652 113 - 22224390
UUUAAGUUCUAUUA------UUCGCCAU-GGAAAUUUAAUUGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGC
.(((((((((((..------......))-)).)))))))..((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))....... ( -31.20)
>DroSec_CAF1 25985 114 - 1
UUUAAGUUUUAUUA------UUCGCCAUUGGAAAUUUAAUUGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGC
..............------..(((................((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))))).... ( -30.30)
>DroEre_CAF1 26740 113 - 1
UCUAAGUUUUAUUA------UUCGCCAU-AGAAAUUUAAUUGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUUUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGC
..............------..(((...-............((((((((((...........))))))))))(((((((.(((((((((.....)))))..)))).)))))))))).... ( -24.00)
>DroYak_CAF1 23150 119 - 1
UUUAAGUUUCAUUGUGGAAACUCGCAAU-GGAAAUUUAAUUGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUUUGUCGAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGCUGC
.((((((((((((((((....)))))))-.)))))))))..((((((((((...........))))))))))..(((((((((....)))))))))........(((((......))))) ( -35.70)
>consensus
UUUAAGUUUUAUUA______UUCGCCAU_GGAAAUUUAAUUGAAUUAGCCAUUUAGCGUUUUUGGCUAAUUUGCAUGUUGUGUCCAAAUAAAACAUUUGAUGAUGCAGCAUGUGCGUUGC
......................(((................((((((((((...........))))))))))(((((((((((((((((.....)))))..))))))))))))))).... (-26.77 = -27.52 +   0.75)

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 10:15:44 2006