Locus 6288

Sequence ID 2R_DroMel_CAF1
Location 19,739,720 – 19,739,850
Length 130
Max. P 0.993480
window10051 window10052 window10053 window10054

overview

Window 1

Location 19,739,720 – 19,739,822
Length 102
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 88.31
Mean single sequence MFE -37.73
Consensus MFE -28.61
Energy contribution -30.05
Covariance contribution 1.44
Combinations/Pair 1.12
Mean z-score -3.07
Structure conservation index 0.76
SVM decision value 1.65
SVM RNA-class probability 0.969814
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19739720 102 + 20766785
AAACUUU-UUUUGGCCAAAUGGAAUGGAAUGGGUAGCUAUAGCU------GUAGCUAUAGCUUUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCCCCAAAAAGUGG
...(.((-(((((((((.......)))...(((((((((((((.------...))))))))...((((((((((...)))))).))))....))))).)))))))).). ( -38.00)
>DroSec_CAF1 49378 101 + 1
AAACUUU-UUUUGGCCAAAUGGAAUGGAAUGGGUACCUAUAGCU------GCAGCUAUAGCUUUGGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCC-CGAAAAGUGG
..(((((-((.((((((...((......((((....)))).(((------(((((((......)))))))))))).))))))..(((......)))..-.))))))).. ( -35.40)
>DroEre_CAF1 49605 102 + 1
AAACUUUUUUUUGGCCAAAUGGAAUGGAAUGGGUAGCUAAAGCU------AUAGCUGCAGCUAUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCC-CCGAAAAAGUGG
...(.(((((((((((....))...((...((..(((((.((((------(((((....)))))))))((((((...)))))))))))..))..))-))))))))).). ( -40.20)
>DroYak_CAF1 50081 108 + 1
AAACUUU-UUUUGGCCAAAUGGAAUGGAAUGGGUAGCUAAAGCUUCAGCAAUAGCUAUAGCUGUAGCUGUAGCCCCUGGCUGCUGGUACUCCUGCCCCCGAAAAUGUGG
..((..(-((((((......((...(((((.((((((((..(((.((((.(((((....))))).)))).)))...)))))))).))..)))..)).))))))).)).. ( -37.30)
>consensus
AAACUUU_UUUUGGCCAAAUGGAAUGGAAUGGGUAGCUAAAGCU______AUAGCUAUAGCUUUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCCCCAAAAAGUGG
..(((((.....(((.....(((.........((((((((((((........))))))))))))((((((((((...)))))).)))).))).)))......))))).. (-28.61 = -30.05 +   1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,739,720 – 19,739,822
Length 102
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 88.31
Mean single sequence MFE -34.70
Consensus MFE -26.66
Energy contribution -27.72
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.80
Structure conservation index 0.77
SVM decision value 1.56
SVM RNA-class probability 0.964082
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19739720 102 - 20766785
CCACUUUUUGGGGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAAAGCUAUAGCUAC------AGCUAUAGCUACCCAUUCCAUUCCAUUUGGCCAAAA-AAAGUUU
....((((((((((((.((....)).((((((...)))))).))...(((((((((...------.))))))))).)))...(((.......)))))))))-)...... ( -37.60)
>DroSec_CAF1 49378 101 - 1
CCACUUUUCG-GGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCCAAAGCUAUAGCUGC------AGCUAUAGGUACCCAUUCCAUUCCAUUUGGCCAAAA-AAAGUUU
..((((((.(-(((((.((....)).((((((...)))))).)))....(((((((...------.)))))))...)))...(((.......))).....)-))))).. ( -33.10)
>DroEre_CAF1 49605 102 - 1
CCACUUUUUCGG-GGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAUAGCUGCAGCUAU------AGCUUUAGCUACCCAUUCCAUUCCAUUUGGCCAAAAAAAAGUUU
..(((((((...-(((.((..(((..((((((...))))))(((((((((....)))))------))))...)))..))....((.......)))))...))))))).. ( -36.50)
>DroYak_CAF1 50081 108 - 1
CCACAUUUUCGGGGGCAGGAGUACCAGCAGCCAGGGGCUACAGCUACAGCUAUAGCUAUUGCUGAAGCUUUAGCUACCCAUUCCAUUCCAUUUGGCCAAAA-AAAGUUU
..........((((((..((((..((((((.....(((((.(((....))).))))).))))))..))))..))).)))...(((.......)))......-....... ( -31.60)
>consensus
CCACUUUUUCGGGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAAAGCUAUAGCUAC______AGCUAUAGCUACCCAUUCCAUUCCAUUUGGCCAAAA_AAAGUUU
..(((((......(((.((((.....((((((...))))))......((((((((((........))))))))))..........)))).....))).....))))).. (-26.66 = -27.72 +   1.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,739,749 – 19,739,850
Length 101
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 88.62
Mean single sequence MFE -32.43
Consensus MFE -28.66
Energy contribution -29.10
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.79
Structure conservation index 0.88
SVM decision value 2.40
SVM RNA-class probability 0.993480
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19739749 101 + 20766785
GGGUAGCUAUAGCU------GUAGCUAUAGCUUUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCCCCAAAAAGUGGAAACUACGCUAAAAGCUUAAACAAAACC
(((((((((((((.------...))))))))...((((((((((...)))))).))))....)))))........(((....).))((.....))............ ( -33.70)
>DroSec_CAF1 49407 100 + 1
GGGUACCUAUAGCU------GCAGCUAUAGCUUUGGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCC-CGAAAAGUGGAAACUACGCUAAAAGCUUAAACAAAACC
(((..((....(((------(((((((......))))))))))....)).....(((......)))))-).....(((....).))((.....))............ ( -29.90)
>DroEre_CAF1 49635 100 + 1
GGGUAGCUAAAGCU------AUAGCUGCAGCUAUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCC-CCGAAAAAGUGGAAACUACGCUAAAAGCUUAAACAAAACC
(((((((((.((((------(((((....)))))))))((((((...))))))))))).....)))-).......(((....).))((.....))............ ( -33.70)
>DroYak_CAF1 50110 107 + 1
GGGUAGCUAAAGCUUCAGCAAUAGCUAUAGCUGUAGCUGUAGCCCCUGGCUGCUGGUACUCCUGCCCCCGAAAAUGUGGAAACUACGCUAAAAGCUUAAACAAAACC
(((((((((..(((.((((.(((((....))))).)))).)))...))))))).((((....)))).))......(((....).))((.....))............ ( -32.40)
>consensus
GGGUAGCUAAAGCU______AUAGCUAUAGCUUUAGCUGUAGCCCCUGGCUACUGGCUCUCCUGCCCCCCAAAAAGUGGAAACUACGCUAAAAGCUUAAACAAAACC
.(((((((((((((........)))))))))).((((.((((((...)))))).(((......))).........(((....).))))))..............))) (-28.66 = -29.10 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,739,749 – 19,739,850
Length 101
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 88.62
Mean single sequence MFE -34.45
Consensus MFE -29.05
Energy contribution -30.18
Covariance contribution 1.13
Combinations/Pair 1.07
Mean z-score -1.87
Structure conservation index 0.84
SVM decision value 0.87
SVM RNA-class probability 0.870851
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19739749 101 - 20766785
GGUUUUGUUUAAGCUUUUAGCGUAGUUUCCACUUUUUGGGGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAAAGCUAUAGCUAC------AGCUAUAGCUACCC
((((((.((...((.....))...((..((.(.....)))..)))).)))))).((((((...))))))......(((((((((...------.))))))))).... ( -36.70)
>DroSec_CAF1 49407 100 - 1
GGUUUUGUUUAAGCUUUUAGCGUAGUUUCCACUUUUCG-GGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCCAAAGCUAUAGCUGC------AGCUAUAGGUACCC
((((((.((...((.....))...((..((.......)-)..)))).)))))).((((((...))))))........(((((((...------.)))))))...... ( -31.90)
>DroEre_CAF1 49635 100 - 1
GGUUUUGUUUAAGCUUUUAGCGUAGUUUCCACUUUUUCGG-GGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAUAGCUGCAGCUAU------AGCUUUAGCUACCC
(((...(((.(((((..((((((((((.((........))-(((.((....)).((((((...)))))).)))..)))))).)))).------))))).))).))). ( -34.10)
>DroYak_CAF1 50110 107 - 1
GGUUUUGUUUAAGCUUUUAGCGUAGUUUCCACAUUUUCGGGGGCAGGAGUACCAGCAGCCAGGGGCUACAGCUACAGCUAUAGCUAUUGCUGAAGCUUUAGCUACCC
(((........(((((((.((...((..((........))..)).((....))....)).)))))))..(((((.((((.((((....)))).)))).)))))))). ( -35.10)
>consensus
GGUUUUGUUUAAGCUUUUAGCGUAGUUUCCACUUUUUCGGGGGCAGGAGAGCCAGUAGCCAGGGGCUACAGCUAAAGCUAUAGCUAC______AGCUAUAGCUACCC
((((((.((...((.....))...((..((........))..)))).)))))).((((((...))))))......((((((((((........)))))))))).... (-29.05 = -30.18 +   1.13)

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 12:07:27 2006