Locus 6776

Sequence ID X_DroMel_CAF1
Location 16,853,895 – 16,854,078
Length 183
Max. P 0.969060
window11097 window11098 window11099 window11100

overview

Window 7

Location 16,853,895 – 16,853,999
Length 104
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 92.32
Mean single sequence MFE -31.60
Consensus MFE -25.78
Energy contribution -24.86
Covariance contribution -0.92
Combinations/Pair 1.29
Mean z-score -1.78
Structure conservation index 0.82
SVM decision value 1.03
SVM RNA-class probability 0.904107
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16853895 104 - 22224390
CCGCAUAAAUCAUUUCUCCUCGAAGGGAGAAGCGUUGUGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUCCAC--UGCAUUCGGAAAAUGGCAUUGAAAAGCUGUU
(((((((.......((((((....))))))((((((((((......)))))))))).))))))).((((((..--.......)))))).(((........)))... ( -34.70)
>DroSec_CAF1 52505 103 - 1
CCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAC-ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUCCAC--UGCAUUCGGAAAAUGGCAUUGAAAAGCUGUU
..(((.....(((((.(((.(((.(((..((.(((-((((((((((....))))))))))))).))..))).)--)).....))))))))((........))))). ( -31.80)
>DroSim_CAF1 36943 103 - 1
CCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU-ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUCCAC--UGCAUUCGGAAAAUGGCAUUGAAAAGCUGUU
..(((.....(((((.(((.(((.(((..((.(((-((((((((((....))))))))))))).))..))).)--)).....))))))))((........))))). ( -29.90)
>DroEre_CAF1 37867 103 - 1
CCGCAUAAAUCAUUUCUCCUUGGAGGGUUAAGCAU-ACGCAGCGUUGCACAGUGCUGUGUGUGGUUUUUCCAC--UGCAUUUGGAAAAUGGCAUUGAAAAGCUGUU
..(((.....(((((.(((.((.((((..((.(((-((((((((((....))))))))))))).))...)).)--).))...))))))))((........))))). ( -30.60)
>DroYak_CAF1 37281 105 - 1
CCGCAUAAAUCAUUUCUCCUUGGAGAGUUAAGCAU-ACGCAGCGUUGCACCGCGUUGUGUGCGGUUUUUCCACAUUGCAUUCGGAAAACGGCAUUGAAAAGCUGUU
((((.........(((((....)))))........-(((((((((......)))))))))))))..(((((...........)))))(((((........))))). ( -31.00)
>consensus
CCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU_ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUCCAC__UGCAUUCGGAAAAUGGCAUUGAAAAGCUGUU
(((..........(((((....)))))....(((..((((((((((....))))))))))((((.....))))..)))...)))..((((((........)))))) (-25.78 = -24.86 +  -0.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,853,929 – 16,854,039
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 90.04
Mean single sequence MFE -30.03
Consensus MFE -25.37
Energy contribution -25.45
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.94
Structure conservation index 0.84
SVM decision value 1.64
SVM RNA-class probability 0.969060
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16853929 110 - 22224390
UUCUACCGUUUCCCAUUUUUUCCGCGCUUUUCCUCGUGCACCGCAUAAAUCAUUUCUCCUCGAAGGGAGAAGCGUUGUGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUC
.......................((((........))))((((((((.......((((((....))))))((((((((((......)))))))))).))))))))..... ( -35.70)
>DroSec_CAF1 52539 109 - 1
UUCCACCGUUUCCAAUUUUUUCCGCGCUUUUCUUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAC-ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUC
....(((................((((........))))................(((....)))))).((.(((-((((((((((....))))))))))))).)).... ( -29.50)
>DroSim_CAF1 36977 109 - 1
UUCCACCGUUUCCCAUUUUUUCCGCGCUUUUCUUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU-ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUC
....((((((((((.........((((........)))).(((.................))).)))..))))((-((((((((((....)))))))))))))))..... ( -28.43)
>DroEre_CAF1 37901 107 - 1
UUCUACCGUUU-CCCGUUUUUCCGCGCUU-UCUUCUUGCACCGCAUAAAUCAUUUCUCCUUGGAGGGUUAAGCAU-ACGCAGCGUUGCACAGUGCUGUGUGUGGUUUUUC
....(((....-...((((..(((((...-...........)))...........(((....)))))..))))((-((((((((((....)))))))))))))))..... ( -26.24)
>DroYak_CAF1 37317 109 - 1
UUCCACCGUUGGCCAGUUUUUCCGCGCUUUUCCUCGUGCACCGCAUAAAUCAUUUCUCCUUGGAGAGUUAAGCAU-ACGCAGCGUUGCACCGCGUUGUGUGCGGUUUUUC
..(((....)))...........((((........))))(((((.........(((((....)))))........-(((((((((......))))))))))))))..... ( -30.30)
>consensus
UUCCACCGUUUCCCAUUUUUUCCGCGCUUUUCUUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU_ACGCAGCGUUGCACAAUGUUGUGUGUGGUUUUUC
.....................((((((........(((((.(((.........(((((....)))))....((.....)).))).)))))........))))))...... (-25.37 = -25.45 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,853,963 – 16,854,078
Length 115
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 88.84
Mean single sequence MFE -22.15
Consensus MFE -17.41
Energy contribution -17.10
Covariance contribution -0.31
Combinations/Pair 1.14
Mean z-score -1.50
Structure conservation index 0.79
SVM decision value 0.13
SVM RNA-class probability 0.598781
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16853963 115 + 22224390
AACGCUUCUCCCUUCGAGGAGAAAUGAUUUAUGCGGUGCACGAGGAAAAGCGCGGAAAAAAUGGGAAACGGUAGAAAACGAUG-AAAGCAUAAAAGAGAAAGUGGAAAGUGAUGAA
..(((((((((......))))))....(((((((.((((..........)))).......((.(....).))...........-...))))))).......)))............ ( -23.90)
>DroSec_CAF1 52573 114 + 1
-GUGCUUAACCCUCCGAGGAGAAAUGAUUUAUGCGGUGCACGAAGAAAAGCGCGGAAAAAAUUGGAAACGGUGGAAAACGAUG-CAAGCAUAAAAGAGAAAGUGGAAAGUGAUGAA
-..((((..(((((....)))......(((((((..((((((........))((......((((....))))......)).))-)).))))))).........)).))))...... ( -22.40)
>DroSim_CAF1 37011 114 + 1
-AUGCUUAACCCUCCGAGGAGAAAUGAUUUAUGCGGUGCACGAAGAAAAGCGCGGAAAAAAUGGGAAACGGUGGAAAGCGAUG-CAAGCAUAAAAGAGAAAGUGGAAAGUGAUGAA
-..((((..(((((....)))......(((((((..((((..........(((.......((.(....).)).....))).))-)).))))))).........)).))))...... ( -22.70)
>DroYak_CAF1 37351 113 + 1
-AUGCUUAACUCUCCAAGGAGAAAUGAUUUAUGCGGUGCACGAGGAAAAGCGCGGAAAAACUGGCCAACGGUGGAAAAUGAUAGAAAGCAUAUGAGAGAAAGUGGAAAGUGAA--G
-...(((.(((.((((.............(((((.((((..........))))......((((.....))))...............)))))..........)))).))).))--) ( -19.60)
>consensus
_AUGCUUAACCCUCCGAGGAGAAAUGAUUUAUGCGGUGCACGAAGAAAAGCGCGGAAAAAAUGGGAAACGGUGGAAAACGAUG_AAAGCAUAAAAGAGAAAGUGGAAAGUGAUGAA
..(((((..(.(((....)))......(((((((.((((..........))))..........(....)..................))))))).........)..)))))..... (-17.41 = -17.10 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,853,963 – 16,854,078
Length 115
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 88.84
Mean single sequence MFE -18.28
Consensus MFE -13.19
Energy contribution -12.88
Covariance contribution -0.31
Combinations/Pair 1.27
Mean z-score -2.19
Structure conservation index 0.72
SVM decision value 0.64
SVM RNA-class probability 0.809320
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16853963 115 - 22224390
UUCAUCACUUUCCACUUUCUCUUUUAUGCUUU-CAUCGUUUUCUACCGUUUCCCAUUUUUUCCGCGCUUUUCCUCGUGCACCGCAUAAAUCAUUUCUCCUCGAAGGGAGAAGCGUU
......................(((((((...-....((.....)).................((((........))))...)))))))...((((((((....)))))))).... ( -19.20)
>DroSec_CAF1 52573 114 - 1
UUCAUCACUUUCCACUUUCUCUUUUAUGCUUG-CAUCGUUUUCCACCGUUUCCAAUUUUUUCCGCGCUUUUCUUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAC-
......(((((((.........(((((((.((-((.((........(((..............)))........))))))..)))))))............))))))).......- ( -17.13)
>DroSim_CAF1 37011 114 - 1
UUCAUCACUUUCCACUUUCUCUUUUAUGCUUG-CAUCGCUUUCCACCGUUUCCCAUUUUUUCCGCGCUUUUCUUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU-
.........................(((((((-....(((((((...(.....).........((((........))))......................))))))))))))))- ( -17.00)
>DroYak_CAF1 37351 113 - 1
C--UUCACUUUCCACUUUCUCUCAUAUGCUUUCUAUCAUUUUCCACCGUUGGCCAGUUUUUCCGCGCUUUUCCUCGUGCACCGCAUAAAUCAUUUCUCCUUGGAGAGUUAAGCAU-
(--((.((((((((..........(((((.............(((....)))...........((((........))))...))))).............)))))))).)))...- ( -19.80)
>consensus
UUCAUCACUUUCCACUUUCUCUUUUAUGCUUG_CAUCGUUUUCCACCGUUUCCCAUUUUUUCCGCGCUUUUCCUCGUGCACCGCAUAAAUCAUUUCUCCUCGGAGGGUUAAGCAU_
..........................((((((.(.............................((((........))))...............((((....))))).)))))).. (-13.19 = -12.88 +  -0.31)

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 12:22:42 2006