Locus 1851

Sequence ID X_DroMel_CAF1
Location 5,105,772 – 5,105,912
Length 140
Max. P 0.777177
window3008 window3009 window3010

overview

Window 8

Location 5,105,772 – 5,105,872
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 87.13
Mean single sequence MFE -19.27
Consensus MFE -12.42
Energy contribution -13.42
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.64
SVM decision value 0.09
SVM RNA-class probability 0.578405
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5105772 100 + 22224390
UGUCUAUUUUUUUUUGUUUUUUUUCAUUUUGAUUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUGAAGUGAAGGGCCAA
.((((.((...(((..((((.((((((((((........((((((((........)))))))).....))))))).))).))))..))).)).))))... ( -22.32)
>DroSim_CAF1 18490 89 + 1
UGUCUAUUUUUUUAUGUU---UUUCAUUUUGAUUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUG--------GGCCAA
.(((((((((.......(---((.(((((((........((((((((........)))))))).....))))))).))).))))))--------)))... ( -20.52)
>DroEre_CAF1 16748 88 + 1
UGUCUAUUU-UUUGUGUU---UUUCAUUUUGAUUGUCUUGAGCACCAACUCUUCUCACUGCUUUAUUAUGAAAUGCAAGUGAAGUG--------AGCCAA
.(..(((((-(...(((.---((((((..(((..((..((((...........))))..)).)))..)))))).)))...))))))--------..)... ( -16.20)
>DroYak_CAF1 17098 89 + 1
AGUCUAUUUUUUUAUGUU---UAUCAUUUUGAUUGUCUUGAGCAGCAACUUUUCUUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUU--------AGCCAA
.(.(((...((((((...---...(((((((........(((((((((......))))))))).....)))))))...)))))).)--------)).).. ( -18.02)
>consensus
UGUCUAUUUUUUUAUGUU___UUUCAUUUUGAUUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUG________AGCCAA
.....................((((((((..(((.....((((((((........))))))))........)))..))))))))................ (-12.42 = -13.42 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,105,804 – 5,105,912
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 87.34
Mean single sequence MFE -28.07
Consensus MFE -21.29
Energy contribution -21.85
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.76
SVM decision value 0.14
SVM RNA-class probability 0.601791
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5105804 108 + 22224390
UUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUGAAGUGAAGGGCCAAAGGCAGCGGAUAUGGCGCUUUCCCGCCUUUACCACCUCUA
((((...((((((((........))))))))....)))).........((.(((..((((((((((...)))((((.......))))......)))))))))).)).. ( -29.30)
>DroSim_CAF1 18519 100 + 1
UUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUG--------GGCCAAAGGCAGCGGAUGUGGCGCUUUCCCGCCUUUGCCACUCCUA
((((...((((((((........))))))))....))))......((.((.(((--------(..(((((((((((.......)))).....))))))))))))))). ( -30.80)
>DroEre_CAF1 16776 100 + 1
UUGUCUUGAGCACCAACUCUUCUCACUGCUUUAUUAUGAAAUGCAAGUGAAGUG--------AGCCAAAGGCACCGGAAAUGGCGCUUUCCCGCUUUUACCAACCCUA
.(((((((((......)))..((((((((((((((....)))).))))..))))--------))...))))))..((.((.((((......)))).)).))....... ( -21.70)
>DroYak_CAF1 17127 100 + 1
UUGUCUUGAGCAGCAACUUUUCUUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUU--------AGCCAAAGGCACCGGAAAUGGCGCUUUCCCGCCGUUACCACCCCUA
.((((((..((...((((((.(((((................))))).))))))--------.))..))))))..((.(((((((......))))))).))....... ( -30.49)
>consensus
UUGUCUUGAGCAGCAACUUUUCCUGCUGCUUUAUUAUAAAAUGCAAGUGAAGUG________AGCCAAAGGCACCGGAAAUGGCGCUUUCCCGCCUUUACCACCCCUA
.((((((..((((((........))))((((((((..........))))))))..........))..))))))..((....((((......))))....))....... (-21.29 = -21.85 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,105,804 – 5,105,912
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 87.34
Mean single sequence MFE -30.69
Consensus MFE -24.37
Energy contribution -24.18
Covariance contribution -0.19
Combinations/Pair 1.24
Mean z-score -1.76
Structure conservation index 0.79
SVM decision value 0.55
SVM RNA-class probability 0.777177
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5105804 108 - 22224390
UAGAGGUGGUAAAGGCGGGAAAGCGCCAUAUCCGCUGCCUUUGGCCCUUCACUUCACUUCACUUGCAUUUUAUAAUAAAGCAGCAGGAAAAGUUGCUGCUCAAGACAA
..(((((((....(((.(((.((((.......))))...))).)))..)))))))......((((.............((((((((......)))))))))))).... ( -30.71)
>DroSim_CAF1 18519 100 - 1
UAGGAGUGGCAAAGGCGGGAAAGCGCCACAUCCGCUGCCUUUGGCC--------CACUUCACUUGCAUUUUAUAAUAAAGCAGCAGGAAAAGUUGCUGCUCAAGACAA
..((((((((((((((.....((((.......)))))))))))..)--------)))))).((((.............((((((((......)))))))))))).... ( -34.21)
>DroEre_CAF1 16776 100 - 1
UAGGGUUGGUAAAAGCGGGAAAGCGCCAUUUCCGGUGCCUUUGGCU--------CACUUCACUUGCAUUUCAUAAUAAAGCAGUGAGAAGAGUUGGUGCUCAAGACAA
..((((.(((....((.(((((......))))).))))).(..(((--------(..((((((.((.............))))))))..))))..).))))....... ( -26.82)
>DroYak_CAF1 17127 100 - 1
UAGGGGUGGUAACGGCGGGAAAGCGCCAUUUCCGGUGCCUUUGGCU--------AACUUCACUUGCAUUUUAUAAUAAAGCAGCAAGAAAAGUUGCUGCUCAAGACAA
...(((..((((((((.(((..(((((......))))).))).)))--------.......(((((.(((......)))...)))))....)))))..)))....... ( -31.00)
>consensus
UAGGGGUGGUAAAGGCGGGAAAGCGCCAUAUCCGCUGCCUUUGGCC________CACUUCACUUGCAUUUUAUAAUAAAGCAGCAAGAAAAGUUGCUGCUCAAGACAA
..((((((.....(((.(((..(((((......))))).))).)))........)))))).((((.............((((((((......)))))))))))).... (-24.37 = -24.18 +  -0.19)

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 10:20:13 2006