Locus 1503

Sequence ID 3R_DroMel_CAF1
Location 4,317,336 – 4,317,496
Length 160
Max. P 0.782490
window2496 window2497 window2498

overview

Window 6

Location 4,317,336 – 4,317,456
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -32.03
Consensus MFE -27.22
Energy contribution -27.67
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.85
SVM decision value 0.08
SVM RNA-class probability 0.575307
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4317336 120 + 27905053
CGUUAAAAUGGCAUUUACAGCGCGGCUCUCGAUGCUGCCAUUUUGCCCCGCUGGCAGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUU
(((((((.(((........(((((((..........)))..((((((.....))))))))))...((((((((....)))))))).................)))..)))))))...... ( -33.40)
>DroSec_CAF1 4706 120 + 1
CGUUAAAAUGGCAUUUACAGCGCGGCUCUCGAUGCUGCCAUUUUGCACCGCUGGCGGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUU
(((((((...(((......(.(((((.......))))))....)))...(((((.((((..(((.((((((((....)))))))).......)))..)))).))))))))))))...... ( -32.20)
>DroEre_CAF1 4714 120 + 1
CGUUAAAAUGGCAUUUACAGCUCGGCUCUCGAUGCUGCCAUUUUGCACCGCUGGCGUAGCGCUAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUU
(((((((...(((....(((((((.....))).))))......)))...(((((.(((.((....((((((((....)))))))))))))...((.....))))))))))))))...... ( -30.50)
>consensus
CGUUAAAAUGGCAUUUACAGCGCGGCUCUCGAUGCUGCCAUUUUGCACCGCUGGCGGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUU
(((((((.(((........(((((((..........)))..(((((.......)))))))))...((((((((....)))))))).................)))..)))))))...... (-27.22 = -27.67 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,317,336 – 4,317,456
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -34.73
Consensus MFE -30.87
Energy contribution -31.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.89
SVM decision value 0.56
SVM RNA-class probability 0.782490
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4317336 120 - 27905053
AAAUGUCGUUAAAGCUGGUGAAAAUCAAAUGUACGAAAUUUUCCAUGGAAAAUUUAUUGCGCUCUGCCAGCGGGGCAAAAUGGCAGCAUCGAGAGCCGCGCUGUAAAUGCCAUUUUAACG
......((((((((((((((.....)....(((..((((((((....))))))))..))).....))))))..((((.....(((((..((.....)).)))))...))))..))))))) ( -35.10)
>DroSec_CAF1 4706 120 - 1
AAAUGUCGUUAAAGCUGGUGAAAAUCAAAUGUACGAAAUUUUCCAUGGAAAAUUUAUUGCGCUCCGCCAGCGGUGCAAAAUGGCAGCAUCGAGAGCCGCGCUGUAAAUGCCAUUUUAACG
......((((((((.((((...........(((..((((((((....))))))))..)))((.(((....))).))......(((((..((.....)).)))))....)))))))))))) ( -33.30)
>DroEre_CAF1 4714 120 - 1
AAAUGUCGUUAAAGCUGGUGAAAAUCAAAUGUACGAAAUUUUCCAUGGAAAAUUUAUAGCGCUACGCCAGCGGUGCAAAAUGGCAGCAUCGAGAGCCGAGCUGUAAAUGCCAUUUUAACG
......((((((((.((((..........(((((.((((((((....))))))))....((((.....))))))))).....(((((.(((.....))))))))....)))))))))))) ( -35.80)
>consensus
AAAUGUCGUUAAAGCUGGUGAAAAUCAAAUGUACGAAAUUUUCCAUGGAAAAUUUAUUGCGCUCCGCCAGCGGUGCAAAAUGGCAGCAUCGAGAGCCGCGCUGUAAAUGCCAUUUUAACG
......((((((((.((((..........(((((.((((((((....))))))))....((((.....))))))))).....(((((..(....)....)))))....)))))))))))) (-30.87 = -31.20 +   0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,317,376 – 4,317,496
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -26.80
Consensus MFE -24.13
Energy contribution -24.13
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.90
SVM decision value -0.02
SVM RNA-class probability 0.522468
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4317376 120 + 27905053
UUUUGCCCCGCUGGCAGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUUUAAUGUGCGUGGAAAACACAAACAGGAAAACAACUUUCCA
.((((((.....))))))(((((...(((((((....)))))))((((....(((........))).....))))........)))))(((.....))).....(((((.....))))). ( -26.90)
>DroSec_CAF1 4746 120 + 1
UUUUGCACCGCUGGCGGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUUUAAUGUGCGUGGAAAACACAAACAGGAAAACAACUUUCCA
....((((.(((((.((((..(((.((((((((....)))))))).......)))..)))).))))).((((.......)))).))))(((.....))).....(((((.....))))). ( -27.80)
>DroEre_CAF1 4754 120 + 1
UUUUGCACCGCUGGCGUAGCGCUAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUUUAAUGUGCGUGGAAAACACAAACAGGAAAACAACUUUCCA
....((((.(((((.(((.((....((((((((....)))))))))))))...((.....))))))).((((.......)))).))))(((.....))).....(((((.....))))). ( -25.70)
>consensus
UUUUGCACCGCUGGCGGAGCGCAAUAAAUUUUCCAUGGAAAAUUUCGUACAUUUGAUUUUCACCAGCUUUAACGACAUUUUAAUGUGCGUGGAAAACACAAACAGGAAAACAACUUUCCA
.......(((((((....(((....((((((((....))))))))))).....((.....)))))))....(((((((....)))).)))))............(((((.....))))). (-24.13 = -24.13 +   0.00)

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 10:12:14 2006