Locus 5573

Sequence ID 2L_DroMel_CAF1
Location 15,842,570 – 15,842,728
Length 158
Max. P 0.979913
window8847 window8848 window8849 window8850

overview

Window 7

Location 15,842,570 – 15,842,689
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -32.50
Consensus MFE -24.98
Energy contribution -25.10
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -2.73
Structure conservation index 0.77
SVM decision value 1.85
SVM RNA-class probability 0.979913
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15842570 119 + 22407834
UGUGUUAUUCAUCGCUUUUCUAGUUGUUUU-UCCCUCAGCUACUUUGUAUGCAGCGACUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAA
.............((((.....((((....-(((..(((((.....(((.(((((....)))))))).)))))..)))....))))....(((.((((....)))))))...)))).... ( -31.10)
>DroPse_CAF1 1546 114 + 1
U---UUGUCCAUCUAUUUUCUUCUUGUUUUAUCCCUGGGCUGCUUUGUAUGCAGCGCCU---GCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACGAGCCCAA
.---...............................((((((((((((.((.(((((.((---(....))).))))).))...))).))).(((.((((....)))))))....)))))). ( -31.80)
>DroSec_CAF1 14735 119 + 1
UUUGUUAUUCAUCGCUUGUCUAGUUGUUUU-UCCCUCGGCUACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAA
.............((((((..((.......-...(((((((...(((...(((((....)))))...)))..(((((....)))))))))))).((((....))))))..)))))).... ( -35.40)
>DroSim_CAF1 15036 119 + 1
UGUGUUAUUCAUAGCUUUUCUAGUUGUUUU-UCCCUCGGCUACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAA
..........((((((.....))))))...-......((((....((...(((((....)))))...))((((((((....)))))))).(((.((((....)))))))....))))... ( -32.40)
>DroPer_CAF1 27301 114 + 1
U---UUGUCCAUCUAUUUUCUUCUUGUUUUAUCCCUGGGCUGCUUUGUAUGCAGCGCCU---GCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACGAGCCCAA
.---...............................((((((((((((.((.(((((.((---(....))).))))).))...))).))).(((.((((....)))))))....)))))). ( -31.80)
>consensus
U_UGUUAUUCAUCGCUUUUCUAGUUGUUUU_UCCCUCGGCUACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAA
.......................(((((.........(((((..(((.((.(((((.(((.......))).))))).))...))))))))(((.((((....))))))))))))...... (-24.98 = -25.10 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,842,570 – 15,842,689
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.43
Mean single sequence MFE -34.22
Consensus MFE -24.06
Energy contribution -26.30
Covariance contribution 2.24
Combinations/Pair 1.04
Mean z-score -3.42
Structure conservation index 0.70
SVM decision value 1.25
SVM RNA-class probability 0.935627
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15842570 119 - 22407834
UUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGUCGCUGCAUACAAAGUAGCUGAGGGA-AAAACAACUAGAAAAGCGAUGAAUAACACA
....((((....((((((....)))).((((((((((....(((........))).(((((....)))))......))))))))))...-.......))....))))............. ( -33.70)
>DroPse_CAF1 1546 114 - 1
UUGGGCUCGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGC---AGGCGCUGCAUACAAAGCAGCCCAGGGAUAAAACAAGAAGAAAAUAGAUGGACAA---A
(((..(((((((((((((....)))).))))))........((((......((....)---)((.(((((.......)))))))..)))).................)).)..)))---. ( -29.60)
>DroSec_CAF1 14735 119 - 1
UUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUAGCCGAGGGA-AAAACAACUAGACAAGCGAUGAAUAACAAA
....(((((((.((((((....)))).((((((((((....(((........))).(((((....)))))......))))))))))...-.......)).)))))))............. ( -41.30)
>DroSim_CAF1 15036 119 - 1
UUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUAGCCGAGGGA-AAAACAACUAGAAAAGCUAUGAAUAACACA
...(((((....((((((....)))).((((((((((....(((........))).(((((....)))))......))))))))))...-.......))....)))))............ ( -36.90)
>DroPer_CAF1 27301 114 - 1
UUGGGCUCGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGC---AGGCGCUGCAUACAAAGCAGCCCAGGGAUAAAACAAGAAGAAAAUAGAUGGACAA---A
(((..(((((((((((((....)))).))))))........((((......((....)---)((.(((((.......)))))))..)))).................)).)..)))---. ( -29.60)
>consensus
UUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUAGCCGAGGGA_AAAACAACUAGAAAAGCGAUGAAUAACA_A
.....((.((((..((((....)))).((((((((((....(((........))).(((((....)))))......))))))))))........)))).))................... (-24.06 = -26.30 +   2.24)

alignment

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secondary structure

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Window 9

Location 15,842,609 – 15,842,728
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.80
Mean single sequence MFE -37.38
Consensus MFE -26.80
Energy contribution -27.40
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.72
SVM decision value 0.42
SVM RNA-class probability 0.729806
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15842609 119 + 22407834
UACUUUGUAUGCAGCGACUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAAAAGCAAAACUCGGGGGCGCGG-CCUACAGAUAUGCAUGUA
(((..(((((((((((((((.......)))))))))...........((((((.((((....))))))).....((((...((.....))...))))..))-).......)))))).))) ( -37.90)
>DroPse_CAF1 1583 105 + 1
UGCUUUGUAUGCAGCGCCU---GCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACGAGCCCAAAAGUAACACUCGAGAGCGCGGGUCUCG------------A
(((.......)))..((((---((..((.((((((((....))))))))((((((.(((((((.((........)).)))))))..)))))).))..))))))....------------. ( -35.00)
>DroSec_CAF1 14774 119 + 1
UACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAAAAGCAAAACUCGAGGGCGCGG-CCUACAGCUAUGCAUGUA
.......((((((((((((..........((((((((....))))))))(((((...((((((.((........)).))))))....))))).))))))((-(.....))).)))))).. ( -38.90)
>DroSim_CAF1 15075 119 + 1
UACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAAAAGCAAAACUCGGGGGCGCGG-CCUACAGAUAUGCAUGUA
...((((((.((.((((((((((....))))((((((....)))))).((((((...((((((.((........)).))))))....)))))))))))).)-).)))))).......... ( -40.10)
>DroPer_CAF1 27338 105 + 1
UGCUUUGUAUGCAGCGCCU---GCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACGAGCCCAAAAGUAACACUCGAGAGCGCGGGUCUCG------------A
(((.......)))..((((---((..((.((((((((....))))))))((((((.(((((((.((........)).)))))))..)))))).))..))))))....------------. ( -35.00)
>consensus
UACUUUGUAUGCAGCGCCUGCUGCUAUCAGUUGUUGGAUUUUCAAUAGCCGAGUGCACUUUUGUGCCUCAACAAGCCCAAAAGCAAAACUCGAGGGCGCGG_CCUACAG_UAUGCAUGUA
.............((((((..........((((((((....))))))))(((((...((((((.((........)).))))))....))))).))))))..................... (-26.80 = -27.40 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,842,609 – 15,842,728
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.80
Mean single sequence MFE -36.99
Consensus MFE -28.70
Energy contribution -28.42
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -2.08
Structure conservation index 0.78
SVM decision value 1.05
SVM RNA-class probability 0.906636
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15842609 119 - 22407834
UACAUGCAUAUCUGUAGG-CCGCGCCCCCGAGUUUUGCUUUUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGUCGCUGCAUACAAAGUA
....(((.((((.((.((-((..((((..(((.....)))..)))).....(((((((....)))).))))))).(((......)))..)).))))(((((....))))).......))) ( -37.30)
>DroPse_CAF1 1583 105 - 1
U------------CGAGACCCGCGCUCUCGAGUGUUACUUUUGGGCUCGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGC---AGGCGCUGCAUACAAAGCA
.------------........(((((..(((((((.((((((((.(((...))).).))))))))))))))((((((...............))))))---.))))).((.......)). ( -35.26)
>DroSec_CAF1 14774 119 - 1
UACAUGCAUAGCUGUAGG-CCGCGCCCUCGAGUUUUGCUUUUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUA
............((((.(-(.(((((..(((((...(((((((.((((....)))).)))))))..)))))((((((...............))))))....))))).)).))))..... ( -38.46)
>DroSim_CAF1 15075 119 - 1
UACAUGCAUAUCUGUAGG-CCGCGCCCCCGAGUUUUGCUUUUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUA
............((((.(-(.(((((..(((((...(((((((.((((....)))).)))))))..)))))((((((...............))))))....))))).)).))))..... ( -38.66)
>DroPer_CAF1 27338 105 - 1
U------------CGAGACCCGCGCUCUCGAGUGUUACUUUUGGGCUCGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGC---AGGCGCUGCAUACAAAGCA
.------------........(((((..(((((((.((((((((.(((...))).).))))))))))))))((((((...............))))))---.))))).((.......)). ( -35.26)
>consensus
UACAUGCAUA_CUGUAGG_CCGCGCCCUCGAGUUUUGCUUUUGGGCUUGUUGAGGCACAAAAGUGCACUCGGCUAUUGAAAAUCCAACAACUGAUAGCAGCAGGCGCUGCAUACAAAGUA
.....................(((((..(((((...(((((((.(((......))).)))))))..)))))((((((...............))))))....)))))............. (-28.70 = -28.42 +  -0.28)

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 11:47:37 2006