Locus 4234

Sequence ID 2L_DroMel_CAF1
Location 12,114,021 – 12,114,221
Length 200
Max. P 0.953247
window6682 window6683 window6684 window6685 window6686

overview

Window 2

Location 12,114,021 – 12,114,141
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.80
Mean single sequence MFE -25.46
Consensus MFE -22.98
Energy contribution -22.86
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.33
Structure conservation index 0.90
SVM decision value 0.72
SVM RNA-class probability 0.832834
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12114021 120 + 22407834
GCCCGUCCGAACUUUUAUCUUUGCAAUCGUUCCGCGAACUUUGGCCAAUCUUAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAU
((..(((((..........(((((.........)))))..(((((((((....((((.....))))....((((......)))).))))))))).......)))))..)).......... ( -25.30)
>DroSec_CAF1 16130 113 + 1
------ACG-ACAUUUAUCUUUGCAAUCGUUCCGCGAACUUUGGCCAAUCUCAUGGACAAAAUCUAAUGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAU
------...-................((((((((((....(((((((((....((((.....))))....((((......)))).))))))))).....))))))...))))........ ( -24.30)
>DroSim_CAF1 15957 119 + 1
CCCCGUCCG-ACAUUUAUCUUUGCAAUCGUUCCGCGAACUUUGGCCAAUCACAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAU
....(((((-.((......(((((.........)))))..(((((((((....((((.....))))....((((......)))).))))))))).....))))))).............. ( -24.30)
>DroEre_CAF1 16375 119 + 1
ACCCAUCAG-ACAUUUAUCUUUGCAAUCGUUCCGCGAGCUUUGGCCAAUCUCAUGGGCAAAAUCUGAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGGGACAUUUCAU
.(((...((-(......)))........((.(((((....(((((((((.(((.((......)))))...((((......)))).))))))))).....)))))))..)))......... ( -25.50)
>DroYak_CAF1 16254 119 + 1
CCCCGUCAG-GCAUUUAUCUUUGCAAUCGUUCCGCGAACUUUGGCCAAUCUCGUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAU
....(((..-(((........)))....((.(((((....(((((((((....((((.....))))....((((......)))).))))))))).....)))))))....)))....... ( -27.90)
>consensus
CCCCGUCCG_ACAUUUAUCUUUGCAAUCGUUCCGCGAACUUUGGCCAAUCUCAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAU
..........................((((((((((....(((((((((....((((.....))))....((((......)))).))))))))).....))))))...))))........ (-22.98 = -22.86 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,114,021 – 12,114,141
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.80
Mean single sequence MFE -32.82
Consensus MFE -27.13
Energy contribution -27.33
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.83
SVM decision value 0.63
SVM RNA-class probability 0.804418
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12114021 120 - 22407834
AUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUAAGAUUGGCCAAAGUUCGCGGAACGAUUGCAAAGAUAAAAGUUCGGACGGGC
..........((((((((((((((..((((((((((........((..((......))..))........)))))))))).((((...))))))))))...((.......)))))))))) ( -35.79)
>DroSec_CAF1 16130 113 - 1
AUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCAUUAGAUUUUGUCCAUGAGAUUGGCCAAAGUUCGCGGAACGAUUGCAAAGAUAAAUGU-CGU------
.((....((((....(((((.(....((((((((((........((..((......))..))........))))))))))....)))))).))))..))..(((....))-)..------ ( -28.59)
>DroSim_CAF1 15957 119 - 1
AUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUGUGAUUGGCCAAAGUUCGCGGAACGAUUGCAAAGAUAAAUGU-CGGACGGGG
...........(((((((((((((..(((((((((((.......((..((......))..)).......))))))))))).((((...))))))))))...(((....))-)))))))). ( -36.94)
>DroEre_CAF1 16375 119 - 1
AUGAAAUGUCCCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUCAGAUUUUGCCCAUGAGAUUGGCCAAAGCUCGCGGAACGAUUGCAAAGAUAAAUGU-CUGAUGGGU
.........((((((((((((((...((((((((((........((..((......))..))........)))))))))).))).)))).))))......((((....))-))...))). ( -32.89)
>DroYak_CAF1 16254 119 - 1
AUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCACGAGAUUGGCCAAAGUUCGCGGAACGAUUGCAAAGAUAAAUGC-CUGACGGGG
......((((..((((((((.(....((((((((((........((..((......))..))........))))))))))....))))).))))..(((........)))-..))))... ( -29.89)
>consensus
AUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUGAGAUUGGCCAAAGUUCGCGGAACGAUUGCAAAGAUAAAUGU_CGGACGGGG
.((....((((....(((((.(....((((((((((........((..((......))..))........))))))))))....)))))).))))..))..................... (-27.13 = -27.33 +   0.20)

alignment

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secondary structure

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Window 4

Location 12,114,061 – 12,114,181
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -26.80
Consensus MFE -25.06
Energy contribution -24.78
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.94
SVM decision value 1.43
SVM RNA-class probability 0.953247
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12114061 120 + 22407834
UUGGCCAAUCUUAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAUGCUUAUCGGCAGUACAACCAGCAAUUAAUCUCCCUUCGGU
(((((((((....((((.....))))....((((......)))).)))))))))...(((((.((.(((((........))))).)).)))))....................(....). ( -26.80)
>DroSec_CAF1 16163 120 + 1
UUGGCCAAUCUCAUGGACAAAAUCUAAUGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAUGCUUAUCGGCGGUACAACCAGCAAUUAAUCUCCCUUCGGU
(((((((((....((((.....))))....((((......)))).)))))))))...(((((.((.(((((........))))).)).)))))....................(....). ( -26.10)
>DroSim_CAF1 15996 120 + 1
UUGGCCAAUCACAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAUGCUUAUCGGCAGUACAACCAGCAAUUAAUCUCCCUUCGGU
(((((((((....((((.....))))....((((......)))).)))))))))...(((((.((.(((((........))))).)).)))))....................(....). ( -26.80)
>DroEre_CAF1 16414 120 + 1
UUGGCCAAUCUCAUGGGCAAAAUCUGAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGGGACAUUUCAUGCUUAUCUGCAGUACAACCAGCAAUUAAUCUAUCUUCGGU
(((.(((......))).)))...((((((.(....)......(((((((........((((((((.(((.((....))...))).))))))))........))))))).....)))))). ( -25.39)
>DroYak_CAF1 16293 120 + 1
UUGGCCAAUCUCGUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAUGCUUAUCGGCAGUACAACCAGCAAUUAAUCGCCCUUCGGC
(((((((((....((((.....))))....((((......)))).)))))))))...(((((.((.(((((........))))).)).))))).................(((....))) ( -28.90)
>consensus
UUGGCCAAUCUCAUGGACAAAAUCUAAAGCGAAAUCUAAUUUUUAAUUGGCCAACAAACUGCGGACAAGCGACAUUUCAUGCUUAUCGGCAGUACAACCAGCAAUUAAUCUCCCUUCGGU
(((((((((....((((.....))))....((((......)))).)))))))))...(((((.((.(((((........))))).)).)))))........................... (-25.06 = -24.78 +  -0.28)

alignment

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secondary structure

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Window 5

Location 12,114,061 – 12,114,181
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -34.02
Consensus MFE -28.99
Energy contribution -29.07
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.85
SVM decision value 1.16
SVM RNA-class probability 0.924619
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12114061 120 - 22407834
ACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUAAGAUUGGCCAA
.((....)).(((.((((((.(((......)))(((((((..........))))))).)))))).)))((((((((........((..((......))..))........)))))))).. ( -34.09)
>DroSec_CAF1 16163 120 - 1
ACCGAAGGGAGAUUAAUUGCUGGUUGUACCGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCAUUAGAUUUUGUCCAUGAGAUUGGCCAA
.((....)).(((.((((((.(((......)))(((((((..........))))))).)))))).)))((((((((........((..((......))..))........)))))))).. ( -33.39)
>DroSim_CAF1 15996 120 - 1
ACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUGUGAUUGGCCAA
.((....)).(((.((((((.(((......)))(((((((..........))))))).)))))).)))(((((((((.......((..((......))..)).......))))))))).. ( -36.34)
>DroEre_CAF1 16414 120 - 1
ACCGAAGAUAGAUUAAUUGCUGGUUGUACUGCAGAUAAGCAUGAAAUGUCCCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUCAGAUUUUGCCCAUGAGAUUGGCCAA
((((..(((......)))..))))...(((((.((((((...((....)).)))))).)))))...((((((((((........((..((......))..))........)))))))))) ( -28.49)
>DroYak_CAF1 16293 120 - 1
GCCGAAGGGCGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCACGAGAUUGGCCAA
(((..((((((((((((((((..(...(((((.(((((((..........))))))).)))))..)..)).)))))))..........))))))).(((((((....))))))))))... ( -37.80)
>consensus
ACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAAAUUAGAUUUCGCUUUAGAUUUUGUCCAUGAGAUUGGCCAA
((((..((........))..))))...(((((.(((((((..........))))))).)))))...((((((((((........((..((......))..))........)))))))))) (-28.99 = -29.07 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,114,101 – 12,114,221
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -34.12
Consensus MFE -27.66
Energy contribution -28.66
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.81
SVM decision value 0.60
SVM RNA-class probability 0.795162
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12114101 120 - 22407834
AGAGAAAGAGAGCAUCUGCUAAGAGAGUCUUCUCCAUUCCACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
..(((.....(((....))).......)))(((((.(((....))).)))))(((((((((..(...(((((.(((((((..........))))))).)))))..)..)).))))))).. ( -35.30)
>DroSec_CAF1 16203 120 - 1
AGAGAAAGAGAGUAUCUGCUAAGAGAGUCUUCUCCACUCCACCGAAGGGAGAUUAAUUGCUGGUUGUACCGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
.((((...(((.(.(((....))).).)))))))..((((.......)))).(((((((..((.....))((((((((((..((....))((......)).))))))))))))))))).. ( -31.70)
>DroSim_CAF1 16036 120 - 1
AGAGAAAGAGAGAAUCUGCUAAGAGAGUCUUCUCCACUCCACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
.(((...((((((.(((....)))...)).))))..)))..((....))...(((((((((..(...(((((.(((((((..........))))))).)))))..)..)).))))))).. ( -36.60)
>DroEre_CAF1 16454 115 - 1
AGAGAAAGAGAGAAUCCGCUAAGAGAGUCUUCUC-----UACCGAAGAUAGAUUAAUUGCUGGUUGUACUGCAGAUAAGCAUGAAAUGUCCCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
......(((((((.(((.....).)).)).))))-----)............(((((((((..(...(((((.((((((...((....)).)))))).)))))..)..)).))))))).. ( -27.00)
>DroYak_CAF1 16333 115 - 1
AGAGAAAGAGAGAAUCUGCUAAGAGAGUCUUCUC-----CGCCGAAGGGCGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
.......((((((.(((....)))...)).))))-----((((....)))).(((((((((..(...(((((.(((((((..........))))))).)))))..)..)).))))))).. ( -40.00)
>consensus
AGAGAAAGAGAGAAUCUGCUAAGAGAGUCUUCUCCA_UCCACCGAAGGGAGAUUAAUUGCUGGUUGUACUGCCGAUAAGCAUGAAAUGUCGCUUGUCCGCAGUUUGUUGGCCAAUUAAAA
.(((((.((.....(((....)))...))))))).......((....))...(((((((((..(...(((((.(((((((..........))))))).)))))..)..)).))))))).. (-27.66 = -28.66 +   1.00)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:03 2006