Locus 158

Sequence ID 4_DroMel_CAF1
Location 1,009,848 – 1,010,008
Length 160
Max. P 0.932382
window253 window254 window255

overview

Window 3

Location 1,009,848 – 1,009,968
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.00
Mean single sequence MFE -39.10
Consensus MFE -32.36
Energy contribution -32.36
Covariance contribution -0.00
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 1.22
SVM RNA-class probability 0.932382
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1009848 120 + 1281640
CACGGAAAACAGCAACGUUGUUAGCUAUCGCUGACUGCAAAUGAAAAGAGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGC
...........((...((.((((((....)))))).))....(((((((.((....((((((((...(((.....))).(((..(....)..))))))))))).....)).))))))))) ( -39.90)
>DroSec_CAF1 49448 120 + 1
CACGGAAAACAGCAACGUUGUUAGCUAUCGCUGACUGUAAAUGAAAAGGGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUGGCCGUUGCUCUUGCCAGUGUUUUUUCGC
..(((((((..((......((((((....)))))).............((.((...((((((((...(((.....))).((((((....)))))))))))))))))).))..))))))). ( -42.10)
>DroSim_CAF1 35340 120 + 1
CACGGAAAACAGCAACGUUGUUAGCUAUCGCUGACUGUAAAUGAAAAGGGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGC
..(((((((..((......((((((....)))))).............((.((...((((((((...(((.....))).(((..(....)..))))))))))))))).))..))))))). ( -37.00)
>DroEre_CAF1 53095 120 + 1
CACGGAAAACAGCACAGUUGUUAGCUACCGAUGACUGCAAUGGAAAAGAGACAACCAGAGCAACGCCGUCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGC
..(((((((..((((.((((((..((.(((.((....)).)))...)).)))))).(((((((((((((....))))).(((..(....)..))))))))))).....))))))))))). ( -38.30)
>DroYak_CAF1 50250 120 + 1
CACGGAAAACAGCAGCGUUGUGAGCUAUCGAUGACUGCAAAGGAAAAGAGACGACAAGAGCAACGACUUCAAAAUGGCUGUCCGAUGUGUUAGCCGUUGCUUUUGCCAGUGUUUUUUCGC
...........(((((((((........))))).))))....(((((((.((..(((((((((((....).....(((((..........)))))))))))))))...)).))))))).. ( -38.20)
>consensus
CACGGAAAACAGCAACGUUGUUAGCUAUCGCUGACUGCAAAUGAAAAGAGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGC
...........((...(..((((((....))))))..)....(((((((.((....(((((((((....).....(((((((......))))))))))))))).....)).))))))))) (-32.36 = -32.36 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,009,848 – 1,009,968
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.00
Mean single sequence MFE -35.66
Consensus MFE -31.74
Energy contribution -31.94
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.24
Structure conservation index 0.89
SVM decision value 0.32
SVM RNA-class probability 0.687941
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1009848 120 - 1281640
GCGAAAAAACACUGGCAAGAGCAACGGCUAACACAUCGGCCAGCCAUUUUGGCGGCGUUGCUCUAGUUGUCUCUUUUCAUUUGCAGUCAGCGAUAGCUAACAACGUUGCUGUUUUCCGUG
(((..((((((...(((((((((((((((........)))).(((.....)))...)))))))((((((((.((...(.......)..)).))))))))......)))))))))).))). ( -36.90)
>DroSec_CAF1 49448 120 - 1
GCGAAAAAACACUGGCAAGAGCAACGGCCAACACAUCGGCCAGCCAUUUUGGCGGCGUUGCUCUAGUUGUCCCUUUUCAUUUACAGUCAGCGAUAGCUAACAACGUUGCUGUUUUCCGUG
(((..((((((...(((((((((((((((........)))).(((.....)))...)))))))((((((((.((...(.......)..)).))))))))......)))))))))).))). ( -38.80)
>DroSim_CAF1 35340 120 - 1
GCGAAAAAACACUGGCAAGAGCAACGGCUAACACAUCGGCCAGCCAUUUUGGCGGCGUUGCUCUAGUUGUCCCUUUUCAUUUACAGUCAGCGAUAGCUAACAACGUUGCUGUUUUCCGUG
(((..((((((...(((((((((((((((........)))).(((.....)))...)))))))((((((((.((...(.......)..)).))))))))......)))))))))).))). ( -36.40)
>DroEre_CAF1 53095 120 - 1
GCGAAAAAACACUGGCAAGAGCAACGGCUAACACAUCGGCCAGCCAUUUUGACGGCGUUGCUCUGGUUGUCUCUUUUCCAUUGCAGUCAUCGGUAGCUAACAACUGUGCUGUUUUCCGUG
(((..((((((...(((((((((((((((........)))).(((........)))))))))))((((((..((...((..((....))..)).))...)))))).))))))))).))). ( -35.80)
>DroYak_CAF1 50250 120 - 1
GCGAAAAAACACUGGCAAAAGCAACGGCUAACACAUCGGACAGCCAUUUUGAAGUCGUUGCUCUUGUCGUCUCUUUUCCUUUGCAGUCAUCGAUAGCUCACAACGCUGCUGUUUUCCGUG
(((..((((((..(((((.((((((((((..((.(..((....))..).)).)))))))))).)))))..............(((((....((....)).....))))))))))).))). ( -30.40)
>consensus
GCGAAAAAACACUGGCAAGAGCAACGGCUAACACAUCGGCCAGCCAUUUUGGCGGCGUUGCUCUAGUUGUCUCUUUUCAUUUGCAGUCAGCGAUAGCUAACAACGUUGCUGUUUUCCGUG
(((((((...((.(((.((((((((((((........)))).(((........))))))))))).)))))...)))))....((((.(((((...........))))))))).....)). (-31.74 = -31.94 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,009,888 – 1,010,008
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.58
Mean single sequence MFE -38.96
Consensus MFE -35.66
Energy contribution -35.30
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.26
Structure conservation index 0.92
SVM decision value 0.50
SVM RNA-class probability 0.759895
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1009888 120 + 1281640
AUGAAAAGAGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((....((((((((...(((.....))).(((..(....)..))))))))))).....)).)))))))((((...(((.((.............)))))..))))..... ( -38.52)
>DroSec_CAF1 49488 120 + 1
AUGAAAAGGGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUGGCCGUUGCUCUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((....((((((((...(((.....))).((((((....)))))))))))))).....)).)))))))((((...(((.((.............)))))..))))..... ( -42.82)
>DroSim_CAF1 35380 120 + 1
AUGAAAAGGGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((....((((((((...(((.....))).(((..(....)..))))))))))).....)).)))))))((((...(((.((.............)))))..))))..... ( -37.72)
>DroEre_CAF1 53135 120 + 1
UGGAAAAGAGACAACCAGAGCAACGCCGUCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((..(.(((((((((((((....))))).(((..(....)..))))))))))).)...)).)))))))((((...(((.((.............)))))..))))..... ( -39.22)
>DroYak_CAF1 50290 120 + 1
AGGAAAAGAGACGACAAGAGCAACGACUUCAAAAUGGCUGUCCGAUGUGUUAGCCGUUGCUUUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((..(((((((((((....).....(((((..........)))))))))))))))...)).)))))))((((...(((.((.............)))))..))))..... ( -36.52)
>consensus
AUGAAAAGAGACAACUAGAGCAACGCCGCCAAAAUGGCUGGCCGAUGUGUUAGCCGUUGCUCUUGCCAGUGUUUUUUCGCAUGAGAGCUCAUUAACGUUUCGCUUGGCUAAGUGCGCACC
..(((((((.((....(((((((((....).....(((((((......))))))))))))))).....)).)))))))((((...(((.((.............)))))..))))..... (-35.66 = -35.30 +  -0.36)

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 09:37:36 2006