Locus 6516

Sequence ID 3L_DroMel_CAF1
Location 17,270,195 – 17,270,475
Length 280
Max. P 0.999265
window10553 window10554 window10555 window10556

overview

Window 3

Location 17,270,195 – 17,270,315
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.17
Mean single sequence MFE -28.90
Consensus MFE -25.78
Energy contribution -26.78
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.89
SVM decision value 0.16
SVM RNA-class probability 0.614249
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17270195 120 + 23771897
UCUUGGCUAAAAUAGUUUGCCAACAGUUGCUCCGCGCUGGCACAUUAACGUGGCCAAGGCGGCAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
....(((..(((((.((((((...(((((((((((..((((.(((....)))))))..))))...............)))))))...))))))..........)))))..)))....... ( -31.96)
>DroSec_CAF1 153657 120 + 1
UCUUGGCUAAAAUAGUUUGCCAACAGUUGCUCCUCGCUUGCACAUUAACGUGGCCAAGGCGGCAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
....(((..(((((.((((((...(((((((.........(((......)))(((.....)))..............)))))))...))))))..........)))))..)))....... ( -25.50)
>DroSim_CAF1 148683 120 + 1
UCUUGGCUAAAAUAGUUUGCCAACAGUUGCUCCUCGCUGGCACAUUAACGUGGCCAAGGCGGCAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
(((((((((...((((.(((((.(((......)).).))))).))))...))))))))).((((..............((........))(((((.........)))))))))....... ( -27.30)
>DroEre_CAF1 156466 120 + 1
UCUUGGCCAAAAUAGUUUGCCAACAGUUGCUCCGCGCUGGCACAUUAACGUGGCCAAGGCGGCAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
....(((..(((((.((((((...(((((((((((..((((.(((....)))))))..))))...............)))))))...))))))..........)))))..)))....... ( -31.06)
>DroYak_CAF1 161280 119 + 1
UCUUGGCUAAAAUAGUUUGCGAACAGUUGCUCCGCGCUGGCACAUUAACGUGGCCAAGGCG-CAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
....(((..(((((.((((((((.(((((((..((((((((.(((....))))))..))))-)...((......)).)))))))))).)))))..........)))))..)))....... ( -28.70)
>consensus
UCUUGGCUAAAAUAGUUUGCCAACAGUUGCUCCGCGCUGGCACAUUAACGUGGCCAAGGCGGCAAAUAAUUCAAUAAAGCAACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUG
....(((..(((((.((((((...(((((((((((..((((.(((....)))))))..))))...............)))))))...))))))..........)))))..)))....... (-25.78 = -26.78 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,270,195 – 17,270,315
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -30.02
Consensus MFE -26.96
Energy contribution -27.96
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.90
SVM decision value 0.88
SVM RNA-class probability 0.873739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17270195 120 - 23771897
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUGCCGCCUUGGCCACGUUAAUGUGCCAGCGCGGAGCAACUGUUGGCAAACUAUUUUAGCCAAGA
..(((((((.(....).)))))))......(((((.(((((((...............((((.(((((.(((....)))))))).))))))))))).))))).................. ( -33.06)
>DroSec_CAF1 153657 120 - 1
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUGCCGCCUUGGCCACGUUAAUGUGCAAGCGAGGAGCAACUGUUGGCAAACUAUUUUAGCCAAGA
..(((((((.(....).)))))))......(((((.(((((((((............(((.....)))..((((........)))).))))))))).))))).................. ( -27.60)
>DroSim_CAF1 148683 120 - 1
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUGCCGCCUUGGCCACGUUAAUGUGCCAGCGAGGAGCAACUGUUGGCAAACUAUUUUAGCCAAGA
..(((((((.(....).)))))))......(((((.(((((((((....((....))..(((..((((.(((....)))))))))).))))))))).))))).................. ( -28.90)
>DroEre_CAF1 156466 120 - 1
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUGCCGCCUUGGCCACGUUAAUGUGCCAGCGCGGAGCAACUGUUGGCAAACUAUUUUGGCCAAGA
..(((((((.(....).)))))))......(((((.(((((((...............((((.(((((.(((....)))))))).))))))))))).))))).................. ( -33.06)
>DroYak_CAF1 161280 119 - 1
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUG-CGCCUUGGCCACGUUAAUGUGCCAGCGCGGAGCAACUGUUCGCAAACUAUUUUAGCCAAGA
..(((((((.(....).)))))))......((.(((((((((((............((-(((..((((.(((....)))))))))))))))))))).))))).................. ( -27.50)
>consensus
CAAAUUAGACAGAAAUAUUUAAUUAAUCUCGCCGAAAGUUGCUUUAUUGAAUUAUUUGCCGCCUUGGCCACGUUAAUGUGCCAGCGCGGAGCAACUGUUGGCAAACUAUUUUAGCCAAGA
..(((((((.(....).)))))))......(((((.(((((((...............((((.(((((.(((....)))))))).))))))))))).))))).................. (-26.96 = -27.96 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,270,275 – 17,270,395
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.92
Mean single sequence MFE -31.66
Consensus MFE -29.38
Energy contribution -29.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.26
Structure conservation index 0.93
SVM decision value 0.21
SVM RNA-class probability 0.635623
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17270275 120 + 23771897
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCAGGGGGUGCGAACUAGAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUA
.(((..(((((((((.........))))).(((......)))(((.....)))...))).)..)))(((..((.....))..))).....(((((((.((((((...))))))))))))) ( -34.00)
>DroSec_CAF1 153737 120 + 1
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCAGGGGGAGCGAACUAAAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUA
..((..(((((((((.........))))).(((......)))(((.....)))...))).)..)).(((..((.....))..))).....(((((((.((((((...))))))))))))) ( -33.10)
>DroSim_CAF1 148763 120 + 1
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCAGGGGGAGCGAACUAAAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUA
..((..(((((((((.........))))).(((......)))(((.....)))...))).)..)).(((..((.....))..))).....(((((((.((((((...))))))))))))) ( -33.10)
>DroEre_CAF1 156546 119 + 1
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCA-GGGGAGCGAACUAAAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGCCAAACUUGCUUA
..(((..((((((((.........))))).(((......)))(((.....)))...))).-.))).(((..((.....))..))).....(((((((.(((((.....)))))))))))) ( -29.30)
>DroYak_CAF1 161359 120 + 1
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCACAGGGAGCGAACUAAAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGCCAAACUUGCUUA
...((((.(((((((.........))))).(((......)))))......((((.(.((((..((......))...)))).)))))))))(((((((.(((((.....)))))))))))) ( -28.80)
>consensus
AACUUUCGGCGAGAUUAAUUAAAUAUUUCUGUCUAAUUUGACGCAAUUUAUGCAAUGCCAGGGGGAGCGAACUAAAGUGGGGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUA
...((((((((((((.........))))).(((......)))(((.....)))...))).......(((..((.....))..))).))))(((((((.(((((.....)))))))))))) (-29.38 = -29.38 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,270,355 – 17,270,475
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -34.89
Consensus MFE -32.26
Energy contribution -32.46
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.92
SVM decision value 3.47
SVM RNA-class probability 0.999265
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17270355 120 + 23771897
GGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUAUCUAUCUGGUGAAACUUUUAUUAAUUACAAAGGAUACACAUCAACAUUAGCCCAAGUGAGCUGCGGAUGUGGCGUCACAU
((.((....((((((((.((((((...)))))))))))))).(((((.((((............))))...))))).............))))..((((((..(....)..)).)))).. ( -33.20)
>DroSec_CAF1 153817 120 + 1
GGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUAUCUAUCUGGUGAAACUUUUAUUAAUUACAAAGGAUAUACAUCAACAUUAGUCCAAGUGAGCUGCGGAAGUGGCGUCACAU
((((((((.((((((((.((((((...))))))))))))))...))))......(((((.........))))).....)))).............((((((..(....)..)).)))).. ( -35.30)
>DroSim_CAF1 148843 120 + 1
GGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUAUCUAUCUGGUGAAACUUUUAUUAAUUACAAAGGAUACACAUCAACAUUAGUCCAAGUGAGCUGCGGAAGUGGCGUCACAU
((((((((.((((((((.((((((...))))))))))))))...))))(((...((((((.....)).))))..))).)))).............((((((..(....)..)).)))).. ( -36.10)
>DroEre_CAF1 156625 120 + 1
GGUGCAGAAAUGAGCAAAGUUUGCCGGCCAAACUUGCUUAUCUAUCUGGUGAAACUUUUAUUAAUUACAAAGGAUACACAUCAACAUUAGCCCAAGUGAGCUGCGGAAGUGGCUUCACAU
((.((....((((((((.(((((.....))))))))))))).(((((.((((............))))...))))).............))))..((((((..(....)..)).)))).. ( -34.70)
>DroYak_CAF1 161439 120 + 1
GGUGCAGAAAUGAGCAAAGUUUGCCGGCCAAACUUGCUUAGCUAUCUGCUGAAACUUUUAUUAAUUACAAAGGAUACACAUCAACAUUAGUCCAAGUGAGCUGCGGAAGUGGCUUCACAU
...(((((..(((((((.(((((.....))))))))))))....)))))......................((((..............))))..((((((..(....)..)).)))).. ( -35.14)
>consensus
GGUGCAGAAAUGAGCAAAGUUUGCCGGGCAAACUUGCUUAUCUAUCUGGUGAAACUUUUAUUAAUUACAAAGGAUACACAUCAACAUUAGUCCAAGUGAGCUGCGGAAGUGGCGUCACAU
((((((((.((((((((.(((((.....)))))))))))))...))))......(((((.........))))).....)))).............((((((..(....)..)).)))).. (-32.26 = -32.46 +   0.20)

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 12:22:23 2006