Locus 6100

Sequence ID 2L_DroMel_CAF1
Location 17,101,425 – 17,101,569
Length 144
Max. P 0.973841
window9702 window9703 window9704 window9705

overview

Window 2

Location 17,101,425 – 17,101,529
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 93.27
Mean single sequence MFE -34.30
Consensus MFE -31.09
Energy contribution -31.34
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.91
SVM decision value 1.31
SVM RNA-class probability 0.940507
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17101425 104 + 22407834
CUCAAUGCGUUUUGUGCGUGGCUUCGGCAGUGAGACUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAAC
(((....(((((.(((((.((((((..(((.....)))))))))))).((((((....)))))))).)))))......)))(((.(((......))).)))... ( -34.60)
>DroSec_CAF1 65413 104 + 1
CUCAAUGCGUUUUGUGCGUGGCUUCGGCAGUUAGACUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAGC
(((....(((((.(((((.((((((..(((.....)))))))))))).((((((....)))))))).)))))......)))(((.(((......))).)))... ( -34.60)
>DroEre_CAF1 66568 101 + 1
CUCAAUGCGUUUUGUGCGUGGCUUUGGCAGUUAGAAUGGUAGCCUGCCGCUGCAUAUUUGCAGCAC-AGACGCACUAAGAGCAGAGUAGA-AAGUACACUGAA-
(((..(((((((.(((((((((...(((..((.....))..))).)))))((((....))))))))-)))))))....)))(((.(((..-...))).)))..- ( -35.50)
>DroYak_CAF1 65774 104 + 1
CUCAAUGCGUUUUGUGCGUGGCUUUGGCAGUUAGAAUGGGAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUACGACCAGAGUAGAGAAAUACACUGAAC
.(((.(((((((.(((((((((...(((.............))).)))))((((....)))))))).)))))..((((.......)))).......)).))).. ( -32.52)
>consensus
CUCAAUGCGUUUUGUGCGUGGCUUCGGCAGUUAGAAUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAAC
(((....(((((.(((((((((...(((.............))).)))))((((....)))))))).)))))......)))(((.(((......))).)))... (-31.09 = -31.34 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,101,425 – 17,101,529
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 93.27
Mean single sequence MFE -34.06
Consensus MFE -29.61
Energy contribution -29.67
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.62
Structure conservation index 0.87
SVM decision value 1.72
SVM RNA-class probability 0.973841
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17101425 104 - 22407834
GUUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAGUCUCACUGCCGAAGCCACGCACAAAACGCAUUGAG
..((((((..((((.......(((............((.(((((((....))))))).))(((((((((.....)))..))))))..))).))))..)))))). ( -33.20)
>DroSec_CAF1 65413 104 - 1
GCUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAGUCUAACUGCCGAAGCCACGCACAAAACGCAUUGAG
.(((((((..((((.......(((............((.(((((((....))))))).))(((((((((.....)))..))))))..))).))))..))))))) ( -35.00)
>DroEre_CAF1 66568 101 - 1
-UUCAGUGUACUU-UCUACUCUGCUCUUAGUGCGUCU-GUGCUGCAAAUAUGCAGCGGCAGGCUACCAUUCUAACUGCCAAAGCCACGCACAAAACGCAUUGAG
-..(((.(((...-..))).)))..((((((((((.(-((((((((....))))))(((((.............)))))..........)))..)))))))))) ( -34.12)
>DroYak_CAF1 65774 104 - 1
GUUCAGUGUAUUUCUCUACUCUGGUCGUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUCCCAUUCUAACUGCCAAAGCCACGCACAAAACGCAUUGAG
..(((((((......((((.......))))...((.((((((((((....))))))(((((.............)))))...)))).)).......))))))). ( -33.92)
>consensus
GUUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAGUCUAACUGCCAAAGCCACGCACAAAACGCAUUGAG
.((((((((........(((........)))..((.((((((((((....))))))(((((.............)))))...)))).)).......)))))))) (-29.61 = -29.67 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,101,460 – 17,101,569
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 84.56
Mean single sequence MFE -26.12
Consensus MFE -18.35
Energy contribution -18.60
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.70
SVM decision value 1.07
SVM RNA-class probability 0.910128
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17101460 109 + 22407834
CUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAACAAAAUGCGGUUCUGCAAACCAAGUACAUAAAUUUUAUUAA
.(((..(.(((..((((((....))))))..))).).........((((((((......)))((((.........)))))))))...)))................... ( -25.00)
>DroSec_CAF1 65448 109 + 1
CUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAGCAAUAUGCAGUACUGCAAACCAAGUACAUAAAUUUUAUUAA
......(((((..((((((....))))))..))).........(..(((.(((......))).)))..).....)).(((((........))))).............. ( -25.90)
>DroEre_CAF1 66603 95 + 1
AUGGUAGCCUGCCGCUGCAUAUUUGCAGCAC-AGACGCACUAAGAGCAGAGUAGA-AAGUACACUGAA------------CUGCAAACCAUGCAGAUACUUUUUAUUAA
.((((.(((((..((((((....)))))).)-))..)))))).......((((((-(((((.......------------(((((.....))))).))))))))))).. ( -27.50)
>DroYak_CAF1 65809 109 + 1
AUGGGAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUACGACCAGAGUAGAGAAAUACACUGAACAAUUCGUGGUACUACAAGCCAAGUACAUAAAUUUUAUUAA
.(((..(.(((..((((((....))))))..))).)..(((((((.(((.(((......))).)))......)))))))........)))................... ( -26.10)
>consensus
AUGGAAGCCUGCCGCUGCAUAUUUGCAGCACCAGACGAACUAAGAGCAGAGUAGAAAAAUACACUGAACAAUAUGCGGUACUGCAAACCAAGUACAUAAAUUUUAUUAA
.(((..(.(((..((((((....))))))..))).)..........(((.(((......))).))).....................)))................... (-18.35 = -18.60 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,101,460 – 17,101,569
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 84.56
Mean single sequence MFE -30.37
Consensus MFE -24.08
Energy contribution -24.32
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.79
SVM decision value 1.66
SVM RNA-class probability 0.970464
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17101460 109 - 22407834
UUAAUAAAAUUUAUGUACUUGGUUUGCAGAACCGCAUUUUGUUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAG
....................(((((...)))))(.(((..(..(((.(((......))).)))..)..))).)(((((.(((((((....))))))).)))))...... ( -28.30)
>DroSec_CAF1 65448 109 - 1
UUAAUAAAAUUUAUGUACUUGGUUUGCAGUACUGCAUAUUGCUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAG
...................(((...((((((.....)))))).(((.(((......))).)))..........(((((.(((((((....))))))).)))))..))). ( -29.40)
>DroEre_CAF1 66603 95 - 1
UUAAUAAAAAGUAUCUGCAUGGUUUGCAG------------UUCAGUGUACUU-UCUACUCUGCUCUUAGUGCGUCU-GUGCUGCAAAUAUGCAGCGGCAGGCUACCAU
..........((..(((((((.(((((((------------(.(((((((((.-..............)))))).))-).)))))))))))))))..)).......... ( -30.76)
>DroYak_CAF1 65809 109 - 1
UUAAUAAAAUUUAUGUACUUGGCUUGUAGUACCACGAAUUGUUCAGUGUAUUUCUCUACUCUGGUCGUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUCCCAU
..............(((((........)))))...((((((.((((.(((......))).))))...))))))(((((.(((((((....))))))).)))))...... ( -33.00)
>consensus
UUAAUAAAAUUUAUGUACUUGGUUUGCAGUACCGCAUAUUGUUCAGUGUAUUUUUCUACUCUGCUCUUAGUUCGUCUGGUGCUGCAAAUAUGCAGCGGCAGGCUUCCAG
...................(((.....................(((.(((......))).)))..........(((((.(((((((....))))))).)))))..))). (-24.08 = -24.32 +   0.25)

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 12:01:25 2006