Locus 4185

Sequence ID X_DroMel_CAF1
Location 10,992,869 – 10,993,038
Length 169
Max. P 0.713876
window6873 window6874 window6875 window6876

overview

Window 3

Location 10,992,869 – 10,992,986
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.70
Mean single sequence MFE -36.33
Consensus MFE -26.69
Energy contribution -27.38
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.73
SVM decision value -0.03
SVM RNA-class probability 0.519945
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10992869 117 + 22224390
GUAUUGGUGAGAACCUGUGGACGCUGCGAAGCGCGCCAA-AAAAUAAAAAUGCCGACAUACAAAUAGUGCAGCGUUUUC--UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGC
.(((.(((....))).)))(((((((((..(..(((((.-......(((((((.(.(((.......)))).))))))).--(((((......))))).)))))..)..)))))).))).. ( -37.90)
>DroSec_CAF1 4971 116 + 1
GUAUUGGUGAGAACCUGUGGACGCUGCGAAGCGCGGCAAAAAAAUAAAAAUGCCGACAUACAAAUAGUGCAGCGUUUUC--UUAGCUCAUUUGCUGGCUGGCAAACAG--CAGCAGUCGC
......(((((.....(..((((((((.....((((((............))))).)..((.....))))))))))..)--....)))))((((((.(((.....)))--)))))).... ( -36.90)
>DroEre_CAF1 4650 116 + 1
GUAUUGGUGAGAACCUGUGGACGCUGCAAAGCGCGCCAA-AA---AAAAAUGCCGACAUACAAAUAAUGCAUCGUUUUUUGUUUGCUCAUUUGCUAGUUGGCGACGAGCGCAGCAGUCGC
.(((.(((....))).)))((((((((....((((((((-..---..(((((..(.((.(((((.((((...)))).))))).))).))))).....)))))).))...))))).))).. ( -35.00)
>DroYak_CAF1 5460 113 + 1
GCAUCGGUGAGAACCUGUGGACGCUGCAAAGCGCGCCAA-AA---AAAAAUGCCGACAUACAAAUAAUGCUGUGUUUUC---UUGCUCAUUUGCUGGCUGGCGACGAGCGCAGCAGUCGC
.(((.(((....))).)))((((((((....(((((((.-..---......(((((((((((.....)).))))))...---..((......)).)))))))).))...))))).))).. ( -35.50)
>consensus
GUAUUGGUGAGAACCUGUGGACGCUGCAAAGCGCGCCAA_AA___AAAAAUGCCGACAUACAAAUAAUGCAGCGUUUUC__UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGC
.(((.(((....))).)))((((((((......(((((........(((((((.(.(((.......)))).)))))))....((((......))))..)))))......))))).))).. (-26.69 = -27.38 +   0.69)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,992,908 – 10,993,026
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.73
Mean single sequence MFE -29.50
Consensus MFE -20.48
Energy contribution -21.29
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.69
SVM decision value 0.38
SVM RNA-class probability 0.713876
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10992908 118 + 22224390
AAAAUAAAAAUGCCGACAUACAAAUAGUGCAGCGUUUUC--UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUUUAUAUAUUCUAA
...(((.((((((.(((........((((.(((......--...)))))))(((((((((.....)))).))))))))((((((........)))))).....)))))).)))....... ( -33.80)
>DroSec_CAF1 5011 116 + 1
AAAAUAAAAAUGCCGACAUACAAAUAGUGCAGCGUUUUC--UUAGCUCAUUUGCUGGCUGGCAAACAG--CAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUUUAUAUAUUCUAA
...(((.((((((.(((........((((.(((......--...)))))))(((((.(((.....)))--))))))))((((((........)))))).....)))))).)))....... ( -30.50)
>DroEre_CAF1 4689 116 + 1
AA---AAAAAUGCCGACAUACAAAUAAUGCAUCGUUUUUUGUUUGCUCAUUUGCUAGUUGGCGACGAGCGCAGCAGUCGCCAUUCACGUGAAAAUCGCCAAUCGCAUU-CUAAAUUCUAA
..---...(((((.((((.(((((.((((...)))).))))).)).)).((..(....(((((((..((...)).))))))).....)..))...........)))))-........... ( -24.90)
>DroYak_CAF1 5499 112 + 1
AA---AAAAAUGCCGACAUACAAAUAAUGCUGUGUUUUC---UUGCUCAUUUGCUGGCUGGCGACGAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUU--UAAAUUCUAA
..---..((((((.(((..........((((((((((..---(((((..((....))..))))).)))))))))))))((((((........)))))).....)))))--)......... ( -28.80)
>consensus
AA___AAAAAUGCCGACAUACAAAUAAUGCAGCGUUUUC__UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUU_AUAAAUUCUAA
.......((((((.(((...(((((...((..............))..)))))...((((((.....)).)))).)))((((((........)))))).....))))))........... (-20.48 = -21.29 +   0.81)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,992,908 – 10,993,026
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.73
Mean single sequence MFE -31.20
Consensus MFE -23.44
Energy contribution -24.69
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.75
SVM decision value 0.14
SVM RNA-class probability 0.601333
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10992908 118 - 22224390
UUAGAAUAUAUAAAUGCGAUUGGCGAUUUUCACGUGAAUCGCGACUGCUGCGCUGUUCGCCAGCCAGCAAAUGAGCUAA--GAAAACGCUGCACUAUUUGUAUGUCGGCAUUUUUAUUUU
((((..(((.....(((((((.(((.......))).)))))))..(((((.((((.....))))))))).)))..))))--(((((.((((.((.........)))))).)))))..... ( -33.90)
>DroSec_CAF1 5011 116 - 1
UUAGAAUAUAUAAAUGCGAUUGGCGAUUUUCACGUGAAUCGCGACUGCUG--CUGUUUGCCAGCCAGCAAAUGAGCUAA--GAAAACGCUGCACUAUUUGUAUGUCGGCAUUUUUAUUUU
((((..(((.....(((((((.(((.......))).)))))))..(((((--(((.....))).))))).)))..))))--(((((.((((.((.........)))))).)))))..... ( -30.60)
>DroEre_CAF1 4689 116 - 1
UUAGAAUUUAG-AAUGCGAUUGGCGAUUUUCACGUGAAUGGCGACUGCUGCGCUCGUCGCCAACUAGCAAAUGAGCAAACAAAAAACGAUGCAUUAUUUGUAUGUCGGCAUUUUU---UU
.........((-(((((..((((((((.(((....))).((((.(....))))).))))))))...(((((((((((............))).))))))))......))))))).---.. ( -29.00)
>DroYak_CAF1 5499 112 - 1
UUAGAAUUUA--AAUGCGAUUGGCGAUUUUCACGUGAAUCGCGACUGCUGCGCUCGUCGCCAGCCAGCAAAUGAGCAA---GAAAACACAGCAUUAUUUGUAUGUCGGCAUUUUU---UU
.........(--(((((((((.(((.......))).)))).((((.((((.((.....))))))..((((((((((..---.........)).))))))))..))))))))))..---.. ( -31.30)
>consensus
UUAGAAUAUAU_AAUGCGAUUGGCGAUUUUCACGUGAAUCGCGACUGCUGCGCUCGUCGCCAGCCAGCAAAUGAGCAAA__GAAAACGCUGCACUAUUUGUAUGUCGGCAUUUUU___UU
............(((((((((.(((.......))).)))).((((.((((.((.....))))))..((((((((((..............)).))))))))..)))))))))........ (-23.44 = -24.69 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,992,947 – 10,993,038
Length 91
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 90.51
Mean single sequence MFE -21.15
Consensus MFE -15.77
Energy contribution -16.40
Covariance contribution 0.63
Combinations/Pair 1.11
Mean z-score -1.66
Structure conservation index 0.75
SVM decision value 0.09
SVM RNA-class probability 0.577556
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10992947 91 + 22224390
-UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUUUAUAUAUUCUAAAUAACAAAUCGA
-((((.....((((((((((.....)))).))))))..((((((...(((.....))).))))))...........))))............ ( -24.20)
>DroSec_CAF1 5050 89 + 1
-UUAGCUCAUUUGCUGGCUGGCAAACAG--CAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUUUAUAUAUUCUAAAUAACAAAUCAA
-((((.....((((((.(((.....)))--))))))..((((((...(((.....))).))))))...........))))............ ( -20.90)
>DroEre_CAF1 4726 91 + 1
GUUUGCUCAUUUGCUAGUUGGCGACGAGCGCAGCAGUCGCCAUUCACGUGAAAAUCGCCAAUCGCAUU-CUAAAUUCUAAAUAACAAAUCAA
(..(((..(((.((....(((((((..((...)).)))))))(((....)))....)).))).)))..-)...................... ( -18.10)
>DroYak_CAF1 5535 88 + 1
--UUGCUCAUUUGCUGGCUGGCGACGAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUU--UAAAUUCUAAAUAACAAAUCAA
--........((((((((((....).))).))))))..((((((...(((.....))).))))))...--...................... ( -21.40)
>consensus
_UUAGCUCAUUUGCUGGCUGGCGAACAGCGCAGCAGUCGCGAUUCACGUGAAAAUCGCCAAUCGCAUU_AUAAAUUCUAAAUAACAAAUCAA
..((((......))))((((((.....)).))))....((((((...(((.....))).))))))........................... (-15.77 = -16.40 +   0.63)

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 11:18:33 2006