Locus 5917

Sequence ID 2L_DroMel_CAF1
Location 16,702,717 – 16,703,027
Length 310
Max. P 0.884830
window9403 window9404 window9405 window9406 window9407

overview

Window 3

Location 16,702,717 – 16,702,828
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.81
Mean single sequence MFE -23.94
Consensus MFE -19.99
Energy contribution -20.30
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.83
SVM decision value 0.93
SVM RNA-class probability 0.884830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702717 111 + 22407834
CGAAAAAAGUGCAGUCCGGUCGUAAAACAUU-----UCCA----UAUAUCUGGCGGACAGUAAAUAAUAAAAAAAAAAAGCUACGACAGCAGCUUGUCGAGUCCACGCGACACAUGAAAA
..................(((((........-----.(((----......))).(((((((..................))).((((((....)))))).))))..)))))......... ( -19.47)
>DroSec_CAF1 157406 102 + 1
CGAAAAAAGUGCAGUCCGGUCGUAAAACAUU-----UCCA----UAUAUCUGGCGGACAAUA---------AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAA
..........((.(((((((......))...-----.(((----......))))))))....---------........(((.....))).)).(((((((....)))))))........ ( -24.00)
>DroSim_CAF1 157336 106 + 1
CGAAAAAAGUGCAGUCCGGUCGUAAAACAUU-----UCCAGAUGUAUAUCUGGCGGAUAAUA---------AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAA
..........((.(((((((......))...-----.((((((....)))))))))))....---------........(((.....))).)).(((((((....)))))))........ ( -27.10)
>DroEre_CAF1 158799 109 + 1
CGAAAAAAGUGCAGUCCGGUCGUAAAACAUUUCAUUUCCA----UAUAUCUGGCGGACAAUA-------AUAAAAAAAAGCAGCGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAA
.............(((((((......)).........(((----......))))))))....-------........((((.((....)).))))((((((....))))))......... ( -25.20)
>consensus
CGAAAAAAGUGCAGUCCGGUCGUAAAACAUU_____UCCA____UAUAUCUGGCGGACAAUA_________AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAA
..........((.(((((((......)).........(((..........)))))))).....................(((.....))).)).(((((((....)))))))........ (-19.99 = -20.30 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,702,717 – 16,702,828
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.81
Mean single sequence MFE -27.52
Consensus MFE -22.16
Energy contribution -22.73
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.50
Structure conservation index 0.81
SVM decision value 0.15
SVM RNA-class probability 0.609559
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702717 111 - 22407834
UUUUCAUGUGUCGCGUGGACUCGACAAGCUGCUGUCGUAGCUUUUUUUUUUUAUUAUUUACUGUCCGCCAGAUAUA----UGGA-----AAUGUUUUACGACCGGACUGCACUUUUUUCG
((((((((((((..((((((.....(((((((....)))))))...................))))))..))))))----))))-----))(((....(....)....)))......... ( -26.85)
>DroSec_CAF1 157406 102 - 1
UUUUUAUGUGUCGCGUGGACGCGACAAGCUGCUGUCGUAGCUUUUUUUU---------UAUUGUCCGCCAGAUAUA----UGGA-----AAUGUUUUACGACCGGACUGCACUUUUUUCG
......(((((((((....))))))(((((((....)))))))......---------....((((((((......----))).-----...(((....)))))))).)))......... ( -27.60)
>DroSim_CAF1 157336 106 - 1
UUUUUAUGUGUCGCGUGGACGCGACAAGCUGCUGUCGUAGCUUUUUUUU---------UAUUAUCCGCCAGAUAUACAUCUGGA-----AAUGUUUUACGACCGGACUGCACUUUUUUCG
......(((((((((....))))))(((((((....)))))))......---------.....((((((((((....)))))).-----...(((....)))))))..)))......... ( -29.10)
>DroEre_CAF1 158799 109 - 1
UUUUUAUGUGUCGCGUGGACGCGACAAGCUGCUGUCGCUGCUUUUUUUUAU-------UAUUGUCCGCCAGAUAUA----UGGAAAUGAAAUGUUUUACGACCGGACUGCACUUUUUUCG
((((((((((((..((((((((((((......)))))).............-------....))))))..))))))----)))))).(((((((....(....)....)))....)))). ( -26.52)
>consensus
UUUUUAUGUGUCGCGUGGACGCGACAAGCUGCUGUCGUAGCUUUUUUUU_________UAUUGUCCGCCAGAUAUA____UGGA_____AAUGUUUUACGACCGGACUGCACUUUUUUCG
......(((((((((....))))))(((((((....)))))))...................((((((((..........))).........(((....)))))))).)))......... (-22.16 = -22.73 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,702,752 – 16,702,868
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.93
Mean single sequence MFE -28.43
Consensus MFE -23.81
Energy contribution -24.38
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.42
Structure conservation index 0.84
SVM decision value 0.07
SVM RNA-class probability 0.569606
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702752 116 + 22407834
----UAUAUCUGGCGGACAGUAAAUAAUAAAAAAAAAAAGCUACGACAGCAGCUUGUCGAGUCCACGCGACACAUGAAAAUAUUGCUUUGUUUUUUCCGCUUUGUAUUUCGGGGAUUGCU
----.((((..((((((.............(((((.(((((..((((((....)))))).(((.....))).............))))).)))))))))))..))))............. ( -22.91)
>DroSec_CAF1 157441 107 + 1
----UAUAUCUGGCGGACAAUA---------AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAAUAUUGCUUUGUUUUUUCCGGUUUGUAUUUCGGGGAUCGCU
----.......(((((.(((((---------......(((((.(....).)))))((((((....)))))).........)))))........(..((((........))))..)))))) ( -29.20)
>DroSim_CAF1 157371 111 + 1
GAUGUAUAUCUGGCGGAUAAUA---------AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAAUAUUGCUUUGUUUUUUCCGCUUUGUAUUUCGGGGAUCGCU
((.(((((...((((((.((((---------((....(((((.(....).)))))((((((....))))))...............))))))...)))))).))))).)).......... ( -31.90)
>DroEre_CAF1 158839 109 + 1
----UAUAUCUGGCGGACAAUA-------AUAAAAAAAAGCAGCGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAAUAUUGCUUUGUUUUUUCCGCUUUGUAUUUCGGGGAUCGCA
----.((((..((((((....(-------(((((...((((.((....)).))))((((((....))))))...............))))))...))))))..))))............. ( -29.70)
>consensus
____UAUAUCUGGCGGACAAUA_________AAAAAAAAGCUACGACAGCAGCUUGUCGCGUCCACGCGACACAUAAAAAUAUUGCUUUGUUUUUUCCGCUUUGUAUUUCGGGGAUCGCU
.....((((..((((((....................(((((.(....).)))))((((((....))))))....(((((((......)))))))))))))..))))............. (-23.81 = -24.38 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,702,828 – 16,702,947
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.40
Mean single sequence MFE -23.20
Consensus MFE -20.26
Energy contribution -21.07
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.15
Structure conservation index 0.87
SVM decision value 0.92
SVM RNA-class probability 0.881005
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702828 119 - 22407834
GCGUAUUUUGAGCGGUGACAAGAUUGCUUACAAAACACACACAAAGUGAAAAA-GUAUUUGUCAAGAAGCUAGAAGGAAAAGCAAUCCCCGAAAUACAAAGCGGAAAAAACAAAGCAAUA
((((((((((...(....)..((((((((........(((.....)))....(-((.(((....))).)))........))))))))..)))))))).....(.......)...)).... ( -23.30)
>DroSec_CAF1 157508 119 - 1
GCGUAUUUUGAGCGGUGACAAGAUUGCUUACAAAACACACACAAAGUGAAAAA-GUAUUUGGCAAGAAGCUAGAAGGAAAAGCGAUCCCCGAAAUACAAACCGGAAAAAACAAAGCAAUA
((((((((((...(....)..((((((((........(((.....))).....-...((((((.....)))))).....))))))))..)))))))).....(.......)...)).... ( -26.80)
>DroSim_CAF1 157442 119 - 1
GCGUAUUUUGAGCGGUGACAAGAUUGGUUACAAAACACACACAAAGUGAAAAA-GUAUUUGGCAAGAAGCUAGAAGGAAAAGCGAUCCCCGAAAUACAAAGCGGAAAAAACAAAGCAAUA
((((((((((...(....)..(((((.((........(((.....))).....-...((((((.....)))))).....)).)))))..)))))))).....(.......)...)).... ( -22.30)
>DroEre_CAF1 158908 118 - 1
GCGUAUUUUGAGCGCUGACAAGAUUGCUUACAAAACA--CACAAAGUGAAAAACACAUUUGGCAAGAAGCUAGAAGGAAAUGCGAUCCCCGAAAUACAAAGCGGAAAAAACAAAGCAAUA
((((((((((.(......)..((((((........((--(.....))).......(.((((((.....)))))).).....))))))..)))))))).....(.......)...)).... ( -20.40)
>consensus
GCGUAUUUUGAGCGGUGACAAGAUUGCUUACAAAACACACACAAAGUGAAAAA_GUAUUUGGCAAGAAGCUAGAAGGAAAAGCGAUCCCCGAAAUACAAAGCGGAAAAAACAAAGCAAUA
((((((((((...(....)..((((((((......(((.......))).........((((((.....)))))).....))))))))..)))))))).....(.......)...)).... (-20.26 = -21.07 +   0.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,702,907 – 16,703,027
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.35
Mean single sequence MFE -30.01
Consensus MFE -24.33
Energy contribution -24.83
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.81
SVM decision value -0.02
SVM RNA-class probability 0.523377
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702907 120 + 22407834
GUGUGUUUUGUAAGCAAUCUUGUCACCGCUCAAAAUACGCCUGCGCAUUUGCCUGGCUCAUUUUAAUGCUUAGAUCAUGCAGAUAGCCAGGCCAACGAACAUUUCAAUGUACAUACAGUG
((((((((((..(((............))))))))))))).((..((((.((((((((.(((....(((.........))))))))))))))....((.....))))))..))....... ( -30.70)
>DroSec_CAF1 157587 108 + 1
GUGUGUUUUGUAAGCAAUCUUGUCACCGCUCAAAAUACGCCUGCGCAUUUGCCUGGCUCAUUAUAAUGCUUAGAUCAUGCAGAUAGCCAGGCCAACG------------UAAGUACAGUG
((((((((((..(((............)))))))))))))(((.......((((((((.(((....(((.........))))))))))))))..((.------------...)).))).. ( -30.70)
>DroSim_CAF1 157521 108 + 1
GUGUGUUUUGUAACCAAUCUUGUCACCGCUCAAAAUACGCCUGCGCAUUUGCCUGGCUCAUUAUAAUGCUUAGAUCAUGCAGAUAGCCAGGCCAACG------------UAAGUACAGUG
((((((((((....................))))))))))(((.......((((((((.(((....(((.........))))))))))))))..((.------------...)).))).. ( -27.95)
>DroEre_CAF1 158988 114 + 1
G--UGUUUUGUAAGCAAUCUUGUCAGCGCUCAAAAUACGCCUGCGCAUUUGCCUGGCUCAUUAUAAUGCCCAGAUCAUGCAGAUAGCCAGGCCAACGAAUAUUUCAA----UGUACAGUG
(--(((((((...((..........))...))))))))..(((..((((.((((((((.(((...(((.......)))...)))))))))))....((.....))))----))..))).. ( -30.70)
>consensus
GUGUGUUUUGUAAGCAAUCUUGUCACCGCUCAAAAUACGCCUGCGCAUUUGCCUGGCUCAUUAUAAUGCUUAGAUCAUGCAGAUAGCCAGGCCAACG____________UAAGUACAGUG
..((((((((..(((............)))))))))))(((((.((((((((.((((((((....)))...)).))).)))))).)))))))............................ (-24.33 = -24.83 +   0.50)

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 11:56:31 2006