Locus 1732

Sequence ID 2L_DroMel_CAF1
Location 4,753,839 – 4,753,983
Length 144
Max. P 0.939116
window2779 window2780 window2781 window2782

overview

Window 9

Location 4,753,839 – 4,753,943
Length 104
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 76.62
Mean single sequence MFE -25.00
Consensus MFE -13.50
Energy contribution -14.06
Covariance contribution 0.56
Combinations/Pair 1.24
Mean z-score -1.81
Structure conservation index 0.54
SVM decision value 0.27
SVM RNA-class probability 0.661653
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4753839 104 + 22407834
UAAAAUAUUAAAUGACCACAAUGUUUAAAGUGC--------AAUAA-------AUUUUCAUCGUGUGGCAUUAAUACCAUUGCCACACCACUGUUCCUGCCACUUUCUGCUGCUUGGCU
...............(((....((..(((((((--------(...(-------((.......((((((((..........))))))))....)))..)).))))))..))....))).. ( -21.30)
>DroSec_CAF1 182306 104 + 1
UGAAAUAUUAAAUGGUCACAAUGUUUAAAGUGC--------AUUAA-------AUUCCCGGCGUGUGGCAUUUAUAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCU
.............(((((....((..(((((((--------(...(-------((.....(.((((((((..........)))))))))...)))..)).))))))..))....))))) ( -24.80)
>DroSim_CAF1 178236 104 + 1
UGAAAUAUUAAAUGGCCACAAUGUUUAAAGUGC--------AAUAA-------AUUUCCGGCGUGUGGCAUUAAAAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCU
.............(((((....((..(((((((--------(...(-------((.....(.((((((((..........)))))))))...)))..)).))))))..))....))))) ( -27.50)
>DroEre_CAF1 190889 103 + 1
UU-AAUAUUAAAUAGCCGCAAUGUUUAAACUGC--------AUUAA-------AUUUCAAGUGUAUAACAUUAAUAUCGUUGCCGCACCACUGUUCCUGCCACCUUUUGCUGCUCGGAU
..-...........((.((((((.((((..(((--------(((..-------......)))))).....))))...)))))).))....(((.....((........))....))).. ( -14.80)
>DroYak_CAF1 188877 117 + 1
-G-AACAUUUUAGUACAGCAGUUUUCAGAUUGAAAGUUUUCGUUAAGUCACAGAUUUUAAGUGUGUGGCAUUAACAUCGUUGCCACACCACUGUUCGUGGCACUUUUUGCUGCUGUGAU
-.-..........(((((((((((((.....))))...........(((((.((.....(((((((((((..........))))))).))))..))))))).......))))))))).. ( -36.60)
>consensus
UGAAAUAUUAAAUGGCCACAAUGUUUAAAGUGC________AUUAA_______AUUUCCAGCGUGUGGCAUUAAUAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCU
...............(((....((..((((((..............................((((((((..........))))))))((.......)).))))))..))....))).. (-13.50 = -14.06 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,753,839 – 4,753,943
Length 104
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 76.62
Mean single sequence MFE -26.86
Consensus MFE -15.91
Energy contribution -16.75
Covariance contribution 0.84
Combinations/Pair 1.33
Mean z-score -2.08
Structure conservation index 0.59
SVM decision value 1.28
SVM RNA-class probability 0.939116
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4753839 104 - 22407834
AGCCAAGCAGCAGAAAGUGGCAGGAACAGUGGUGUGGCAAUGGUAUUAAUGCCACACGAUGAAAAU-------UUAUU--------GCACUUUAAACAUUGUGGUCAUUUAAUAUUUUA
.((......))...(((((((....((((((((((((((..........))))))))(((((....-------)))))--------..........)))))).)))))))......... ( -27.00)
>DroSec_CAF1 182306 104 - 1
AGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUAUAAAUGCCACACGCCGGGAAU-------UUAAU--------GCACUUUAAACAUUGUGACCAUUUAAUAUUUCA
.((((............)))).((.((((((((((((((..........))))))))........(-------((((.--------.....)))))))))))..))............. ( -26.20)
>DroSim_CAF1 178236 104 - 1
AGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUUUUAAUGCCACACGCCGGAAAU-------UUAUU--------GCACUUUAAACAUUGUGGCCAUUUAAUAUUUCA
.((......))...(((((((....((((((((((((((..........))))))))((.(.....-------...).--------))........)))))).)))))))......... ( -29.40)
>DroEre_CAF1 190889 103 - 1
AUCCGAGCAGCAAAAGGUGGCAGGAACAGUGGUGCGGCAACGAUAUUAAUGUUAUACACUUGAAAU-------UUAAU--------GCAGUUUAAACAUUGCGGCUAUUUAAUAUU-AA
.....(((.((((.(((((.....((((.(((((((....)).))))).))))...)))))....(-------((((.--------.....)))))..)))).)))..........-.. ( -21.60)
>DroYak_CAF1 188877 117 - 1
AUCACAGCAGCAAAAAGUGCCACGAACAGUGGUGUGGCAACGAUGUUAAUGCCACACACUUAAAAUCUGUGACUUAACGAAAACUUUCAAUCUGAAAACUGCUGUACUAAAAUGUU-C-
...(((((((....(((((((((.....)))))((((((..........)))))).(((.........))))))).........((((.....)))).)))))))...........-.- ( -30.10)
>consensus
AGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUAUUAAUGCCACACGCUGGAAAU_______UUAAU________GCACUUUAAACAUUGUGGCCAUUUAAUAUUUCA
..............(((((((....((((((((((((((..........))))))))................(((................))).)))))).)))))))......... (-15.91 = -16.75 +   0.84)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,753,872 – 4,753,983
Length 111
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 86.69
Mean single sequence MFE -28.96
Consensus MFE -18.46
Energy contribution -18.90
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -2.58
Structure conservation index 0.64
SVM decision value 0.44
SVM RNA-class probability 0.737911
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4753872 111 + 22407834
-AAUAA-------AUUUUCAUCGUGUGGCAUUAAUACCAUUGCCACACCACUGUUCCUGCCACUUUCUGCUGCUUGGCUGCCUGGCACUCUUGUGCUAAUUUCGAUUUAAUUUUAUUUG
-(((((-------(.((..(((((((((((..........))))))))..........((((............))))....((((((....)))))).....)))..)).)))))).. ( -27.20)
>DroSec_CAF1 182339 111 + 1
-AUUAA-------AUUCCCGGCGUGUGGCAUUUAUAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCUGCAUGGCACUCUUGUGCUAAUUUCGAUUUAAUUUUAUUUG
-(((((-------(((....((((((((((..........))))))))..........((((............)))).)).((((((....)))))).....))))))))........ ( -29.00)
>DroSim_CAF1 178269 111 + 1
-AAUAA-------AUUUCCGGCGUGUGGCAUUAAAAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCUGCCUGGCACUCUUGUGCUAAUUUCGAUUUAAUUUUAUUUG
-..(((-------(((...(((((((((((..........))))))))..........((((............)))).)))((((((....)))))).....)))))).......... ( -30.90)
>DroEre_CAF1 190921 111 + 1
-AUUAA-------AUUUCAAGUGUAUAACAUUAAUAUCGUUGCCGCACCACUGUUCCUGCCACCUUUUGCUGCUCGGAUGCCUGGCACUCUGGUGCUAAUUUCGAUUUAAUUUUAUUUG
-.....-------...........((((.(((((.((((.....((((((..((.((.((..((...........))..))..)).))..))))))......))))))))).))))... ( -21.00)
>DroYak_CAF1 188915 119 + 1
CGUUAAGUCACAGAUUUUAAGUGUGUGGCAUUAACAUCGUUGCCACACCACUGUUCGUGGCACUUUUUGCUGCUGUGAUGCCUGGCACUCUGGUGCUAAUUUCGAUUUAAUUUUAUUUG
.((((((((.(((......(((((((((((..........))))))).))))..(((..((((.....).)))..)))...)))((((....)))).......))))))))........ ( -36.70)
>consensus
_AUUAA_______AUUUCCAGCGUGUGGCAUUAAUAUCGUUGCCACACCACUGUUCCUGCCACUUUUUGCUGCUUGGCUGCCUGGCACUCUUGUGCUAAUUUCGAUUUAAUUUUAUUUG
......................((((((((..........)))))))).......................((......)).((((((....))))))..................... (-18.46 = -18.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,753,872 – 4,753,983
Length 111
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 86.69
Mean single sequence MFE -26.70
Consensus MFE -17.80
Energy contribution -17.72
Covariance contribution -0.08
Combinations/Pair 1.16
Mean z-score -1.97
Structure conservation index 0.67
SVM decision value 0.10
SVM RNA-class probability 0.585608
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4753872 111 - 22407834
CAAAUAAAAUUAAAUCGAAAUUAGCACAAGAGUGCCAGGCAGCCAAGCAGCAGAAAGUGGCAGGAACAGUGGUGUGGCAAUGGUAUUAAUGCCACACGAUGAAAAU-------UUAUU-
..((((((.((..(((.......((((....))))......((((..(....)....))))..........((((((((..........)))))))))))..)).)-------)))))- ( -25.50)
>DroSec_CAF1 182339 111 - 1
CAAAUAAAAUUAAAUCGAAAUUAGCACAAGAGUGCCAUGCAGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUAUAAAUGCCACACGCCGGGAAU-------UUAAU-
......(((((...(((......((((....))))...((.((((............))))..........((((((((..........))))))))))))).)))-------))...- ( -26.50)
>DroSim_CAF1 178269 111 - 1
CAAAUAAAAUUAAAUCGAAAUUAGCACAAGAGUGCCAGGCAGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUUUUAAUGCCACACGCCGGAAAU-------UUAUU-
..((((((...............((((....))))..(((.((((............))))..........((((((((..........))))))))))).....)-------)))))- ( -28.70)
>DroEre_CAF1 190921 111 - 1
CAAAUAAAAUUAAAUCGAAAUUAGCACCAGAGUGCCAGGCAUCCGAGCAGCAAAAGGUGGCAGGAACAGUGGUGCGGCAACGAUAUUAAUGUUAUACACUUGAAAU-------UUAAU-
...((((.((((((((.......((((((..((.((.(.((.((...........)))).).)).))..))))))(....)))).))))).))))...........-------.....- ( -24.10)
>DroYak_CAF1 188915 119 - 1
CAAAUAAAAUUAAAUCGAAAUUAGCACCAGAGUGCCAGGCAUCACAGCAGCAAAAAGUGCCACGAACAGUGGUGUGGCAACGAUGUUAAUGCCACACACUUAAAAUCUGUGACUUAACG
.......................((((....))))......((((((.......(((((((((.....))))(((((((..........)))))))))))).....))))))....... ( -28.70)
>consensus
CAAAUAAAAUUAAAUCGAAAUUAGCACAAGAGUGCCAGGCAGCCAAGCAGCAAAAAGUGGCAGGAACAGUGGUGUGGCAACGAUAUUAAUGCCACACGCUGGAAAU_______UUAAU_
........................(((.....((((..((......)).((.....))))))......)))((((((((..........))))))))...................... (-17.80 = -17.72 +  -0.08)

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 10:09:44 2006