Locus 7713

Sequence ID X_DroMel_CAF1
Location 19,211,620 – 19,211,775
Length 155
Max. P 0.998518
window12649 window12650 window12651

overview

Window 9

Location 19,211,620 – 19,211,735
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -25.61
Consensus MFE -20.26
Energy contribution -19.86
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -2.30
Structure conservation index 0.79
SVM decision value 1.76
SVM RNA-class probability 0.975859
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19211620 115 + 22224390
UCUUCUCAGCCACCU-----CCUAACCGAGCAACACUCGGCUAAAUUAGUUAAGUACCACUUUUACACUACACAGCAGGCAGACAGUUUUCCCGAGUGUAGAUCUACAAUUUAGACCCUA
...............-----.....(((((.....)))))(((((((.((.(((.....)))..)).((((((....((.(((....))).))..))))))......)))))))...... ( -20.00)
>DroSec_CAF1 32956 94 + 1
--------------------CCUAACCA--CCGCACUCGGCUAAAUUAGUUAAGUACCACUUUUACACUACACAGCAGGU----AGUUUUCCCGAGUGUAGGUCUACAAUUUGGACCCUA
--------------------........--..((((((((........((.(((.....)))..))(((((.......))----)))....)))))))).((((((.....))))))... ( -24.10)
>DroSim_CAF1 7702 94 + 1
--------------------CCUAACCA--CCGCACUCGGCUAAAUUAGUUAAGUACCACUUUUACACUGCACAGCAGGC----AGUUUUCCCGAGUGUAGGUCCACAAUUUGGACCCUA
--------------------........--..((((((((..(((((.((.(((.....)))..)).((((...))))..----)))))..)))))))).((((((.....))))))... ( -29.50)
>DroEre_CAF1 30086 103 + 1
UCUUCUCAG--------UCCCCUAA-----CCACACUCGGGUAAAUUAGUUAAGUGCCACUUUUACACUACACAGCAGGC----UGUUUUCCCGAGUGUAGGUCUGCAAUUUGGACCCUA
........(--------(((.(..(-----(((((((((((.(((.......((((.........))))..((((....)----))))))))))))))).)))..)......)))).... ( -28.10)
>DroYak_CAF1 30908 110 + 1
UCUCCUCGGCC-CUUCCUCCCCUAA-----CCGCACUCGGGUAAAUUAGUUAAGUGCCACUUUUACACUACACAGCAGGC----AGUUUUCCCGAGUGUAGGUCUGCAAUUUGGACCCUA
.......((.(-(........(..(-----(((((((((((.((((........((((...................)))----))))).))))))))).)))..)......)).))... ( -26.35)
>consensus
UCU_CUC_G___________CCUAACC___CCGCACUCGGCUAAAUUAGUUAAGUACCACUUUUACACUACACAGCAGGC____AGUUUUCCCGAGUGUAGGUCUACAAUUUGGACCCUA
................................((((((((..(((((.((.(((.....)))..)).((.......))......)))))..)))))))).((((((.....))))))... (-20.26 = -19.86 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,211,620 – 19,211,735
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.63
Mean single sequence MFE -31.54
Consensus MFE -21.08
Energy contribution -20.60
Covariance contribution -0.48
Combinations/Pair 1.14
Mean z-score -1.73
Structure conservation index 0.67
SVM decision value 0.30
SVM RNA-class probability 0.677975
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19211620 115 - 22224390
UAGGGUCUAAAUUGUAGAUCUACACUCGGGAAAACUGUCUGCCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAGCCGAGUGUUGCUCGGUUAGG-----AGGUGGCUGAGAAGA
..(((((((.....)))))))((((((((....(((...(((((((...)))).)))..)))(((.....))).......))))))))..((((((((..-----...)))))))).... ( -32.00)
>DroSec_CAF1 32956 94 - 1
UAGGGUCCAAAUUGUAGACCUACACUCGGGAAAACU----ACCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAGCCGAGUGCGG--UGGUUAGG--------------------
((((..(((..((....((((((((.((((......----.))))..)))))).)).))..)))..)))).(((((...((((....)))--).))))).-------------------- ( -26.80)
>DroSim_CAF1 7702 94 - 1
UAGGGUCCAAAUUGUGGACCUACACUCGGGAAAACU----GCCUGCUGUGCAGUGUAAAAGUGGUACUUAACUAAUUUAGCCGAGUGCGG--UGGUUAGG--------------------
..(((((((.....))))))).(((((((....(((----(((....).)))))...(((.((((.....)))).)))..)))))))...--........-------------------- ( -29.90)
>DroEre_CAF1 30086 103 - 1
UAGGGUCCAAAUUGCAGACCUACACUCGGGAAAACA----GCCUGCUGUGUAGUGUAAAAGUGGCACUUAACUAAUUUACCCGAGUGUGG-----UUAGGGGA--------CUGAGAAGA
...(((((......(.((((.(((((((((...(((----(....))))..(((((.......)))))...........)))))))))))-----)).).)))--------))....... ( -35.10)
>DroYak_CAF1 30908 110 - 1
UAGGGUCCAAAUUGCAGACCUACACUCGGGAAAACU----GCCUGCUGUGUAGUGUAAAAGUGGCACUUAACUAAUUUACCCGAGUGCGG-----UUAGGGGAGGAAG-GGCCGAGGAGA
...(((((...((.(.((((..((((((((...(((----(((....).))))).....(((........)))......)))))))).))-----))...).))...)-))))....... ( -33.90)
>consensus
UAGGGUCCAAAUUGUAGACCUACACUCGGGAAAACU____GCCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAGCCGAGUGCGG___GGUUAGG___________C_GAG_AGA
..(((((.........))))).(((((((...........((((((...)))).))...(((........))).......)))))))................................. (-21.08 = -20.60 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,211,655 – 19,211,775
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.39
Mean single sequence MFE -31.56
Consensus MFE -28.88
Energy contribution -28.52
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -2.07
Structure conservation index 0.92
SVM decision value 3.13
SVM RNA-class probability 0.998518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19211655 120 - 22224390
CGGGUGUUUAACCUCAACUAACACCUCUGCCACAUCCACUUAGGGUCUAAAUUGUAGAUCUACACUCGGGAAAACUGUCUGCCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAG
.(((((((...........))))))).((((((...((((..(((((((.....)))))))((((.((((...........))))..)))))))).....)))))).............. ( -29.30)
>DroSec_CAF1 32974 116 - 1
CGGGUGUUCAACCUCAACUAACACCUCUGCCACAUCCACUUAGGGUCCAAAUUGUAGACCUACACUCGGGAAAACU----ACCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAG
.(((((((...........))))))).((((((((((.....))))...........((((((((.((((......----.))))..)))))).))....)))))).............. ( -29.30)
>DroSim_CAF1 7720 116 - 1
CGGGUGUUUAACCUCAACUAACACCUCUGCCACAUCCACUUAGGGUCCAAAUUGUGGACCUACACUCGGGAAAACU----GCCUGCUGUGCAGUGUAAAAGUGGUACUUAACUAAUUUAG
.(((((((...........))))))).((((((.(((.....(((((((.....))))))).......)))..(((----(((....).)))))......)))))).............. ( -34.70)
>DroEre_CAF1 30113 116 - 1
CGGGUGUUUAACCUCAACUAACACCUCUGCCACAUCCACUUAGGGUCCAAAUUGCAGACCUACACUCGGGAAAACA----GCCUGCUGUGUAGUGUAAAAGUGGCACUUAACUAAUUUAC
.(((((((...........))))))).((((((((((.....)))).....(((((...((((((.((((......----.))))..)))))))))))..)))))).............. ( -33.40)
>DroYak_CAF1 30942 116 - 1
CGGGUGUUUAACCUCAACUAACACCUCUGCCAUAUCCACUUAGGGUCCAAAUUGCAGACCUACACUCGGGAAAACU----GCCUGCUGUGUAGUGUAAAAGUGGCACUUAACUAAUUUAC
.(((((((...........))))))).((((((((((.....)))).....(((((...((((((.((((......----.))))..)))))))))))..)))))).............. ( -31.10)
>consensus
CGGGUGUUUAACCUCAACUAACACCUCUGCCACAUCCACUUAGGGUCCAAAUUGUAGACCUACACUCGGGAAAACU____GCCUGCUGUGUAGUGUAAAAGUGGUACUUAACUAAUUUAG
.(((((((...........))))))).((((((((((.....))))...........((((((((.((((...........))))..)))))).))....)))))).............. (-28.88 = -28.52 +  -0.36)

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 12:45:42 2006