Locus 1843

Sequence ID 2L_DroMel_CAF1
Location 5,083,368 – 5,083,501
Length 133
Max. P 0.975534
window2961 window2962 window2963 window2964

overview

Window 1

Location 5,083,368 – 5,083,461
Length 93
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.97
Mean single sequence MFE -30.64
Consensus MFE -13.75
Energy contribution -13.43
Covariance contribution -0.31
Combinations/Pair 1.18
Mean z-score -3.41
Structure conservation index 0.45
SVM decision value 1.03
SVM RNA-class probability 0.902781
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5083368 93 + 22407834
AUUUAUUAUUACCUACUUUGGGUGAAAAUCUGUACACGC---GGCCAGGCAAUCAAUUCAUAGUUA------UUUUUUAAUGAAUUGCC-------------UGGC-----UGUUGGCGA
........((((((.....)))))).....(((....((---(((((((((((....((((.....------.......))))))))))-------------))))-----)))..))). ( -28.90)
>DroSec_CAF1 12760 93 + 1
AUUUAUUACUACCCACUUUGGGUGAAAAUCUGUACACGC---GGCCAGGCAAUCAAUUCAUAUUUA------UUUUUUAAUGAAUUGCC-------------UGGC-----UGUUGGCGA
.........(((((.....)))))......(((....((---(((((((((((....((((.....------.......))))))))))-------------))))-----)))..))). ( -29.90)
>DroSim_CAF1 15008 93 + 1
AUUUAUUACUACCUACUUUGGGUGAAAAUCUGUACACGC---GGCCAGGCAAUCAAUUCAUAUUUA------UUUUUUAAUGGAUUGCC-------------UGGC-----UGUUGGCGA
.........(((((.....)))))......(((....((---((((((((((((............------..........)))))))-------------))))-----)))..))). ( -29.05)
>DroYak_CAF1 14301 119 + 1
AUUUAUAACCAACC-UUUUGGGGGAAAAUCUGUACUUGCAGCAGCCAGGCAAUCAAUUCAUAGUUACAUAUUUUUUGUAAUGAAUUGCUGUAGCUGCUGUGUUGGCAGUUGUGUUGGCGA
.....(((((((((-(....)))......((((...(((((((((...(((..((((((((...((((.......)))))))))))).))).)))))))))...))))))).)))).... ( -34.70)
>consensus
AUUUAUUACUACCCACUUUGGGUGAAAAUCUGUACACGC___GGCCAGGCAAUCAAUUCAUAGUUA______UUUUUUAAUGAAUUGCC_____________UGGC_____UGUUGGCGA
.........(((((.....)))))...................(((((.((...(((((((..................)))))))(((..............))).....))))))).. (-13.75 = -13.43 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,083,368 – 5,083,461
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.97
Mean single sequence MFE -26.38
Consensus MFE -9.75
Energy contribution -10.56
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -3.40
Structure conservation index 0.37
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5083368 93 - 22407834
UCGCCAACA-----GCCA-------------GGCAAUUCAUUAAAAAA------UAACUAUGAAUUGAUUGCCUGGCC---GCGUGUACAGAUUUUCACCCAAAGUAGGUAAUAAUAAAU
..(((.((.-----((((-------------(((((((.(((......------........))).))))))))))).---(.(((..........))).)...)).))).......... ( -23.54)
>DroSec_CAF1 12760 93 - 1
UCGCCAACA-----GCCA-------------GGCAAUUCAUUAAAAAA------UAAAUAUGAAUUGAUUGCCUGGCC---GCGUGUACAGAUUUUCACCCAAAGUGGGUAGUAAUAAAU
.(((.....-----((((-------------(((((((.(((......------........))).))))))))))).---))).............((((.....)))).......... ( -25.04)
>DroSim_CAF1 15008 93 - 1
UCGCCAACA-----GCCA-------------GGCAAUCCAUUAAAAAA------UAAAUAUGAAUUGAUUGCCUGGCC---GCGUGUACAGAUUUUCACCCAAAGUAGGUAGUAAUAAAU
..(((.((.-----((((-------------(((((((.(((......------........))).))))))))))).---(.(((..........))).)...)).))).......... ( -25.24)
>DroYak_CAF1 14301 119 - 1
UCGCCAACACAACUGCCAACACAGCAGCUACAGCAAUUCAUUACAAAAAAUAUGUAACUAUGAAUUGAUUGCCUGGCUGCUGCAAGUACAGAUUUUCCCCCAAAA-GGUUGGUUAUAAAU
..((((((....(((......((((((((((((((((((((((((.......))))...)))))))).)))..)))))))))......))).((((.....))))-.))))))....... ( -31.70)
>consensus
UCGCCAACA_____GCCA_____________GGCAAUUCAUUAAAAAA______UAAAUAUGAAUUGAUUGCCUGGCC___GCGUGUACAGAUUUUCACCCAAAGUAGGUAGUAAUAAAU
..(((.........((((.............(((((((.(((....................))).)))))))))))....(.(((..........))).)......))).......... ( -9.75 = -10.56 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,083,407 – 5,083,501
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -33.16
Consensus MFE -17.08
Energy contribution -16.71
Covariance contribution -0.37
Combinations/Pair 1.08
Mean z-score -3.06
Structure conservation index 0.52
SVM decision value 0.85
SVM RNA-class probability 0.865155
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5083407 94 + 22407834
--GGCCAGGCAAUCAAUUCAUAGUUA------UUUUUUAAUGAAUUGCC-------------UGGC-----UGUUGGCGAAGGUCAUGUCCCGUUGAUGACAAACACGAAACAGCGACAA
--(((((((((((....((((.....------.......))))))))))-------------))))-----)..((((....))))(((((.(((..((.....))...))).).)))). ( -28.20)
>DroSec_CAF1 12799 94 + 1
--GGCCAGGCAAUCAAUUCAUAUUUA------UUUUUUAAUGAAUUGCC-------------UGGC-----UGUUGGCGAAGGUCGUGUCCCGUUCAUGACAAACACGAAAGACCGACAA
--(((((((((((....((((.....------.......))))))))))-------------))))-----)(((((.....((((((.......)))))).....(....).))))).. ( -33.00)
>DroSim_CAF1 15047 94 + 1
--GGCCAGGCAAUCAAUUCAUAUUUA------UUUUUUAAUGGAUUGCC-------------UGGC-----UGUUGGCGAAGGUCAUGUCCCGUUGAUGACAAACACGAAAGACCGACAA
--((((((((((((............------..........)))))))-------------))))-----)(((((.....(((((.........))))).....(....).))))).. ( -31.65)
>DroYak_CAF1 14340 120 + 1
GCAGCCAGGCAAUCAAUUCAUAGUUACAUAUUUUUUGUAAUGAAUUGCUGUAGCUGCUGUGUUGGCAGUUGUGUUGGCGAAGGUCGUGUCCCGGCGAUGACAAACACGAAAAACCGACAA
(((((...(((..((((((((...((((.......)))))))))))).))).)))))..((((((...((((((((((....))).((((........)))))))))))....)))))). ( -39.80)
>consensus
__GGCCAGGCAAUCAAUUCAUAGUUA______UUUUUUAAUGAAUUGCC_____________UGGC_____UGUUGGCGAAGGUCAUGUCCCGUUGAUGACAAACACGAAAGACCGACAA
...((((((((....((((((..................)))))))))).............)))).....(((((((....))).((((........)))).............)))). (-17.08 = -16.71 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,083,407 – 5,083,501
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.09
Mean single sequence MFE -30.75
Consensus MFE -17.85
Energy contribution -17.91
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -3.15
Structure conservation index 0.58
SVM decision value 1.75
SVM RNA-class probability 0.975534
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5083407 94 - 22407834
UUGUCGCUGUUUCGUGUUUGUCAUCAACGGGACAUGACCUUCGCCAACA-----GCCA-------------GGCAAUUCAUUAAAAAA------UAACUAUGAAUUGAUUGCCUGGCC--
..((((.(((..(((...........)))..)))))))...........-----((((-------------(((((((.(((......------........))).))))))))))).-- ( -29.64)
>DroSec_CAF1 12799 94 - 1
UUGUCGGUCUUUCGUGUUUGUCAUGAACGGGACACGACCUUCGCCAACA-----GCCA-------------GGCAAUUCAUUAAAAAA------UAAAUAUGAAUUGAUUGCCUGGCC--
..((((((((((((((.....))))))..)))).))))...........-----((((-------------(((((((.(((......------........))).))))))))))).-- ( -32.34)
>DroSim_CAF1 15047 94 - 1
UUGUCGGUCUUUCGUGUUUGUCAUCAACGGGACAUGACCUUCGCCAACA-----GCCA-------------GGCAAUCCAUUAAAAAA------UAAAUAUGAAUUGAUUGCCUGGCC--
.(((.(((...((((((((((.....)).)))))))).....))).)))-----((((-------------(((((((.(((......------........))).))))))))))).-- ( -30.24)
>DroYak_CAF1 14340 120 - 1
UUGUCGGUUUUUCGUGUUUGUCAUCGCCGGGACACGACCUUCGCCAACACAACUGCCAACACAGCAGCUACAGCAAUUCAUUACAAAAAAUAUGUAACUAUGAAUUGAUUGCCUGGCUGC
.(((.(((..((.(((((((((........))))((.....))..)))))))..))).)))..((((((((((((((((((((((.......))))...)))))))).)))..))))))) ( -30.80)
>consensus
UUGUCGGUCUUUCGUGUUUGUCAUCAACGGGACACGACCUUCGCCAACA_____GCCA_____________GGCAAUUCAUUAAAAAA______UAAAUAUGAAUUGAUUGCCUGGCC__
(((.(((....((((((((..........))))))))...))).))).......((((.............(((((((.(((....................))).)))))))))))... (-17.85 = -17.91 +   0.06)

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 10:12:39 2006