Locus 8556

Sequence ID 3R_DroMel_CAF1
Location 22,857,622 – 22,857,716
Length 94
Max. P 0.938925
window13748 window13749

overview

Window 8

Location 22,857,622 – 22,857,716
Length 94
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 76.78
Mean single sequence MFE -27.17
Consensus MFE -17.48
Energy contribution -17.42
Covariance contribution -0.06
Combinations/Pair 1.32
Mean z-score -1.90
Structure conservation index 0.64
SVM decision value 1.27
SVM RNA-class probability 0.938925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22857622 94 + 27905053
UUUAAAGCUUUAACUUCUUGAGCAACUACUUGUGUUAUUUU--CCGA-----GACGG----AUUUUGGGGCUGUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
..................((((((.((((..((.(((...(--(((.-----..)))----)...))).)).))))..(((((((....)))))))..)))))). ( -28.90)
>DroPse_CAF1 4039 80 + 1
GGUAUGGGUUUGGG------------------UUUGGUUUU--UGGG-----AUUGGGCCUAGGCUGGGUCUUUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
....(.((((((((------------------((..(((..--...)-----))..)))))))))).)......(((((((((((....)))))))..))))... ( -30.60)
>DroSec_CAF1 3845 94 + 1
UUUAAAGCUUUAACUUCUUGAGCAACUACUUGUGUUAUUUU--UCGA-----GUCGG----AUUUUGGGGCUGUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
..................((((((........((((((.(.--.(((-----(....----..))))..)..))))))(((((((....)))))))..)))))). ( -26.80)
>DroSim_CAF1 3864 94 + 1
UUUAAAGCUUUAACUUCUUGAGCAACUACUUGUGUUAUUUU--UCGA-----GGCGG----AUUUUGGGGCUGUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
.....(((((((((((((((((.((..((....))..)).)--))))-----)).))----...))))))))(((((((((((((....)))))))..))).))) ( -27.30)
>DroEre_CAF1 3895 101 + 1
CUUGAAGUUUUAACUUCUUAAGCAAUUUUCUGUGUUUUUUUUUUGGGCUGUUGGCGU----AUUUUGGGGCUGUGGCAGCGUGUCAAAUGGCAUGUAAUGCUCAC
((..((((.(((((..((((((.((.............)).))))))..)))))...----))))..))...(((((((((((((....)))))))..))).))) ( -21.82)
>DroYak_CAF1 3744 96 + 1
UUUGAAGCUUUACCUUCUUAAGCAACUAUUUGUGUCUUUUUUUUUGG-----GACGG----AUUUUGGGGCUGUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
...((((......))))...(((..(....(.((((((.......))-----)))).----)....)..)))(((((((((((((....)))))))..))).))) ( -27.60)
>consensus
UUUAAAGCUUUAACUUCUUGAGCAACUACUUGUGUUAUUUU__UCGA_____GACGG____AUUUUGGGGCUGUGGCAGCGUGCCAAAUGGCAUGUAAUGCUCAC
.....((((((((........((((....))))..........(((........))).......))))))))(((((((((((((....)))))))..))).))) (-17.48 = -17.42 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,857,622 – 22,857,716
Length 94
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 76.78
Mean single sequence MFE -18.75
Consensus MFE -10.33
Energy contribution -12.17
Covariance contribution 1.83
Combinations/Pair 1.11
Mean z-score -1.78
Structure conservation index 0.55
SVM decision value 0.44
SVM RNA-class probability 0.736105
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22857622 94 - 27905053
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCACAGCCCCAAAAU----CCGUC-----UCGG--AAAAUAACACAAGUAGUUGCUCAAGAAGUUAAAGCUUUAAA
.((((((((((.((((....)))).((((...)))).......(----(((..-----.)))--)...........)))).)))))).(((((....)))))... ( -24.80)
>DroPse_CAF1 4039 80 - 1
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCAAAGACCCAGCCUAGGCCCAAU-----CCCA--AAAACCAAA------------------CCCAAACCCAUACC
.((.((((...))))))((((((.....))))))......((....)).....-----....--.........------------------.............. ( -11.40)
>DroSec_CAF1 3845 94 - 1
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCACAGCCCCAAAAU----CCGAC-----UCGA--AAAAUAACACAAGUAGUUGCUCAAGAAGUUAAAGCUUUAAA
.((((((((((.((((....)))).((((...))))........----.....-----....--............)))).)))))).(((((....)))))... ( -22.20)
>DroSim_CAF1 3864 94 - 1
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCACAGCCCCAAAAU----CCGCC-----UCGA--AAAAUAACACAAGUAGUUGCUCAAGAAGUUAAAGCUUUAAA
.((((((((((.((((....)))).((((...))))........----.....-----....--............)))).)))))).(((((....)))))... ( -22.20)
>DroEre_CAF1 3895 101 - 1
GUGAGCAUUACAUGCCAUUUGACACGCUGCCACAGCCCCAAAAU----ACGCCAACAGCCCAAAAAAAAAACACAGAAAAUUGCUUAAGAAGUUAAAACUUCAAG
.((((((.....((...((((....((((...))))..))))..----..((.....))..............))......)))))).(((((....)))))... ( -13.60)
>DroYak_CAF1 3744 96 - 1
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCACAGCCCCAAAAU----CCGUC-----CCAAAAAAAAAGACACAAAUAGUUGCUUAAGAAGGUAAAGCUUCAAA
.((((((..((.((((....)))).((((...))))........----..(((-----...........))).......)))))))).((((......))))... ( -18.30)
>consensus
GUGAGCAUUACAUGCCAUUUGGCACGCUGCCACAGCCCCAAAAU____CCGAC_____CCGA__AAAAUAACACAAGUAGUUGCUCAAGAAGUUAAAGCUUUAAA
.((((((.....((((....)))).((((...)))).............................................)))))).((((......))))... (-10.33 = -12.17 +   1.83)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:01 2006