Locus 6518

Sequence ID 3L_DroMel_CAF1
Location 17,271,066 – 17,271,195
Length 129
Max. P 0.733903
window10558 window10559

overview

Window 8

Location 17,271,066 – 17,271,181
Length 115
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 90.12
Mean single sequence MFE -28.05
Consensus MFE -22.60
Energy contribution -23.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.81
SVM decision value 0.43
SVM RNA-class probability 0.733903
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271066 115 + 23771897
GCUUUUCCACACACACCCACACACACACCCGAUGGAAAACACGGCAGAGAGUGAAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAGGACUGCA
((...(((........((((........(((.((.....)))))..(((.((....-..))))).(((((......)))))..)))).......((((.....)))).)))..)). ( -26.30)
>DroSec_CAF1 154505 114 + 1
GCUUUUCCACACACACCCACACACACACACGUUGGAAAACACGGUGGAGAGUGAAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG-ACUGCA
((............................(((((....(((...((((.((....-..))))))(((((......)))))..))).)))))..((((.....))))..-...)). ( -28.30)
>DroEre_CAF1 157329 112 + 1
GCUUUUCCACACACAC--ACACACACACCCGUUGGAAAACACGGCGGAGAGUGGAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAGCACUCACAG-UCUGCA
((..............--............(((((....(((...((((.((....-..))))))(((((......)))))..))).)))))..((((.....))))..-...)). ( -28.60)
>DroYak_CAF1 162165 105 + 1
GCUUUUCCACACA----------CACACCCGCUGGAAAACACGGCGUAGAGUGAAAAAAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG-UGUGCA
...........((----------(((...(((((.......)))))..(((((............(((((......)))))..(((.....)))......)))))...)-)))).. ( -29.00)
>consensus
GCUUUUCCACACACAC__ACACACACACCCGUUGGAAAACACGGCGGAGAGUGAAA_AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG_ACUGCA
((............................(((((....(((...((((.((.......))))))(((((......)))))..))).)))))..((((.....))))......)). (-22.60 = -23.60 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,271,102 – 17,271,195
Length 93
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.26
Mean single sequence MFE -25.76
Consensus MFE -18.20
Energy contribution -18.44
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.71
SVM decision value 0.03
SVM RNA-class probability 0.549001
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271102 93 + 23771897
AAACACGGCAGAGAGUGAAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAGGACUGCACUGAGAACAUUCAU--------------------------
......(((.(((.((....-..)))))..)))(((((.((((((..(((.....)))((((.....))))..)))).)).)))))........-------------------------- ( -20.10)
>DroSec_CAF1 154541 118 + 1
AAACACGGUGGAGAGUGAAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG-ACUGCACUGAGAACUUUCAUAUGUAAUGAAGGUAUGAAAAAUAUCU
......(.(((((.((....-..))))))).).(((((.((((((..(((.....)))((((.....)))).)-))).)).)))))((((((((.....))))))))............. ( -30.50)
>DroSim_CAF1 149571 118 + 1
AAACACGGCGGAGAGUGAAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG-AAUGCACUGAGAACAUUCAUAUGUAAUGAAGGUAUGAAUAAUAUCU
......(((((((.((....-..))))))(((((......))))).....))).(((..((((....((.(((-......))).))...))))..))).....((((((.....)))))) ( -29.00)
>DroEre_CAF1 157363 109 + 1
AAACACGGCGGAGAGUGGAA-AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAGCACUCACAG-UCUGCACUGAAAACAUUAAUUUUUAAUGAAGA---------UGCAC
......(((((((.((....-..))))))(((((......))))).....))).....((((.....)))).(-(((.((.((((((......)))))).)).)))---------).... ( -27.10)
>DroYak_CAF1 162191 110 + 1
AAACACGGCGUAGAGUGAAAAAAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG-UGUGCACUGAGAACAUUCAUUAUUAAUGAAGA---------UUUAU
..((((...((.(((((............(((((......)))))..(((.....)))......))))))).)-))).......(((..(((((.....)))))..---------))).. ( -22.10)
>consensus
AAACACGGCGGAGAGUGAAA_AAACCUCCGGCUUUUUAAUGAGUCAAGUGGCCAACACGUGAAACACUCACAG_ACUGCACUGAGAACAUUCAUAUGUAAUGAAGA_________UAUAU
......(((((((.((.......))))))(((((......))))).....))).....((((.....))))................................................. (-18.20 = -18.44 +   0.24)

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 12:22:26 2006