Locus 3387

Sequence ID 2R_DroMel_CAF1
Location 11,448,837 – 11,448,934
Length 97
Max. P 0.971569
window5536 window5537

overview

Window 6

Location 11,448,837 – 11,448,934
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.91
Mean single sequence MFE -23.42
Consensus MFE -12.86
Energy contribution -13.22
Covariance contribution 0.36
Combinations/Pair 1.24
Mean z-score -1.78
Structure conservation index 0.55
SVM decision value 0.56
SVM RNA-class probability 0.780567
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11448837 97 + 20766785
UUCAGCUGAAUUGAGGCA--------GCUA---------ACAAGACAUUUCUUGUUUGUAUACAA---AA-AUAUCAUUGAUACUUUCGACCGGGAUUUUCCUG--GCCUCAUUUACGCU
...((((((((.(((((.--------((.(---------((((((....))))))).))......---..-......((((.....)))).((((.....))))--)))))))))).))) ( -27.00)
>DroSec_CAF1 1240 95 + 1
UUCAGCUGAAUUGAGGCAA-------GAC------------AAGAAAUUUCUUGUUUGUAUACAA---AA-AUAUCAGUGAUACUUUCGACCGGGAUUUCCCUG--GCCUCAUUUACGCU
...((((((((.(((((.(-------(((------------((((....))))))))((((((..---..-......)).))))........(((....)))..--)))))))))).))) ( -26.00)
>DroSim_CAF1 1240 98 + 1
UUCAGCUAAAUUGAGGCAA-------GACA---------ACAAGAAAUUUCUUGUUUGUAUACAA---AA-AUAUCAGUGAUACUUUUGACCGGGAUUUUCCUG--GCGUCAUUUACGCU
...((((((((.((.((..-------.(((---------((((((....))))).))))...(((---((-.((((...)))).)))))..((((.....))))--)).))))))).))) ( -24.70)
>DroEre_CAF1 1251 120 + 1
UUCAGCUGAAUUGAGUUAAUUAGGCAGCUUACAUAUUUCACAAGUCAUUUCUUGUUUGUAUACAAACAAACGUUUUAGAGAUUAUUUCUACUGGGUUUUCCCUUAUUUCUUAUUUACGCU
...(((((..((((.....)))).)))))......................(((((((....))))))).(((...((((((..........(((....)))..)))))).....))).. ( -18.50)
>DroYak_CAF1 1226 115 + 1
UUCAGUUGAAUUGUGUUAAUUUGGCAGCUUACAUAUUUCACAAGACUUUUCUUGUUUGUAUACAA---AAGGUUUCCGAGAUUAUUUCGAAUGGGAUUUUCCUG--CGCUUAUUUACGCU
............((((.(((..(((.((....((((...((((((....))))))..))))....---.(((.(((((.((.....))...)))))....))))--)))).))).)))). ( -20.90)
>consensus
UUCAGCUGAAUUGAGGCAA_______GCUA_________ACAAGACAUUUCUUGUUUGUAUACAA___AA_AUAUCAGUGAUACUUUCGACCGGGAUUUUCCUG__GCCUCAUUUACGCU
...((((((((.(((((......................(((((......))))).....................................(((....)))....)))))))))).))) (-12.86 = -13.22 +   0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,448,837 – 11,448,934
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.91
Mean single sequence MFE -23.42
Consensus MFE -7.94
Energy contribution -7.82
Covariance contribution -0.12
Combinations/Pair 1.18
Mean z-score -2.21
Structure conservation index 0.34
SVM decision value 1.68
SVM RNA-class probability 0.971569
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11448837 97 - 20766785
AGCGUAAAUGAGGC--CAGGAAAAUCCCGGUCGAAAGUAUCAAUGAUAU-UU---UUGUAUACAAACAAGAAAUGUCUUGU---------UAGC--------UGCCUCAAUUCAGCUGAA
(((.....((((((--..((......))(((((((((((((...)))))-))---)))......(((((((....))))))---------).))--------))))))).....)))... ( -26.90)
>DroSec_CAF1 1240 95 - 1
AGCGUAAAUGAGGC--CAGGGAAAUCCCGGUCGAAAGUAUCACUGAUAU-UU---UUGUAUACAAACAAGAAAUUUCUU------------GUC-------UUGCCUCAAUUCAGCUGAA
(((.....((((((--..(((....)))(..((((((((((...)))))-))---)))....)..((((((....))))------------)).-------..)))))).....)))... ( -28.40)
>DroSim_CAF1 1240 98 - 1
AGCGUAAAUGACGC--CAGGAAAAUCCCGGUCAAAAGUAUCACUGAUAU-UU---UUGUAUACAAACAAGAAAUUUCUUGU---------UGUC-------UUGCCUCAAUUUAGCUGAA
(((.(((((((.((--.((((.......(..((((((((((...)))))-))---)))....).(((((((....))))))---------).))-------)))).)).))))))))... ( -23.00)
>DroEre_CAF1 1251 120 - 1
AGCGUAAAUAAGAAAUAAGGGAAAACCCAGUAGAAAUAAUCUCUAAAACGUUUGUUUGUAUACAAACAAGAAAUGACUUGUGAAAUAUGUAAGCUGCCUAAUUAACUCAAUUCAGCUGAA
.(((((.(((((......(((....)))..((((.......)))).....((((((((....))))))))......)))))....))))).(((((...((((.....)))))))))... ( -21.00)
>DroYak_CAF1 1226 115 - 1
AGCGUAAAUAAGCG--CAGGAAAAUCCCAUUCGAAAUAAUCUCGGAAACCUU---UUGUAUACAAACAAGAAAAGUCUUGUGAAAUAUGUAAGCUGCCAAAUUAACACAAUUCAACUGAA
(((....(((..((--(((((........(((((.......)))))....((---((((......))))))....)))))))...)))....)))......................... ( -17.80)
>consensus
AGCGUAAAUGAGGC__CAGGAAAAUCCCGGUCGAAAGUAUCACUGAUAU_UU___UUGUAUACAAACAAGAAAUGUCUUGU_________AAGC_______UUGCCUCAAUUCAGCUGAA
..................((.....))((((.(((....................(((....)))(((((......))))).............................))).)))).. ( -7.94 =  -7.82 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:20 2006