Locus 718

Sequence ID 2R_DroMel_CAF1
Location 3,530,722 – 3,530,849
Length 127
Max. P 0.976438
window1260 window1261 window1262

overview

Window 0

Location 3,530,722 – 3,530,826
Length 104
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 79.85
Mean single sequence MFE -44.60
Consensus MFE -31.24
Energy contribution -34.16
Covariance contribution 2.92
Combinations/Pair 1.18
Mean z-score -1.70
Structure conservation index 0.70
SVM decision value 0.43
SVM RNA-class probability 0.735154
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530722 104 + 20766785
CGCCCUGUCUCCCUCCCACCGCCGUCCGGCUGCCAUUGGCAAUGGGGGCGUGGCGAGGCCCGUUUCACGCCCC--UGCUGCAGUGCAAGCGAGACAACCGUAUGGC
.(((.((((((.((..(((.(((....)))........(((..((((((((((((.....)))..))))))))--)..))).)))..)).)))))).......))) ( -43.40)
>DroSim_CAF1 24595 104 + 1
CGCCCUGUCUCCCUCCCACCGCCGUGCGGCUGCCAUUGGCAAAGGGGGCGUGGUAAGACCUCAUCCACGCCCC--UGCUGCAGUGCGAGCGAGACAACCGUAUGGC
.(((.((((((.(((.(((.....((((((((((...))))..((((((((((...........)))))))))--)))))))))).))).)))))).......))) ( -48.80)
>DroEre_CAF1 23224 103 + 1
CGCACUGUCUCCCUCCCACCAGCGUGCGGCUGCCAUUGGCAAAGG-GGCGUGGCGUGGCCUCAUCCACGCCCC--UGCAGCAGUGCGAGCGAGACAACCGUAUGGC
.....((((((.(((.(((..((.(((...((((...)))).(((-(((((((.(((....))))))))))))--)))))).))).))).)))))).......... ( -47.80)
>DroYak_CAF1 22339 104 + 1
CGCACUGUCUCCCUCCCACCGCCGUGUGGCUGCCAUUGGCAAAGGGGGCGUGGCGUGGCCUCAUCCACGCCCC--UGCUGCAGUGCGAGGGAGACAACCGUAUGAC
.....((((((((((.(((.....((..((((((...))))..((((((((((.(((....))))))))))))--)))..))))).)))))))))).......... ( -54.70)
>DroAna_CAF1 18065 95 + 1
CUCACUCUCUCUAUA----------UCGGCUGCCAUUGGCAAAGG-GGCGUGACAGGGCCAUGGCCACGCCUAGACGCUCAAGUGGAAAAGAGACAACCGUAUGAG
((((((((.(((((.----------(.(((((((...))))...(-(((((.....(((....)))))))))....))).).)))))..))))((....)).)))) ( -28.30)
>consensus
CGCACUGUCUCCCUCCCACCGCCGUGCGGCUGCCAUUGGCAAAGGGGGCGUGGCGAGGCCUCAUCCACGCCCC__UGCUGCAGUGCGAGCGAGACAACCGUAUGGC
.....((((((.(((.(((.....((((((((((...))))...(((((((((.(((....))))))))))))...))))))))).))).)))))).......... (-31.24 = -34.16 +   2.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,530,722 – 3,530,826
Length 104
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 79.85
Mean single sequence MFE -50.12
Consensus MFE -36.72
Energy contribution -39.04
Covariance contribution 2.32
Combinations/Pair 1.22
Mean z-score -2.32
Structure conservation index 0.73
SVM decision value 1.77
SVM RNA-class probability 0.976438
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530722 104 - 20766785
GCCAUACGGUUGUCUCGCUUGCACUGCAGCA--GGGGCGUGAAACGGGCCUCGCCACGCCCCCAUUGCCAAUGGCAGCCGGACGGCGGUGGGAGGGAGACAGGGCG
(((......(((((((.(((.((((((....--((((((((...((.....)).))))))))..(((((...))))).......)))))).))).)))))))))). ( -50.00)
>DroSim_CAF1 24595 104 - 1
GCCAUACGGUUGUCUCGCUCGCACUGCAGCA--GGGGCGUGGAUGAGGUCUUACCACGCCCCCUUUGCCAAUGGCAGCCGCACGGCGGUGGGAGGGAGACAGGGCG
(((......(((((((.(((.((((((.((.--(((((((((.(((....))))))))))))..(((((...)))))..))...)))))).))).)))))))))). ( -58.10)
>DroEre_CAF1 23224 103 - 1
GCCAUACGGUUGUCUCGCUCGCACUGCUGCA--GGGGCGUGGAUGAGGCCACGCCACGCC-CCUUUGCCAAUGGCAGCCGCACGCUGGUGGGAGGGAGACAGUGCG
(((....)))((((((.(((.((((((((((--(((((((((.((......)))))))))-)))(((((...)))))..))).)).)))).))).))))))..... ( -54.50)
>DroYak_CAF1 22339 104 - 1
GUCAUACGGUUGUCUCCCUCGCACUGCAGCA--GGGGCGUGGAUGAGGCCACGCCACGCCCCCUUUGCCAAUGGCAGCCACACGGCGGUGGGAGGGAGACAGUGCG
.........(((((((((((.((((((....--(((((((((.((......)))))))))))..(((((...))))).......)))))).))))))))))).... ( -57.20)
>DroAna_CAF1 18065 95 - 1
CUCAUACGGUUGUCUCUUUUCCACUUGAGCGUCUAGGCGUGGCCAUGGCCCUGUCACGCC-CCUUUGCCAAUGGCAGCCGA----------UAUAGAGAGAGUGAG
((((((((((((((..........(((.(((....((((((((.........))))))))-....)))))).)))))))).----------))).)))........ ( -30.80)
>consensus
GCCAUACGGUUGUCUCGCUCGCACUGCAGCA__GGGGCGUGGAUGAGGCCACGCCACGCCCCCUUUGCCAAUGGCAGCCGCACGGCGGUGGGAGGGAGACAGUGCG
.........(((((((.(((.((((((......(((((((((.((......)))))))))))..(((((...))))).......)))))).))).))))))).... (-36.72 = -39.04 +   2.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,530,753 – 3,530,849
Length 96
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 67.93
Mean single sequence MFE -37.35
Consensus MFE -20.32
Energy contribution -21.98
Covariance contribution 1.67
Combinations/Pair 1.20
Mean z-score -1.48
Structure conservation index 0.54
SVM decision value 0.54
SVM RNA-class probability 0.775773
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530753 96 + 20766785
GCCAUUGGCAAUGGGGGCGUGGCGAGGCCCGUUUCACGCCCC--UGCUGCAGUGCAAGCGAGACAACCGUAU-GGCGGAGGGCUGCCAGGCAAG----UGUAU-------------
(((....(((..((((((((((((.....)))..))))))))--)..))).......(((.......))).(-(((((....)))))))))...----.....------------- ( -40.60)
>DroPse_CAF1 12124 111 + 1
UCCAUUGGCAAAGAGGGCGUGUCGAGAGUUGG-UCACGCCCC---ACUAUAGCAGAAAAGAGACAACCAUAUAGAUGGAACUCUUGAAGGGAAAAUACUUAAUGAACAUAC-UACU
(((....((..((.(((((((((((...))))-.))))))).---.))...))....(((((....((((....))))..)))))....)))...................-.... ( -25.10)
>DroSim_CAF1 24626 96 + 1
GCCAUUGGCAAAGGGGGCGUGGUAAGACCUCAUCCACGCCCC--UGCUGCAGUGCGAGCGAGACAACCGUAU-GGCGGAGGGCUGCCAGGCAAG----UGUAU-------------
(((..(((((..((((((((((...........)))))))))--).((((.(((((.(........))))))-.)))).....))))))))...----.....------------- ( -42.00)
>DroEre_CAF1 23255 108 + 1
GCCAUUGGCAAAGG-GGCGUGGCGUGGCCUCAUCCACGCCCC--UGCAGCAGUGCGAGCGAGACAACCGUAU-GGCCGAGCGCCGCCAGGCAAG----UGUAUGUACAUACAUACA
(((..((((..(((-(((((((.(((....))))))))))))--)......((((..((.(.((....)).)-.))...)))).)))))))...----(((((((....))))))) ( -47.50)
>DroYak_CAF1 22370 96 + 1
GCCAUUGGCAAAGGGGGCGUGGCGUGGCCUCAUCCACGCCCC--UGCUGCAGUGCGAGGGAGACAACCGUAU-GACGGAGGGCCGCCAGGCAAG----UGUAU-------------
(((..((((...((((((((((.(((....))))))))))))--).(((..(((((..(....)...)))))-..)))......)))))))...----.....------------- ( -43.90)
>DroAna_CAF1 18086 87 + 1
GCCAUUGGCAAAGG-GGCGUGACAGGGCCAUGGCCACGCCUAGACGCUCAAGUGGAAAAGAGACAACCGUAU-GAG----------UAGACUAU----GUUAU-------------
.....(((((.(((-(((((.....(((....)))))))))....(((((..(((...........)))..)-)))----------)...)).)----)))).------------- ( -25.00)
>consensus
GCCAUUGGCAAAGGGGGCGUGGCGAGGCCUCAUCCACGCCCC__UGCUGCAGUGCAAGCGAGACAACCGUAU_GACGGAGGGCUGCCAGGCAAG____UGUAU_____________
(((...((((...(((((((((...........)))))))))..))))..................((((....))))..........)))......................... (-20.32 = -21.98 +   1.67)

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 09:45:28 2006