Locus 2490

Sequence ID 3R_DroMel_CAF1
Location 6,821,205 – 6,821,396
Length 191
Max. P 0.990930
window4079 window4080

overview

Window 9

Location 6,821,205 – 6,821,317
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.34
Mean single sequence MFE -34.42
Consensus MFE -26.18
Energy contribution -27.27
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.76
SVM decision value -0.03
SVM RNA-class probability 0.519812
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6821205 112 + 27905053
GCCGAACGUGCAGUUUCCGGACUGCAGUUAACGGCUUCAGCUU--UGGCAAAACAGACCACC-----AGACAAUGGC-AAAUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAAC
(((((((.(((((((....))))))))))..))))......((--((((......(.....)-----.((..(((((-...((((((((...)))))))).)))))..)))))))).... ( -37.50)
>DroSec_CAF1 80332 113 + 1
GCCGAACGUGCAGUUUCCGGACUGCAGUUAACGGCUUCAGCUU--UGGCAAAACAGACGACC-----AGACAAUUGCUAAAUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAAC
(.((((..(((((((....)))))))......(((((..((((--((((((((((......(-----((....))).....)))))))....))))))))))))...)))).)....... ( -32.40)
>DroSim_CAF1 86219 112 + 1
GCCGAACGUGCAGUUUCCGGACUGCAGUUAACGGCUUCAGCUU--UGGCAAAACAGACGACC-----AGACAAUGGC-AAAUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAAC
(((((((.(((((((....))))))))))..))))......((--((((......(.....)-----.((..(((((-...((((((((...)))))))).)))))..)))))))).... ( -37.50)
>DroEre_CAF1 65263 112 + 1
GCCGAACGUGCAGUUUCCGGACUGCAGUUAACGGCAUCAACUU--UGGCAAAACAAACAACC-----AGACAAUGGC-AAAUGUUUUAGUAACCAAAGCGAGCCAUCUUCGCCAGGUAAC
(((.(((.(((((((....))))))))))...(((......((--((......)))).....-----.((..(((((-...((((((.......)))))).)))))..))))).)))... ( -30.10)
>DroYak_CAF1 78498 117 + 1
GCCGAACGUGCAGUUGCCGGACUGCAGUUAACGGCAUCAACUU--UGGCAAAACAGACGACCAGACCAGACAAUGGC-AAAUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAAC
(((((((.(((((((....))))))))))..))))......((--((((........(.....)....((..(((((-...((((((((...)))))))).)))))..)))))))).... ( -38.10)
>DroAna_CAF1 37066 108 + 1
GCCGAACGUGCACUUUCCCGAGUGCAGUUAACGGCUCUAGCUGAAUGGCAAA-----CAA-U-----GAACAAUGCC-GAAAAUUUUGGUAACCAGAGCGGUCCAUUUUGUCCCUCUAAU
(((((((.(((((((....))))))))))..((((....))))..))))...-----...-.-----......((((-((.....))))))...((((.((.(......).))))))... ( -30.90)
>consensus
GCCGAACGUGCAGUUUCCGGACUGCAGUUAACGGCUUCAGCUU__UGGCAAAACAGACGACC_____AGACAAUGGC_AAAUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAAC
(((((((.(((((((....))))))))))..))))..........((((...................((..(((((....((((((((...)))))))).)))))..))))))...... (-26.18 = -27.27 +   1.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,821,277 – 6,821,396
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 94.71
Mean single sequence MFE -33.32
Consensus MFE -29.98
Energy contribution -30.86
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.90
SVM decision value 2.24
SVM RNA-class probability 0.990930
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6821277 119 + 27905053
AUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGGGCCAUUAAAGGGCUGGCUUUGCUUUCAAAUGAAAUCAGCACUUCA
..((.(((((...((((((.((((.(((((((((.......))))..(((.....))).)))))((((.....)))).......)))).))))))..(((....)))))))).)).... ( -33.10)
>DroSec_CAF1 80405 119 + 1
AUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGAGCCAUUAAAGGGCUUGCUUUGCUUUCGAAUGAAAUCUGCACUUCA
....(((((.((.(((((((((((.(((((((((.......))))..(((.....))).)))))((((.....)))).......))))))))))).)))))))((((........)))) ( -33.80)
>DroSim_CAF1 86291 119 + 1
AUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGGGCCAUUAAAGGGCUUGCUUUGCUUUCGAAUGAAAUCUGCACUUUA
....(((((.((.(((((((((((.(((((((((.......))))..(((.....))).)))))((((.....)))).......))))))))))).)))))))................ ( -33.60)
>DroEre_CAF1 65335 114 + 1
AUGUUUUAGUAACCAAAGCGAGCCAUCUUCGCCAGGUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGGG-CAUUAAAGGGCUUGCUUUGCUUUGC----AAAUCUGCACUCCA
.............(((((((((((.(((((((((.(...).))))..(((.....))).))))).(((.....))-).......)))))))))))...(((----(....))))..... ( -31.80)
>DroYak_CAF1 78575 119 + 1
AUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGGGCCAUUAAAGGGCUUGCUUUGCUUUCAAAUGAAAUCUGCACUGCA
.(((....(((..(((((((((((.(((((((((.......))))..(((.....))).)))))((((.....)))).......))))))))))).((((....))))..)))...))) ( -34.30)
>consensus
AUGUUUUGGUAACCAAAGCGAGCCAUCUUCGCCAGAUAACGUGGCCAUUGAAAUUCAGAGAAGAGGUUAAAAGGGCCAUUAAAGGGCUUGCUUUGCUUUCAAAUGAAAUCUGCACUUCA
....(((((.((.(((((((((((.(((((((((.......))))..(((.....))).)))))((((.....)))).......))))))))))).)))))))................ (-29.98 = -30.86 +   0.88)

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 10:37:43 2006