Locus 1296

Sequence ID 3R_DroMel_CAF1
Location 3,819,782 – 3,819,916
Length 134
Max. P 0.961354
window2113 window2114 window2115

overview

Window 3

Location 3,819,782 – 3,819,879
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.38
Mean single sequence MFE -30.32
Consensus MFE -20.40
Energy contribution -21.32
Covariance contribution 0.92
Combinations/Pair 1.05
Mean z-score -1.26
Structure conservation index 0.67
SVM decision value -0.04
SVM RNA-class probability 0.511899
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3819782 97 - 27905053
UUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA-CUAGUUGCCAGUUGGCUAUGGGCGGCUAUG---------------------GGCUAUCGGGUCUGG-GUU
..((((..((((.((((....))))))))((((((((((((........-...)))))))))..)))..))))((((.((---------------------((((....)))))))-))) ( -34.00)
>DroSec_CAF1 47576 84 - 1
UUGCCUCUUUUGACACUGAAAAGUGCACAGGCGCUGGCGGCGAAUUUUA-CUAG--GCCAGUUGGCUAU---CGGUUAUG-----------------------------GGUAUUG-GUU
..((((....((.((((....)))))).))))((..(((((........-....--))).))..)).((---((((....-----------------------------...))))-)). ( -23.20)
>DroSim_CAF1 52164 84 - 1
UUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA-CUAG--GCCAGUUGGCUAU---CGGGUAUG-----------------------------GGUCUUG-GUU
.(((((((((((.((((....)))))))))).((..(((((........-....--))).))..))...---.)))))..-----------------------------.......-... ( -26.00)
>DroEre_CAF1 38980 113 - 1
UUGCCCCUUUUGACACUGAAAAGUGCAAAGACGCUGGCGGCGAAUUUAA-CUGG--GCCAGUUGGCUAU---CGGCAAUGGGCUACGGGCUAUGGGCUAUGGGCUAUGG-GCUAUGGGGU
..((((((((((.((((....))))))))).(((.....))).......-...(--(((...(((((..---.(((.((((.(....).))))..)))...)))))..)-)))..))))) ( -43.90)
>DroYak_CAF1 51401 79 - 1
UUGCCUCUUUUGACACUGAAAAGUGCAAAGACGCUGGCGGCGAAUUAAACCUGG--GCCAGUUGGCUAU---CGG-----------------------------------GCUGUU-GUU
..((((.(((((.((((....)))))))))..((..(((((.............--))).))..))...---.))-----------------------------------))....-... ( -24.52)
>consensus
UUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA_CUAG__GCCAGUUGGCUAU___CGGCUAUG_____________________________GGUCUUG_GUU
..(((.((((((.((((....)))))))))).((..(((((...............))).))..)).......)))............................................ (-20.40 = -21.32 +   0.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,819,800 – 3,819,916
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 91.71
Mean single sequence MFE -26.08
Consensus MFE -21.05
Energy contribution -20.85
Covariance contribution -0.20
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.81
SVM decision value 0.46
SVM RNA-class probability 0.743833
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3819800 116 + 27905053
CAUAGCCGCCCAUAGCCAACUGGCAACUAG-UAAAAUUCGCCGCCAGCGCCUUUGCACUUUUCAGUGUCAAAAGAGGCAACACAAAAAUGCGGCAAAAGUCCCAGUCGAAAAUAAAA
....(((((..........(((((......-...........))))).(((((((((((....)))))....))))))...........)))))....................... ( -28.33)
>DroSec_CAF1 47586 111 + 1
CAUAACCG---AUAGCCAACUGGC--CUAG-UAAAAUUCGCCGCCAGCGCCUGUGCACUUUUCAGUGUCAAAAGAGGCAACACAAAAAUGCGGCAAAAGUCCCAGUCAAAAAUAAAA
........---...(((..(((((--...(-.......)...))))).((((.((((((....)))))....).)))).............)))....................... ( -22.50)
>DroSim_CAF1 52174 111 + 1
CAUACCCG---AUAGCCAACUGGC--CUAG-UAAAAUUCGCCGCCAGCGCCUUUGCACUUUUCAGUGUCAAAAGAGGCAACACAAAAAUGCGGCAAAAGUCCCAGUCGAAAAUAAAA
......((---((.(((....)))--....-........(((((....(((((((((((....)))))....))))))...........)))))..........))))......... ( -25.46)
>DroEre_CAF1 39019 110 + 1
CAUUGCCG---AUAGCCAACUGGC--CCAG-UUAAAUUCGCCGCCAGCGUCUUUGCACUUUUCAGUGUCAAAAGGGGCAAC-CAAAAAUGCGGCAAAAGUCCCAGUCGAAAAUAAAA
.(((..((---((.(((....)))--....-........(((((......(((((((((....)))))..))))((....)-)......)))))..........))))..))).... ( -27.60)
>DroYak_CAF1 51410 107 + 1
-----CCG---AUAGCCAACUGGC--CCAGGUUUAAUUCGCCGCCAGCGUCUUUGCACUUUUCAGUGUCAAAAGAGGCAACACAAAAAUGCGGCAAAAGUCCCAGUCGAAAAUAAAU
-----.((---((.(((..(((((--...(((.......))))))))..((((((((((....)))))..))))))))..........((.(((....))).))))))......... ( -26.50)
>consensus
CAUAGCCG___AUAGCCAACUGGC__CUAG_UAAAAUUCGCCGCCAGCGCCUUUGCACUUUUCAGUGUCAAAAGAGGCAACACAAAAAUGCGGCAAAAGUCCCAGUCGAAAAUAAAA
..............(((..(((((..................))))).(((((((((((....)))))....)))))).............)))....................... (-21.05 = -20.85 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,819,800 – 3,819,916
Length 116
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 91.71
Mean single sequence MFE -35.62
Consensus MFE -29.36
Energy contribution -29.76
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.82
SVM decision value 1.53
SVM RNA-class probability 0.961354
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3819800 116 - 27905053
UUUUAUUUUCGACUGGGACUUUUGCCGCAUUUUUGUGUUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA-CUAGUUGCCAGUUGGCUAUGGGCGGCUAUG
.........(((((((....((((((((((....)))).(((.((((((.((((....))))))))))....))))))))).....-)))))))..(((((.(....).)))))... ( -38.60)
>DroSec_CAF1 47586 111 - 1
UUUUAUUUUUGACUGGGACUUUUGCCGCAUUUUUGUGUUGCCUCUUUUGACACUGAAAAGUGCACAGGCGCUGGCGGCGAAUUUUA-CUAG--GCCAGUUGGCUAU---CGGUUAUG
.........(((((((((..((((((((.((((.(((((.........))))).))))(((((....))))).))))))))..)).-...(--(((....)))).)---)))))).. ( -35.40)
>DroSim_CAF1 52174 111 - 1
UUUUAUUUUCGACUGGGACUUUUGCCGCAUUUUUGUGUUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA-CUAG--GCCAGUUGGCUAU---CGGGUAUG
.......(((((((((....((((((((((....)))).(((.((((((.((((....))))))))))....))))))))).....-))))--(((....)))..)---)))).... ( -36.60)
>DroEre_CAF1 39019 110 - 1
UUUUAUUUUCGACUGGGACUUUUGCCGCAUUUUUG-GUUGCCCCUUUUGACACUGAAAAGUGCAAAGACGCUGGCGGCGAAUUUAA-CUGG--GCCAGUUGGCUAU---CGGCAAUG
.........(((((((..(.((((((((......(-(.....))(((((.((((....)))))))))......)))))))).....-..).--.)))))))((...---..)).... ( -32.70)
>DroYak_CAF1 51410 107 - 1
AUUUAUUUUCGACUGGGACUUUUGCCGCAUUUUUGUGUUGCCUCUUUUGACACUGAAAAGUGCAAAGACGCUGGCGGCGAAUUAAACCUGG--GCCAGUUGGCUAU---CGG-----
.........((((..((...((((((((......(((((......((((.((((....)))))))))))))..)))))))).....))..)--(((....)))..)---)).----- ( -34.80)
>consensus
UUUUAUUUUCGACUGGGACUUUUGCCGCAUUUUUGUGUUGCCUCUUUUGACACUGAAAAGUGCAAAGGCGCUGGCGGCGAAUUUUA_CUAG__GCCAGUUGGCUAU___CGGCUAUG
........((((((((..((((((((((((....)))).(((.((((((.((((....))))))))))....)))))))))........))...))))))))............... (-29.36 = -29.76 +   0.40)

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 10:05:56 2006