Locus 1437

Sequence ID 3R_DroMel_CAF1
Location 4,152,749 – 4,152,843
Length 94
Max. P 0.949452
window2396 window2397

overview

Window 6

Location 4,152,749 – 4,152,843
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.12
Mean single sequence MFE -33.08
Consensus MFE -15.60
Energy contribution -16.68
Covariance contribution 1.08
Combinations/Pair 1.20
Mean z-score -2.02
Structure conservation index 0.47
SVM decision value 1.39
SVM RNA-class probability 0.949452
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4152749 94 + 27905053
CAACGAAAUGGAGACGGAUACGGAGAAUGCUUUUGUC------------------------UGAUCGGUAAAUAUUUGCCCAUGGAUUUUCGUCUCCGGGACUC--GUAGUCCUUUCGCA
...((((((((((((((((.((((.((.....)).))------------------------)))))(((((....)))))..........))))))))((((..--...))))))))).. ( -31.90)
>DroPse_CAF1 2282 115 + 1
AAACGAAAUGGAGAUGCAUAUGGCC-GUGCCCUUGCCUCUAACAGCCCUAGCCCUGGGCCCUAUUUGGUCAAUAUUUGCUCAUGGAUUCUCGUCUCCA--UUCC--GUUGUCCUUUCGGA
.((((.((((((((((.......((-(((..((((((.......((((.......)))).......)).))).....)..))))).....))))))))--)).)--))).(((....))) ( -33.14)
>DroSim_CAF1 1396 96 + 1
CAGCGAAAUGGAGACGGAGAAGGAGACUGCUUUUGUC------------------------UGAUCGGUAAAUAUUUGCCCAUGGAUUUUCGUCUCCGGGACUCCGGGAGUCCUUUCGCA
..((((((((((((((((((...((((.......)))------------------------)....(((((....)))))......))))))))))))((((((...)))))))))))). ( -39.80)
>DroYak_CAF1 1614 94 + 1
CAACGAAAUGGAGACGG------AGACUGCUUUUGUC-----------------UGAUGUCUGAUCGGUAAAUAUUUGCCCAUGGAUUUUCGUCUC-GGGACUC--GUAGUCCUUUCGCA
...((((...(((((((------((((.......)))-----------------....((((.((.(((((....))))).)))))).))))))))-(((((..--...))))))))).. ( -27.80)
>DroPer_CAF1 2228 115 + 1
AAACGAAAUGGAGAUGCAUAUGGCC-GUGCCCUUGCCUCUAACAGCCCUAGCCCUGGGCCCUAUUUGGUCAAUAUUUGCUCAUGGAUUCUCGUCUCCG--UUCC--GUUGUCCUUUCGGA
.((((.((((((((((.......((-(((..((((((.......((((.......)))).......)).))).....)..))))).....))))))))--)).)--))).(((....))) ( -32.74)
>consensus
CAACGAAAUGGAGACGGAUAUGGAGACUGCUUUUGUC_________________UG____CUGAUCGGUAAAUAUUUGCCCAUGGAUUUUCGUCUCCGGGACUC__GUAGUCCUUUCGCA
...(((((((((((((............((....))..............................(((((....)))))..........))))))))(((((.....)))))))))).. (-15.60 = -16.68 +   1.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,152,749 – 4,152,843
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.12
Mean single sequence MFE -31.36
Consensus MFE -10.23
Energy contribution -13.15
Covariance contribution 2.92
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.33
SVM decision value 0.95
SVM RNA-class probability 0.887200
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4152749 94 - 27905053
UGCGAAAGGACUAC--GAGUCCCGGAGACGAAAAUCCAUGGGCAAAUAUUUACCGAUCA------------------------GACAAAAGCAUUCUCCGUAUCCGUCUCCAUUUCGUUG
.((((((((((...--..)))).(((((((.........((...........))((((.------------------------((.((.....)).)).).)))))))))).)))))).. ( -23.40)
>DroPse_CAF1 2282 115 - 1
UCCGAAAGGACAAC--GGAA--UGGAGACGAGAAUCCAUGAGCAAAUAUUGACCAAAUAGGGCCCAGGGCUAGGGCUGUUAGAGGCAAGGGCAC-GGCCAUAUGCAUCUCCAUUUCGUUU
(((....))).(((--((((--((((((.......((.((.((...((((.....))))..)).))))((...((((((.....((....))))-))))....)).))))))))))))). ( -41.30)
>DroSim_CAF1 1396 96 - 1
UGCGAAAGGACUCCCGGAGUCCCGGAGACGAAAAUCCAUGGGCAAAUAUUUACCGAUCA------------------------GACAAAAGCAGUCUCCUUCUCCGUCUCCAUUUCGCUG
.((((((((((((...)))))).(((((((.........((...........))((..(------------------------(((.......))))...))..))))))).)))))).. ( -32.50)
>DroYak_CAF1 1614 94 - 1
UGCGAAAGGACUAC--GAGUCCC-GAGACGAAAAUCCAUGGGCAAAUAUUUACCGAUCAGACAUCA-----------------GACAAAAGCAGUCU------CCGUCUCCAUUUCGUUG
.((((((((((...--..)))).-((((((........(((...........)))..........(-----------------(((.......))))------.))))))..)))))).. ( -22.60)
>DroPer_CAF1 2228 115 - 1
UCCGAAAGGACAAC--GGAA--CGGAGACGAGAAUCCAUGAGCAAAUAUUGACCAAAUAGGGCCCAGGGCUAGGGCUGUUAGAGGCAAGGGCAC-GGCCAUAUGCAUCUCCAUUUCGUUU
(((....))).(((--((((--.(((((.......((.((.((...((((.....))))..)).))))((...((((((.....((....))))-))))....)).))))).))))))). ( -37.00)
>consensus
UGCGAAAGGACUAC__GAGUCCCGGAGACGAAAAUCCAUGGGCAAAUAUUUACCGAUCAG____CA_________________GACAAAAGCACUCUCCAUAUCCGUCUCCAUUUCGUUG
.(((((((((((.....))))).(((((((...........((...............................................))............))))))).)))))).. (-10.23 = -13.15 +   2.92)

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 10:10:36 2006