Locus 1756

Sequence ID 2L_DroMel_CAF1
Location 4,802,043 – 4,802,133
Length 90
Max. P 0.999409
window2819 window2820

overview

Window 9

Location 4,802,043 – 4,802,133
Length 90
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -28.90
Consensus MFE -21.10
Energy contribution -21.54
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -3.03
Structure conservation index 0.73
SVM decision value 3.09
SVM RNA-class probability 0.998409
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4802043 90 + 22407834
GCAGCUGCUGCUGCAGCGAAGCUUUGGCAGCAGCAAA-----GGCAAAAGGCAGCCCAUAUAGCCAUAUAGCCAUAUAGCCAUAUAGCAGC-------------------AAAA
((.((((((((((.(((...))).))))))))))...-----(((....(((..........))).((((....))))))).....))...-------------------.... ( -32.10)
>DroSec_CAF1 4901 86 + 1
GCAGCUGCUGCUGCAGCGAAGCUUUGGCAGCAGCGAA-----GGCAUAUAG----ACAUAUAGCCAUACAGCCAUAUAGCCAUAUAGCAGC-------------------AAAG
((.((((((((((.(((...))).))))))))))...-----(((.((((.----...))))))).....((.((((....)))).)).))-------------------.... ( -30.90)
>DroSim_CAF1 2254 86 + 1
GCAGCUGCUGCUGCAGCGAAGCUUUGGCAGCAGCAAA-----GGCAUAUAG----CCAUAUAGCCAUACAGCCAUAUAGCCAUAUAGCAGC-------------------AAAG
((.((((((((((.(((...))).))))))))))...-----.((((((.(----(.((((.((......)).)))).)).)))).)).))-------------------.... ( -32.30)
>DroEre_CAF1 4969 94 + 1
GCAGCUUCUGCUGCAGCGAAGCUUUGGCAGCAGCAAAAGGCAGCCAUAUAG----ACAUAUAGCCAUACAGCCAUAUAGCAAUAUAGC----------------CAUAUAACAG
(((((....))))).((...(((.((((.((.((.....)).))..((((.----...))))))))...)))..((((....))))))----------------.......... ( -23.60)
>DroYak_CAF1 5040 110 + 1
GCAACUUCUGCUGCAGCGAAGCUUUGGCAGCAGCAAAAGGCAGCCAUAUAG----ACAUAUAGCCAUAUAGCCAUAUAGCAGUAUAGCAGUAUAGCACUAUAGCCAUAUAACAG
.......((((((((((...)))...))))))).....(((.((.((((..----..)))).))......((.((((.((......)).)))).))......)))......... ( -25.60)
>consensus
GCAGCUGCUGCUGCAGCGAAGCUUUGGCAGCAGCAAA_____GGCAUAUAG____ACAUAUAGCCAUACAGCCAUAUAGCCAUAUAGCAGC___________________AAAG
((.((((((((((.(((...))).)))))))))).......................((((.((.(((......))).)).)))).)).......................... (-21.10 = -21.54 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,802,043 – 4,802,133
Length 90
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 78.81
Mean single sequence MFE -38.36
Consensus MFE -27.74
Energy contribution -28.70
Covariance contribution 0.96
Combinations/Pair 1.11
Mean z-score -4.93
Structure conservation index 0.72
SVM decision value 3.58
SVM RNA-class probability 0.999409
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4802043 90 - 22407834
UUUU-------------------GCUGCUAUAUGGCUAUAUGGCUAUAUGGCUAUAUGGGCUGCCUUUUGCC-----UUUGCUGCUGCCAAAGCUUCGCUGCAGCAGCAGCUGC
....-------------------((((((((((((((....))))))))))).....((((........)))-----)..((((((((...(((...))))))))))))))... ( -38.30)
>DroSec_CAF1 4901 86 - 1
CUUU-------------------GCUGCUAUAUGGCUAUAUGGCUGUAUGGCUAUAUGU----CUAUAUGCC-----UUCGCUGCUGCCAAAGCUUCGCUGCAGCAGCAGCUGC
....-------------------(((((.((((((.(((((((((....))))))))).----)))))))).-----...((((((((...(((...))))))))))))))... ( -35.50)
>DroSim_CAF1 2254 86 - 1
CUUU-------------------GCUGCUAUAUGGCUAUAUGGCUGUAUGGCUAUAUGG----CUAUAUGCC-----UUUGCUGCUGCCAAAGCUUCGCUGCAGCAGCAGCUGC
....-------------------((.(((((((((((((((((((....))))))))))----)))))))..-----..(((((((((...(((...)))))))))))))).)) ( -41.90)
>DroEre_CAF1 4969 94 - 1
CUGUUAUAUG----------------GCUAUAUUGCUAUAUGGCUGUAUGGCUAUAUGU----CUAUAUGGCUGCCUUUUGCUGCUGCCAAAGCUUCGCUGCAGCAGAAGCUGC
..((((((((----------------(.(((((.(((((((....))))))).))))).----))))))))).((.(((((((((.((.........)).)))))))))))... ( -35.80)
>DroYak_CAF1 5040 110 - 1
CUGUUAUAUGGCUAUAGUGCUAUACUGCUAUACUGCUAUAUGGCUAUAUGGCUAUAUGU----CUAUAUGGCUGCCUUUUGCUGCUGCCAAAGCUUCGCUGCAGCAGAAGUUGC
..(((((((((.((((..((((((..((((((......))))))..))))))..)))).----)))))))))...((((((((((.((.........)).)))))))))).... ( -40.30)
>consensus
CUUU___________________GCUGCUAUAUGGCUAUAUGGCUGUAUGGCUAUAUGU____CUAUAUGCC_____UUUGCUGCUGCCAAAGCUUCGCUGCAGCAGCAGCUGC
..........................(((((((((((....)))))))))))((((((......))))))..........((((((((...(((...)))...))))))))... (-27.74 = -28.70 +   0.96)

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 10:10:22 2006