Locus 2816

Sequence ID 3R_DroMel_CAF1
Location 7,535,341 – 7,535,475
Length 134
Max. P 0.917216
window4552 window4553 window4554

overview

Window 2

Location 7,535,341 – 7,535,435
Length 94
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 74.71
Mean single sequence MFE -27.37
Consensus MFE -12.70
Energy contribution -13.43
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -2.19
Structure conservation index 0.46
SVM decision value 1.11
SVM RNA-class probability 0.917216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7535341 94 - 27905053
GCUGGAGCUGAAGCUGCAGGAUGCUGAAUGGA---AG--G--------------AGUGGGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG---GCUUCAUGUCUUCAGCUU
((((((((((((((((..(.(((((.(.....---..--.--------------..).)))))(.(((((((......))))))).)...)..))---)))))).).))))))).. ( -32.10)
>DroSec_CAF1 30728 94 - 1
GCUGGAGCUGAAGCUGCUGGAUGCUGAAUGGA---GG--G--------------AGUGGGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG---GCUCCAUGUCUUCAGCUU
.(..((((....))).)..)..((((((.((.---.(--(--------------(((.(.((((.(((((((......))))))).)..))).).---)))))...)))))))).. ( -32.70)
>DroSim_CAF1 31611 79 - 1
GCU---------------AGAUGCUGAAUGGA---GG--G--------------AGUGGGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG---GCUCCAUGUCUUCAGCUU
...---------------....((((((.((.---.(--(--------------(((.(.((((.(((((((......))))))).)..))).).---)))))...)))))))).. ( -27.00)
>DroEre_CAF1 32585 87 - 1
GCU------AAAGCUGCA-GAAGCUGAAUAGA---GG--G--------------AGUGAGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG---GCUCCAUGUCUUCAGCUU
((.------......)).-.((((((((....---.(--(--------------(((...((((.(((((((......))))))).)..)))...---))))).....)))))))) ( -26.60)
>DroYak_CAF1 30676 98 - 1
GCU------AAAGCUA----AAGCUAAAUAGA---GA--GAGAGAGAGAGUGGGAAUGGGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG---GCUCCAUGUCUUCAGCUU
(((------..(((..----..))).......---((--.(((.(..((((.(......((((((.((((.......))))))))))......).---))))..).)))))))).. ( -21.90)
>DroPer_CAF1 30025 86 - 1
---------------GGUGCAUGCUGCCUGGUGCAGGCCA--------------AGAGGGAGUGGAUAAUGAGUUAAAUUAUUAUGCAAACGACGGCGGCUCCAUGUCUUGAGA-U
---------------..........(((((...)))))((--------------(((.((((((.(((((((......))))))).)...((....)))))))...)))))...-. ( -23.90)
>consensus
GCU_______AAGCUGC_GGAUGCUGAAUGGA___GG__G______________AGUGGGCGUGGGUAAUGAGUUAAAUUAUUAUGCAAACGACG___GCUCCAUGUCUUCAGCUU
......................(((((..............................(((((((((((((((......)))))))((...........)).))))))))))))).. (-12.70 = -13.43 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,535,375 – 7,535,475
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 81.60
Mean single sequence MFE -19.56
Consensus MFE -10.71
Energy contribution -11.78
Covariance contribution 1.06
Combinations/Pair 1.11
Mean z-score -2.73
Structure conservation index 0.55
SVM decision value 0.95
SVM RNA-class probability 0.887959
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7535375 100 + 27905053
AUUUAACUCAUUACCCACGCCCACUCCUUCCAUUCAGCAUCCUGCAGCUUCAGCUCCAGCUUCUGCUCUAGCUUAGGGUUCUGCUCCUUUUGGGCCAGAA
..................(((((...........(((.((((((.((((..(((..........)))..)))))))))).))).......)))))..... ( -23.97)
>DroSec_CAF1 30762 94 + 1
AUUUAACUCAUUACCCACGCCCACUCCCUCCAUUCAGCAUCCAGCAGCUUCAGCUCCAGCUUC------AGCUUGGGGUUCUGCUCCUUAUGGGCCAGAA
..................(((((.............((.....))(((...(((((((((...------.)).)))))))..))).....)))))..... ( -23.10)
>DroSim_CAF1 31645 79 + 1
AUUUAACUCAUUACCCACGCCCACUCCCUCCAUUCAGCAUCU---------------AGCUUC------AGCUUGGGUUUCUGCUCCUUUUGGGCCAGAA
............(((((.((...............(((....---------------.)))..------.)).)))))(((((..((....))..))))) ( -14.97)
>DroEre_CAF1 32619 87 + 1
AUUUAACUCAUUACCCACGCUCACUCCCUCUAUUCAGCUUC-UGCAGCUUU------AGCUUC------AGCUUCAGCUUCUGCUCCUUUUGGGCCAGAA
....................................((...-.))((((..------(((...------.)))..))))((((..((....))..)))). ( -16.20)
>consensus
AUUUAACUCAUUACCCACGCCCACUCCCUCCAUUCAGCAUCCUGCAGCUUC______AGCUUC______AGCUUGGGGUUCUGCUCCUUUUGGGCCAGAA
..................(((((.............((.....))............((((........)))))))))(((((..((....))..))))) (-10.71 = -11.78 +   1.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,535,375 – 7,535,475
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 81.60
Mean single sequence MFE -24.62
Consensus MFE -15.41
Energy contribution -15.97
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -1.84
Structure conservation index 0.63
SVM decision value 0.21
SVM RNA-class probability 0.636306
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7535375 100 - 27905053
UUCUGGCCCAAAAGGAGCAGAACCCUAAGCUAGAGCAGAAGCUGGAGCUGAAGCUGCAGGAUGCUGAAUGGAAGGAGUGGGCGUGGGUAAUGAGUUAAAU
(((..(((((......((...(((((...(((.((((....(((.(((....))).)))..))))...))).))).))..)).)))))...)))...... ( -29.20)
>DroSec_CAF1 30762 94 - 1
UUCUGGCCCAUAAGGAGCAGAACCCCAAGCU------GAAGCUGGAGCUGAAGCUGCUGGAUGCUGAAUGGAGGGAGUGGGCGUGGGUAAUGAGUUAAAU
(((..((((((.....((...(((((.((((------..(((....)))..))))((.....))........))).))..))))))))...)))...... ( -28.20)
>DroSim_CAF1 31645 79 - 1
UUCUGGCCCAAAAGGAGCAGAAACCCAAGCU------GAAGCU---------------AGAUGCUGAAUGGAGGGAGUGGGCGUGGGUAAUGAGUUAAAU
(((((..((....))..)))))(((((.(((------.(..((---------------...(.(.....).).))..).))).)))))............ ( -20.50)
>DroEre_CAF1 32619 87 - 1
UUCUGGCCCAAAAGGAGCAGAAGCUGAAGCU------GAAGCU------AAAGCUGCA-GAAGCUGAAUAGAGGGAGUGAGCGUGGGUAAUGAGUUAAAU
(((..(((((......((((.((((......------..))))------....)))).-...(((.(..........).))).)))))...)))...... ( -20.60)
>consensus
UUCUGGCCCAAAAGGAGCAGAACCCCAAGCU______GAAGCU______GAAGCUGCAGGAUGCUGAAUGGAGGGAGUGGGCGUGGGUAAUGAGUUAAAU
(((..(((((......((..(..(((.((((........))))........(((........))).......)))..)..)).)))))...)))...... (-15.41 = -15.97 +   0.56)

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 10:45:22 2006