Locus 1495

Sequence ID 3L_DroMel_CAF1
Location 4,331,282 – 4,331,516
Length 234
Max. P 0.974906
window2328 window2329 window2330

overview

Window 8

Location 4,331,282 – 4,331,397
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.00
Mean single sequence MFE -15.15
Consensus MFE -12.70
Energy contribution -12.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.84
SVM decision value 0.13
SVM RNA-class probability 0.600398
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4331282 115 + 23771897
--U-UAAAUGCCAGCAAAAGAGGAAAUGUUUACAGCACAGCCAA--CUGCAAUCCAUUAGCUAUUUUUAUAGCAGCACAAAAGCACAAAAAUAAUAAACAAAAUCUACACAUAUUUCUUU
--.-...............((((((((((.....(((.......--.))).....(((((((((....))))).((......)).......))))...............)))))))))) ( -15.00)
>DroSec_CAF1 17790 114 + 1
--U-UAAAUGCCAGCAA-AGAGGAAAUGUUUACAGCACAGCCAA--CUGCAAUCCAUUAGCUAUUUUUAUAGCAGCACAAAAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUA
--.-.............-..(((((((((.....(((.......--.))).........(((((....))))).((......))..........................))))))))). ( -14.30)
>DroSim_CAF1 16384 115 + 1
--UUUAUAUGCCAGCAA-AGAGGAAAUGUUUACAGCACAGCCAA--CUGCAAUCCAUUAGCUAUUUUUAUAGCAGCACAAAAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUA
--...............-..(((((((((.....(((.......--.))).........(((((....))))).((......))..........................))))))))). ( -14.30)
>DroEre_CAF1 17778 108 + 1
UUU-UAAAUGCCAGCAA-AGAGGAAAUGUUUACAGCACUGCCAA--CUGCAAUCCAUUAGCUAUUUUUAUAGCAGCAC--------AGAAAUAACAAACAAAAUCUACACAUAUUUCUUU
...-....(((..(((.-...((...(((.....)))...))..--.))).........(((((....))))).))).--------(((((((..................))))))).. ( -14.27)
>DroYak_CAF1 16963 108 + 1
--U-GAAAUGCCAGCAA-AGAGGAAAUGUUUACAGCACUGCCAACACUGCAAUGCAUUAGCUAUUUUUAUAGCAGCAC--------AAAAAUAACAAACAAAAUCUACACAUAUUUCUUU
--.-.............-.((((((((((.....(((.(((.......))).)))....(((((....))))).....--------........................)))))))))) ( -17.90)
>consensus
__U_UAAAUGCCAGCAA_AGAGGAAAUGUUUACAGCACAGCCAA__CUGCAAUCCAUUAGCUAUUUUUAUAGCAGCACAAAAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUU
........(((..(((.....((...(((.....)))...)).....))).........(((((....))))).)))........................................... (-12.70 = -12.70 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,331,357 – 4,331,477
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.11
Mean single sequence MFE -23.39
Consensus MFE -20.56
Energy contribution -19.92
Covariance contribution -0.64
Combinations/Pair 1.16
Mean z-score -1.33
Structure conservation index 0.88
SVM decision value 0.42
SVM RNA-class probability 0.730788
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4331357 120 + 23771897
AAGCACAAAAAUAAUAAACAAAAUCUACACAUAUUUCUUUGAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAGAGGGGAAAUGGUGAGUAUAAAACGUAGACAC
.......................(((((...(((((((......)))))))(..(((((((((((....)))..((.((....)))).....))))))))..).........)))))... ( -25.20)
>DroSec_CAF1 17864 120 + 1
AAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUAGAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGGAAAUGCAGGGGGGAAAUGGCGGGUAUAAAACGCAGACAC
..((...........................(((((((......)))))))((((((((((((((....)))..((.((....)))).....))))))))))).........))...... ( -23.40)
>DroSim_CAF1 16459 120 + 1
AAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUAGAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGGAAAUGCAGGGGGGAAAUGGCGGGUAUAAAACGCAGACAC
..((...........................(((((((......)))))))((((((((((((((....)))..((.((....)))).....))))))))))).........))...... ( -23.40)
>DroEre_CAF1 17852 113 + 1
------AGAAAUAACAAACAAAAUCUACACAUAUUUCUUUGAGCGGGCAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAA-GGGGAAAUGGCGAGUAUAAAACGAAGACAC
------.............................((((((.(....)...(((((((((((.(((.((((((...)))))).)))...-..)))))))))))........))))))... ( -22.50)
>DroYak_CAF1 17037 113 + 1
------AAAAAUAACAAACAAAAUCUACACAUAUUUCUUUGAGCGCGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAA-GGGGAAGUGGCGAGUAUAAAACGAAGACAC
------.............................((((((..........(((((((((((.(((.((((((...)))))).)))...-..)))))))))))........))))))... ( -22.47)
>consensus
AAGCACAAAAAUAACAAACAAAAUCUACACAUAUUUCUUUGAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAG_GGGGAAAUGGCGAGUAUAAAACGAAGACAC
.......................(((.(...(((((((......)))))))(((((((((((.(((.((((((...)))))).)))......))))))))))).........).)))... (-20.56 = -19.92 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,331,397 – 4,331,516
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.81
Mean single sequence MFE -33.42
Consensus MFE -32.44
Energy contribution -31.56
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -1.44
Structure conservation index 0.97
SVM decision value 1.74
SVM RNA-class probability 0.974906
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4331397 119 + 23771897
GAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAGAGGGGAAAUGGUGAGUAUAAAACGUAGACACU-UUACUUGGCGGGUGGGAAAACUUGAUCAAUUUCCUGCA
..(((((((..(..(((((((((((....)))..((.((....)))).....))))))))..).........(((((...)-))))(((((((((......))))).)))).))))))). ( -33.20)
>DroSec_CAF1 17904 120 + 1
GAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGGAAAUGCAGGGGGGAAAUGGCGGGUAUAAAACGCAGACACUUUUACUUGGCGGGUGGGAAAACUUGAUCAAUUUCCUGCA
..(((((((..((((((((((((((....)))..((.((....)))).....))))))))))).......................(((((((((......))))).)))).))))))). ( -34.10)
>DroSim_CAF1 16499 120 + 1
GAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGGAAAUGCAGGGGGGAAAUGGCGGGUAUAAAACGCAGACACUUUUACUUGGCGGGUGGGAAAACUUGAUCAAUUUCCUGCA
..(((((((..((((((((((((((....)))..((.((....)))).....))))))))))).......................(((((((((......))))).)))).))))))). ( -34.10)
>DroEre_CAF1 17886 118 + 1
GAGCGGGCAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAA-GGGGAAAUGGCGAGUAUAAAACGAAGACACU-UUAGUUGGCGGGUGGGAAAGCUUGAUCAAUUUCCUGCA
..(((((....(((((((((((.(((.((((((...)))))).)))...-..)))))))))))..................-..(((((((((((......))))).)))))).))))). ( -33.40)
>DroYak_CAF1 17071 118 + 1
GAGCGCGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAA-GGGGAAGUGGCGAGUAUAAAACGAAGACACU-UUAGUUGGCGGGUGGGAAAGCUUGAUCAAUUUCCUGCA
...(((.(((.(((((((((((.(((.((((((...)))))).)))...-..))))))))))).........((((...))-)).))).))).(..(((((..........)))))..). ( -32.30)
>consensus
GAGCGGGAAUAUUGCCAUUUCCAUAUAUUUAUGAGCCAUGAAAGUGCAG_GGGGAAAUGGCGAGUAUAAAACGAAGACACU_UUACUUGGCGGGUGGGAAAACUUGAUCAAUUUCCUGCA
..(((((((..(((((((((((.(((.((((((...)))))).)))......))))))))))).......................(((((((((......))))).)))).))))))). (-32.44 = -31.56 +  -0.88)

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 10:09:10 2006