Locus 4586

Sequence ID X_DroMel_CAF1
Location 12,021,459 – 12,021,768
Length 309
Max. P 0.927719
window7544 window7545 window7546

overview

Window 4

Location 12,021,459 – 12,021,571
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -26.58
Consensus MFE -20.98
Energy contribution -22.34
Covariance contribution 1.36
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 0.79
SVM decision value 1.19
SVM RNA-class probability 0.927719
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12021459 112 - 22224390
CUGGUUGAAAAGAUUGCUGCUUUUUGUAUACAAGAGGCAUGCAAAUGGUUUUUUAAUGGGGUUUCAGAUUUAUCAACAAAGUGAAACUGUAAACUAAAGUAAUAAAAAUUCC--------
((.(((((((((.(((((((((((((....))))))))).))))....))))))))).))(((((((.(((((.......))))).))).))))..................-------- ( -28.00)
>DroSec_CAF1 54783 120 - 1
CUGGUUGAAAAGAUUGCUGCUUUUUGUUUACAAGAGCCUUGCAAAUGGUUUUUUAAUGGGGUUUCAGAUUUAUCAACAAAGUGAAACUGUAAACUAAAGUAAUAAAAAUUCCGUGAAAUA
..((........((((((.......(((((((((((((........)))))))......(((((((..(((......))).)))))))))))))...)))))).......))........ ( -22.56)
>DroSim_CAF1 53510 120 - 1
CUGGUUGAAAAGAUUGCUGCUUUUUGUUUACAAGAGCCAUGCAAAUGGUUUUUUAAUGGGGUUUCAGAUUUAUCAACAAAGUGAAACUGUAAACUAAAGUAAUAAAAAUUCCAUGAAAUA
.(((........((((((.......(((((((((((((((....)))))))))......(((((((..(((......))).)))))))))))))...)))))).......)))....... ( -25.76)
>DroEre_CAF1 51887 120 - 1
CUGUUUGAAAAGAUUGCUGCACUUUGUUUACAAACGGCAUGCAAAUGGUUUUUUAAUGGGGUUUCAGAUUUAUCAACAAAGUGAAACUGUAAACUAAAGUAAUAAAAAUUCCAUGGAACA
..((((.......(((((((..((((....))))..))).))))((((.((((((((..((((((((.(((((.......))))).))).)))))...))..))))))..)))).)))). ( -24.10)
>DroYak_CAF1 53059 119 - 1
CUGGUUGAAAAGAUUGCAGCUUUUUGUUUACAAAAGGCAUGCAAAUGGUUUUUUAAUGGGGUUUCAGUUUUAAAAACAAAGUGAAACUGCAAACUAAAGUAAUAA-AAUUCCAUGGAAUA
((.(((((((((.(((((((((((((....)))))))).)))))....))))))))).))((((((((((((.........)))))))).))))...........-.((((....)))). ( -32.50)
>consensus
CUGGUUGAAAAGAUUGCUGCUUUUUGUUUACAAGAGGCAUGCAAAUGGUUUUUUAAUGGGGUUUCAGAUUUAUCAACAAAGUGAAACUGUAAACUAAAGUAAUAAAAAUUCCAUGAAAUA
((.(((((((((.(((((((((((((....))))))))).))))....))))))))).))(((((((.(((((.......))))).))).)))).......................... (-20.98 = -22.34 +   1.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,021,571 – 12,021,691
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -20.95
Consensus MFE -17.55
Energy contribution -17.18
Covariance contribution -0.37
Combinations/Pair 1.19
Mean z-score -1.48
Structure conservation index 0.84
SVM decision value 0.11
SVM RNA-class probability 0.586457
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12021571 120 - 22224390
AGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAUUUAACAACUAGCACAGUACAUUUUGUAUAGUAUCAAUUUGCAAAAGCAAAUAGGGAUUUUCGUUAAACAAAUGCAGAAUA
....((((((.(((((....))))).)))))).......((((((.((((..((((......)))).)))).((.((((((....)))))).)).......))))))............. ( -22.30)
>DroSec_CAF1 54903 120 - 1
AGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAUUUAACAACUAGCACAGUACAUUUUGUAUAGUAUCAAUUUGCAAAAGCAAAUAGGAAUUUUCGUUAAACAAAUGCAAAAUA
....((((((.(((((....))))).)))))).......((((((.((((..((((......)))).)))).((.((((((....)))))).)).......))))))............. ( -22.30)
>DroSim_CAF1 53630 120 - 1
AGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAUUUAACAACUAGCUCAGUACAUUUUGUAUAGUAUCAAUUUGCAAAAACAAAUAGGGAUUUUCGUUAAACAAAUGCAAAAUA
....((((((.(((((....))))).)))))).......((((((.((((...(((......)))..)))).((.(((((......))))).)).......))))))............. ( -17.40)
>DroYak_CAF1 53178 120 - 1
AAAAUAGCUUCGUGGGGCAACUUGCUAAUUUAAAAUCAAUUUAACAACAAUGAUAGUAAAUUUUGUAUAGUAUCAAUUUGCAAAAGCAAAUAGGGAUUUUCGUUAAAUAAAUGCAAAAUA
......((...(..((....))..).............(((((((.....(((((.((.........)).)))))((((((....))))))..........)))))))....))...... ( -21.80)
>consensus
AGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAUUUAACAACUAGCACAGUACAUUUUGUAUAGUAUCAAUUUGCAAAAGCAAAUAGGGAUUUUCGUUAAACAAAUGCAAAAUA
....((((((.(((((....))))).)))))).......((((((.((((...(((......)))..)))).((.((((((....)))))).)).......))))))............. (-17.55 = -17.18 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,021,651 – 12,021,768
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 95.43
Mean single sequence MFE -22.80
Consensus MFE -20.10
Energy contribution -20.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.88
SVM decision value 0.82
SVM RNA-class probability 0.858002
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12021651 117 - 22224390
AACAGUUUUUAUUGGCUAACUACCAAUUUUUACCACCUCUUUCAAUUUUUUUCAGAUUCUGAGAAAAAUUAAAAACGAGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAU
....(((((((((((.......)))))................((((((((((((...))))))))))))))))))((...((((((.(((((....))))).))))))...))... ( -24.80)
>DroSec_CAF1 54983 116 - 1
AACAGUUUUUAUCGGCUAAUUACCAAUUUCUACCACCUCUUUCACU-UUUUUCAGAUACUGAGAAAAAUUAAAAACGAGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAU
....(((((((..((.......)).....................(-((((((((...)))))))))..)))))))((...((((((.(((((....))))).))))))...))... ( -21.10)
>DroSim_CAF1 53710 116 - 1
AACCGUUUUUAUCGGCUAAUUACCAAUUUUUACCACCUCUUUCACU-UUUUUCAGAUUCUGAGAAAAAGUAAAAACGAGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAU
...(((((((((.((.......)).....................(-((((((((...))))))))).)))))))))....((((((.(((((....))))).))))))........ ( -22.50)
>consensus
AACAGUUUUUAUCGGCUAAUUACCAAUUUUUACCACCUCUUUCACU_UUUUUCAGAUUCUGAGAAAAAUUAAAAACGAGAAUGAAUUUGUAAGGGAGCUUACUAAUUUAAAAUCAAU
....(((((((..((.......)).......................((((((((...))))))))...)))))))((...((((((.(((((....))))).))))))...))... (-20.10 = -20.10 +  -0.00)

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 11:28:52 2006