Locus 2231

Sequence ID 2R_DroMel_CAF1
Location 8,235,395 – 8,235,492
Length 97
Max. P 0.921367
window3673 window3674

overview

Window 3

Location 8,235,395 – 8,235,492
Length 97
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -20.54
Consensus MFE -10.18
Energy contribution -10.40
Covariance contribution 0.22
Combinations/Pair 1.11
Mean z-score -2.09
Structure conservation index 0.50
SVM decision value -0.02
SVM RNA-class probability 0.525513
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8235395 97 + 20766785
GCAUUUGCAUUCGAGUUAUGUGCGCUAAUUUCACGUUAUGAAAUU-UUUAUUUCGCACAUUUGCUCGUCGCAGUUUUCUUGCCUCGUUUUUC-----AUCUGA----------------
(((.((((...(((((.(((((((..(((((((.....)))))))-.......)))))))..)))))..))))......)))..........-----......---------------- ( -24.00)
>DroVir_CAF1 34317 110 + 1
GCAUUUGCAUUCGAGUUAUUUGCGCUCAUUUCACGUUAUGAAAUU-UUUAUUUCGCACAUUUGCGCAACGCA-UUUUCGUGCCUCGUUUUUC-----AUUCGCUGC--CGCUUUCCGCU
......((...((((....((((((........((..((((....-.))))..)).......)))))).(((-(....))))))))......-----....((...--.)).....)). ( -18.96)
>DroGri_CAF1 39866 112 + 1
GCAUUUGCAUUCGAGUUAUGUGCGCUAAUUUCACGUUAUGAAUUU-UGUAUUUCGCAAAUUUGCGCAUCACA-UUUUCUUGCCACGUUUUUC-----AUUCUUUUUUUUGUUUUGUGUU
((....))....(((..(((((.((((((.....)))).(((...-(((..(.((((....)))).)..)))-..)))..)))))))..)))-----...................... ( -16.70)
>DroSec_CAF1 22801 102 + 1
GCAUUUGCAUUCGAGUUAUGUGCGCUAAUUUCACGUUAUGAAAUU-UUUAUUUCGCACAUUUGCUCGUCGCAGUUUUCUUGCCUCAUUUUUUAUUUCAUCUGC----------------
(((.((((...(((((.(((((((..(((((((.....)))))))-.......)))))))..)))))..))))......))).....................---------------- ( -24.00)
>DroSim_CAF1 24823 99 + 1
GCAUUUGCAUUCGAGUUAUGUGCGCUAAUUUCACGUUAUGAAAUU-UUUAUUUCGCACAUUUGCUCGUCGCAGUUUUCUUGCCUCGUUUUUCGUUU---CUGA----------------
(((.((((...(((((.(((((((..(((((((.....)))))))-.......)))))))..)))))..))))......)))..............---....---------------- ( -24.00)
>DroMoj_CAF1 39533 94 + 1
GCAUUUGCAUUCAAGUUAUUUGCGCUAAUUUCACGUUAUGAAAUUUUUUAUUUCGCACAUUUGCACAACGCG-UUUGCUUGCCUCGUUUUUC-----AUU-------------------
((....))...(((((.....((((.(((((((.....))))))).........(((....))).....)))-)..)))))...........-----...------------------- ( -15.60)
>consensus
GCAUUUGCAUUCGAGUUAUGUGCGCUAAUUUCACGUUAUGAAAUU_UUUAUUUCGCACAUUUGCUCAUCGCA_UUUUCUUGCCUCGUUUUUC_____AUCUGA________________
((....))...((((.....((((...............(((((.....)))))(((....)))....)))).....))))...................................... (-10.18 = -10.40 +   0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,235,395 – 8,235,492
Length 97
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -20.46
Consensus MFE -12.66
Energy contribution -13.08
Covariance contribution 0.42
Combinations/Pair 1.15
Mean z-score -2.42
Structure conservation index 0.62
SVM decision value 1.14
SVM RNA-class probability 0.921367
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8235395 97 - 20766785
----------------UCAGAU-----GAAAAACGAGGCAAGAAAACUGCGACGAGCAAAUGUGCGAAAUAAA-AAUUUCAUAACGUGAAAUUAGCGCACAUAACUCGAAUGCAAAUGC
----------------......-----......((((..........(((.....))).(((((((.......-((((((((...))))))))..)))))))..))))........... ( -21.00)
>DroVir_CAF1 34317 110 - 1
AGCGGAAAGCG--GCAGCGAAU-----GAAAAACGAGGCACGAAAA-UGCGUUGCGCAAAUGUGCGAAAUAAA-AAUUUCAUAACGUGAAAUGAGCGCAAAUAACUCGAAUGCAAAUGC
.(((....((.--...))....-----......(((((((......-))).((((((...(((.....)))..-.(((((((...)))))))..))))))....))))..)))...... ( -24.10)
>DroGri_CAF1 39866 112 - 1
AACACAAAACAAAAAAAAGAAU-----GAAAAACGUGGCAAGAAAA-UGUGAUGCGCAAAUUUGCGAAAUACA-AAAUUCAUAACGUGAAAUUAGCGCACAUAACUCGAAUGCAAAUGC
..(((.................-----.......)))(((.((...-((((.(((((.((((((((.......-..........))).))))).)))))))))..))...)))...... ( -16.79)
>DroSec_CAF1 22801 102 - 1
----------------GCAGAUGAAAUAAAAAAUGAGGCAAGAAAACUGCGACGAGCAAAUGUGCGAAAUAAA-AAUUUCAUAACGUGAAAUUAGCGCACAUAACUCGAAUGCAAAUGC
----------------(((..................(((.......)))..((((...(((((((.......-((((((((...))))))))..)))))))..))))..)))...... ( -22.80)
>DroSim_CAF1 24823 99 - 1
----------------UCAG---AAACGAAAAACGAGGCAAGAAAACUGCGACGAGCAAAUGUGCGAAAUAAA-AAUUUCAUAACGUGAAAUUAGCGCACAUAACUCGAAUGCAAAUGC
----------------....---..........((((..........(((.....))).(((((((.......-((((((((...))))))))..)))))))..))))........... ( -21.00)
>DroMoj_CAF1 39533 94 - 1
-------------------AAU-----GAAAAACGAGGCAAGCAAA-CGCGUUGUGCAAAUGUGCGAAAUAAAAAAUUUCAUAACGUGAAAUUAGCGCAAAUAACUUGAAUGCAAAUGC
-------------------...-----..........(((..(((.-....((((((...(((.....)))...((((((((...)))))))).)))))).....)))..)))...... ( -17.10)
>consensus
________________GCAAAU_____GAAAAACGAGGCAAGAAAA_UGCGACGAGCAAAUGUGCGAAAUAAA_AAUUUCAUAACGUGAAAUUAGCGCACAUAACUCGAAUGCAAAUGC
.................................((((..........(((.....)))..(((((.........((((((((...)))))))).))))).....))))........... (-12.66 = -13.08 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:26 2006