Locus 1473

Sequence ID 3L_DroMel_CAF1
Location 4,289,328 – 4,289,442
Length 114
Max. P 0.927848
window2293 window2294

overview

Window 3

Location 4,289,328 – 4,289,419
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.45
Mean single sequence MFE -22.67
Consensus MFE -14.23
Energy contribution -14.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.63
SVM decision value 1.19
SVM RNA-class probability 0.927848
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4289328 91 - 23771897
CGCCGCCUUGUGCAAUUUUCACGCAGUUUUU-CAUGGCAGCGUGAAAAUGU--------CAAACAA-CAACGGGAUAG---------AAAGAAA------AAAGAAAAGC----GACCGA
..(((..((((...((((((((((.(((...-...))).))))))))))..--------...))))-...))).....---------.......------..........----...... ( -20.50)
>DroPse_CAF1 13661 99 - 1
CGCCGCCUUCUGCAAUUUUCACGCAGUUUUUCCAUGGCAGCGUGAAAAUGU--------CAGGCAGGCAA----ACAG---------AAAGAAAAAAUUGAAAGAAAAACCAGAAAACAA
.(((((((...(((.(((((((((.(((.......))).))))))))))))--------.)))).)))..----....---------................................. ( -25.90)
>DroSec_CAF1 12881 91 - 1
CGCCGCCUUGUGCAAUUUUCACGCAGUUUUU-CAUGGCAGCGUGAAAAUGU--------CAAACAA-CAACAGGAUAG---------AAAGAAA------AAAGAAAAGC----GACCAA
..((...((((...((((((((((.(((...-...))).))))))))))..--------...))))-.....))....---------.......------..........----...... ( -18.00)
>DroWil_CAF1 13649 96 - 1
CGCCACCU-AAGCAAUUUUCACGCAGUUUUU-CAUGGCAGCGUGAAAAUGUUAACAAAGCAAACAA-CAGCAGCAAGG---------CAGGCAA------CAACAACAAC----GAC--A
.(((.(((-..((.((((((((((.(((...-...))).)))))))))).........((......-..)).)).)))---------..)))..------..........----...--. ( -24.80)
>DroYak_CAF1 13193 91 - 1
CGCCGCCUUGUGCAAUUUUCACGCAGUUUUU-CAUGGCAGCGUGAAAAUGU--------CAAACAA-CAACGGGCUAG---------AAAGAAA------AUAGAAAAGC----GACCGA
..(((..((((...((((((((((.(((...-...))).))))))))))..--------...))))-...)))(((..---------.......------.......)))----...... ( -21.19)
>DroAna_CAF1 12803 103 - 1
CGCCGCCUUGUGCAAUUUUCACGCAGUUUUU-CAUGGCAGCGUGAAAAUGU--------CAAACAA-CAACGGCAUGGCUUAAAAAAAAAGAAA---CAGAAAGAAAAGC----GUCCAA
.((((..((((...((((((((((.(((...-...))).))))))))))..--------...))))-...))))...((((.............---.........))))----...... ( -25.65)
>consensus
CGCCGCCUUGUGCAAUUUUCACGCAGUUUUU_CAUGGCAGCGUGAAAAUGU________CAAACAA_CAACGGGAUAG_________AAAGAAA______AAAGAAAAGC____GACCAA
.((........)).((((((((((.(((.......))).))))))))))....................................................................... (-14.23 = -14.23 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,289,351 – 4,289,442
Length 91
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 85.86
Mean single sequence MFE -26.55
Consensus MFE -19.59
Energy contribution -19.48
Covariance contribution -0.11
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.74
SVM decision value -0.03
SVM RNA-class probability 0.518006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4289351 91 + 23771897
--CUAUCCCGUUG-UUGUUUGACAUUUUCACGCUGCCAUG-AAAAACUGCGUGAAAAUUGCACAAGGCGGCG-AGACAAUUGCCGUUAAUUU--GAAA
--........(((-(.((.....((((((((((.......-.......)))))))))).))))))(((((((-(.....)))))))).....--.... ( -24.04)
>DroPse_CAF1 13694 89 + 1
--CUGU----UUGCCUGCCUGACAUUUUCACGCUGCCAUGGAAAAACUGCGUGAAAAUUGCAGAAGGCGGCG-AGACAAUUGCCGUUAAUUU--GAGA
--....----..((((..(((..((((((((((...............))))))))))..))).))))((((-(.....)))))........--.... ( -29.86)
>DroGri_CAF1 14287 83 + 1
--CUGU------G-UUUU-----GUGUUCACGCUGUGUUGGAAAAACUGCGUGAAAAUUGCACA-GGCGGCAAAGACAAUUGCCGUUAAUUUUAAAAA
--((((------(-(..(-----...(((((((...(((.....))).))))))).)..)))))-)(((((((......)))))))............ ( -30.10)
>DroSec_CAF1 12904 91 + 1
--CUAUCCUGUUG-UUGUUUGACAUUUUCACGCUGCCAUG-AAAAACUGCGUGAAAAUUGCACAAGGCGGCG-AGACAAUUGCCGUUAAUUU--GAAA
--........(((-(.((.....((((((((((.......-.......)))))))))).))))))(((((((-(.....)))))))).....--.... ( -24.04)
>DroYak_CAF1 13216 91 + 1
--CUAGCCCGUUG-UUGUUUGACAUUUUCACGCUGCCAUG-AAAAACUGCGUGAAAAUUGCACAAGGCGGCG-AGACAAUUGCCGUUAAUUU--GAAA
--...(((..(((-(.((.....((((((((((.......-.......)))))))))).)))))))))((((-(.....)))))........--.... ( -24.94)
>DroAna_CAF1 12836 93 + 1
AGCCAUGCCGUUG-UUGUUUGACAUUUUCACGCUGCCAUG-AAAAACUGCGUGAAAAUUGCACAAGGCGGCG-AGACAAUUGCCGUUAAUUU--GAAA
......(((.(((-(.((.....((((((((((.......-.......)))))))))).)))))))))((((-(.....)))))........--.... ( -26.34)
>consensus
__CUAUCCCGUUG_UUGUUUGACAUUUUCACGCUGCCAUG_AAAAACUGCGUGAAAAUUGCACAAGGCGGCG_AGACAAUUGCCGUUAAUUU__GAAA
.......................((((((((((...............)))))))))).......(((((((........)))))))........... (-19.59 = -19.48 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:35 2006