Locus 1218

Sequence ID X_DroMel_CAF1
Location 3,625,178 – 3,625,273
Length 95
Max. P 0.999953
window1956 window1957

overview

Window 6

Location 3,625,178 – 3,625,273
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.42
Mean single sequence MFE -36.79
Consensus MFE -25.36
Energy contribution -26.54
Covariance contribution 1.19
Combinations/Pair 1.12
Mean z-score -3.19
Structure conservation index 0.69
SVM decision value 4.82
SVM RNA-class probability 0.999953
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3625178 95 + 22224390
---GCAGCUGCUUUCCGUUUUGGAUUGGAAGUUCG----------UUGGAAUGGAAGGCAGCAGC----AAAAGAA----GA-AGAAGAAGCUGCAACGCC---GCGAAGCUGGCAGCGC
---((.((((((((((((((..(...((....)).----------)..)))))))))))))).))----.......----..-.......(((((...((.---.....))..))))).. ( -36.80)
>DroSec_CAF1 4528 95 + 1
---GCAGCUGCUUUCCGUUUUGGAUUGGAAGUUCG----------UUGGAAUGGAAGGCAGCAGC----GAAAGAA----GA-AGAAGAAGCUGCAACGCC---GCGAAGCUGGCAGCGC
---((.((((((((((((((..(...((....)).----------)..)))))))))))))).))----.......----..-.......(((((...((.---.....))..))))).. ( -36.80)
>DroEre_CAF1 4573 95 + 1
GCAGCAGCUGCUUUCCGUUUUGGAUUGGAAGUUCG----------GUGGAAUGGAAGGCAGCAGC----AAAAGAA----G----AAGAAGCUGCAACGCC---GCGAAGCUGGCAGCGC
((.((.(((((((((((((((((((.....)))))----------...)))))))))))))).))----.......----.----.....(((((...((.---.....))..))))))) ( -37.40)
>DroAna_CAF1 9693 110 + 1
---GCAGCUGCUUUCCGU-------UGGAAGUUGCUGGCUAUGUUGUGGAAUGGUAAGAAAUAGAGGGGAAGGGAAGCAGGAAGGAAGAGGCUGCAGCGCUAAAGCGACGCAGUCAGCGU
---((..(((((((((..-------.........((.(((((........))))).)).............))))))))).........((((((..(((....)))..)))))).)).. ( -36.15)
>consensus
___GCAGCUGCUUUCCGUUUUGGAUUGGAAGUUCG__________GUGGAAUGGAAGGCAGCAGC____AAAAGAA____GA_AGAAGAAGCUGCAACGCC___GCGAAGCUGGCAGCGC
...((.(((((((((((((((..........................)))))))))))))))............................(((((..(((....)))......))))))) (-25.36 = -26.54 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,625,178 – 3,625,273
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.42
Mean single sequence MFE -23.61
Consensus MFE -16.53
Energy contribution -17.59
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.70
SVM decision value 0.04
SVM RNA-class probability 0.552400
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3625178 95 - 22224390
GCGCUGCCAGCUUCGC---GGCGUUGCAGCUUCUUCU-UC----UUCUUUU----GCUGCUGCCUUCCAUUCCAA----------CGAACUUCCAAUCCAAAACGGAAAGCAGCUGC---
..(((((..(((....---)))...))))).......-..----.......----((.(((((.((((.......----------...................)))).))))).))--- ( -24.77)
>DroSec_CAF1 4528 95 - 1
GCGCUGCCAGCUUCGC---GGCGUUGCAGCUUCUUCU-UC----UUCUUUC----GCUGCUGCCUUCCAUUCCAA----------CGAACUUCCAAUCCAAAACGGAAAGCAGCUGC---
..(((((..(((....---)))...))))).......-..----.......----((.(((((.((((.......----------...................)))).))))).))--- ( -25.07)
>DroEre_CAF1 4573 95 - 1
GCGCUGCCAGCUUCGC---GGCGUUGCAGCUUCUU----C----UUCUUUU----GCUGCUGCCUUCCAUUCCAC----------CGAACUUCCAAUCCAAAACGGAAAGCAGCUGCUGC
(((((((.......))---))))).(((((.....----.----.......----...(((((.((((.......----------...................)))).))))).))))) ( -26.60)
>DroAna_CAF1 9693 110 - 1
ACGCUGACUGCGUCGCUUUAGCGCUGCAGCCUCUUCCUUCCUGCUUCCCUUCCCCUCUAUUUCUUACCAUUCCACAACAUAGCCAGCAACUUCCA-------ACGGAAAGCAGCUGC---
..((((.(((((.(((....))).)))))........((((((((...((..............................))..)))).......-------..))))..))))...--- ( -18.01)
>consensus
GCGCUGCCAGCUUCGC___GGCGUUGCAGCUUCUUCU_UC____UUCUUUU____GCUGCUGCCUUCCAUUCCAA__________CGAACUUCCAAUCCAAAACGGAAAGCAGCUGC___
..(((((..((.........))...))))).........................((.(((((.((((....................................)))).))))).))... (-16.53 = -17.59 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:10 2006