Locus 2176

Sequence ID X_DroMel_CAF1
Location 5,899,664 – 5,899,807
Length 143
Max. P 0.994186
window3528 window3529

overview

Window 8

Location 5,899,664 – 5,899,770
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.21
Mean single sequence MFE -20.10
Consensus MFE -17.00
Energy contribution -17.20
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.85
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5899664 106 - 22224390
GCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAAAAAAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGACCGCUGAUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
...(((-.....))).............(((....((((-------------(((.((.((((((...((.(((.....))).))....))))))....))...))))))).)))..... ( -19.20)
>DroSec_CAF1 16357 104 - 1
GCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGACCGCUGAUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
((((((-(.....................(....--)..-------------(((.((...((((.......))))....)).))).))))))).......................... ( -19.10)
>DroSim_CAF1 13702 104 - 1
GCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGACCGCUGAUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
((((((-(.....................(....--)..-------------(((.((...((((.......))))....)).))).))))))).......................... ( -19.10)
>DroEre_CAF1 16466 103 - 1
GCCGCU--AAAAAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CCGAGGGUGUUGCAAAAGGGGUAAAUGACCGCUGGUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
((((((--(...(((...................--...-------------((....(.....)....))(((.....))))))..))))))).......................... ( -21.60)
>DroYak_CAF1 16597 118 - 1
GCCGCUUAAAAAAGCCAAGAAAAUAAUGAUGAAA--AAAAAAUUAAAAACAGCAGAGGGUGUUGCAAACGGGGUAAAUGACCGCUGAUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
((.((((....))))...................--.........((((((.(((....((((((...((((((.....))).)))...))))))....)))...))))))))....... ( -21.50)
>consensus
GCCGCU_AAAAGAGCCAAGAAAAUAAUGAUGAAA__AAA_____________CAGAGGGUGUUGCAAAAGGGGUAAAUGACCGCUGAUGGCGGCAAAAAUUGAAUUGUUUUGCAUAAAUU
((((((......))).....................................(((.((...((((.......))))....)).)))..))).((((((.........))))))....... (-17.00 = -17.20 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,899,704 – 5,899,807
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.24
Mean single sequence MFE -27.72
Consensus MFE -22.56
Energy contribution -22.60
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.81
SVM decision value 2.46
SVM RNA-class probability 0.994186
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5899704 103 - 22224390
UUUGCCGUGUGUUGC---GCCCUGCAGCAAAAUGAUGGGUGCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAAAAAAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGA
((((((.(.(((.((---((((((((.(.........).))).(((-.....)))........................-------------...))))))).)))...).))))))... ( -25.70)
>DroSec_CAF1 16397 101 - 1
UUUGCCGUGUGUUGC---GCCCUGCAGCAAAAUGAUGGGUGCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGA
((((((.(.(((.((---((((((((.(.........).))).(((-.....)))...................--...-------------...))))))).)))...).))))))... ( -25.70)
>DroSim_CAF1 13742 101 - 1
UUUGCCGUGUGUUGC---GCCCUGCAGCAAAAUGAUGGGUGCCGCU-AAAAGAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CAGAGGGUGUUGCAAAAGGGGUAAAUGA
((((((.(.(((.((---((((((((.(.........).))).(((-.....)))...................--...-------------...))))))).)))...).))))))... ( -25.70)
>DroEre_CAF1 16506 100 - 1
UUUGCCGUGUGUAGC---GCCCUGCAGCAAAAUGAUGGGUGCCGCU--AAAAAGCCAAGAAAAUAAUGAUGAAA--AAA-------------CCGAGGGUGUUGCAAAAGGGGUAAAUGA
((((((.(.((((((---((((((((.(.........).))).(((--....)))...................--...-------------...)))))))))))...).))))))... ( -28.90)
>DroYak_CAF1 16637 118 - 1
UUUGCCGUGUGUUGUGAAGCCCUGCAGCCAAAUGAUGGGUGCCGCUUAAAAAAGCCAAGAAAAUAAUGAUGAAA--AAAAAAUUAAAAACAGCAGAGGGUGUUGCAAACGGGGUAAAUGA
((((((.(((.(((..(.((((((((.(((.....))).))).((((....))))...................--...................))))).)..)))))).))))))... ( -32.60)
>consensus
UUUGCCGUGUGUUGC___GCCCUGCAGCAAAAUGAUGGGUGCCGCU_AAAAGAGCCAAGAAAAUAAUGAUGAAA__AAA_____________CAGAGGGUGUUGCAAAAGGGGUAAAUGA
((((((.(...((((...((((((((.(.........).))).(((......)))........................................)))))...))))..).))))))... (-22.56 = -22.60 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:59 2006