Locus 3966

Sequence ID 2L_DroMel_CAF1
Location 11,581,859 – 11,581,953
Length 94
Max. P 0.818800
window6254 window6255

overview

Window 4

Location 11,581,859 – 11,581,953
Length 94
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 86.60
Mean single sequence MFE -40.32
Consensus MFE -34.48
Energy contribution -35.04
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.68
Structure conservation index 0.86
SVM decision value 0.67
SVM RNA-class probability 0.818800
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11581859 94 + 22407834
A-GUGA-AAAACGAGGCACGAGGACGCUGCCGAGAGAGGAGGCCGAACUCCGCUUGGUUUCCACUUGGCGGAGGCGUCUGCCUGCCUGGAAAUCCG-----------------
.-....-....(.(((((.(.(((((((.(((.(((.(((((((((.......))))))))).)))..))).))))))).).))))).).......----------------- ( -42.20)
>DroSec_CAF1 36243 94 + 1
A-GUGA-AGAACGAGGCACGAGGACGCUGCCGAGAGAGAAGGCCGAACUCCGCCUGGUUUCCACUUGGCGGAGGCGUCUGCCUGCCUGGAAAUCCG-----------------
.-....-....(.(((((.(.((((((.(((.........)))....(((((((.(((....))).))))))))))))).).))))).).......----------------- ( -40.10)
>DroSim_CAF1 38518 113 + 1
ACGUGAAAGAACGAGGCACGAGGACGCUGCCGAGAGAGAAGGCCGUAAUCGUCCUGGUUUCCACUUGGCGGAGGAGUCUGCCUGCCUGGAAAUCCGUGGAGCCCCNNNNNNNN
.(((......))).(((.(((..(((..(((.........))))))..)))((((((((((((...((((((....))))))....)))))).))).)))))).......... ( -38.60)
>DroEre_CAF1 67007 93 + 1
A-GUGA-A-AACGAGGCACGAGGACGCUGCCGAGAGAGGAGGCCGAACUCCGCCUGCUUUUCACUUGGCGGAGGCGUCCGCCUGCCUGGAAAUCCG-----------------
.-((..-.-.)).(((((.(.(((((((((((((((((.((((.(....).)))).))))...))))))...))))))).).)))))((....)).----------------- ( -43.20)
>DroYak_CAF1 37637 93 + 1
A-GUGC-A-AACGAGGCACGAGGACGCUGCCGAGAGAGGAGGCCGAACGCCGCCUGGUUUUCACUUGGCGGAGGCGUCUGCCUGCCUGGAAAUCCG-----------------
.-....-.-..(.(((((.(.(((((((.(((.(((.((((((((.........)))))))).)))..))).))))))).).))))).).......----------------- ( -37.50)
>consensus
A_GUGA_A_AACGAGGCACGAGGACGCUGCCGAGAGAGGAGGCCGAACUCCGCCUGGUUUCCACUUGGCGGAGGCGUCUGCCUGCCUGGAAAUCCG_________________
...........(.(((((.(.(((((((.(((.(((.((((((((.........)))))))).)))..))).))))))).).))))).)........................ (-34.48 = -35.04 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,581,859 – 11,581,953
Length 94
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 86.60
Mean single sequence MFE -37.58
Consensus MFE -30.66
Energy contribution -32.06
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.82
SVM decision value 0.64
SVM RNA-class probability 0.809063
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11581859 94 - 22407834
-----------------CGGAUUUCCAGGCAGGCAGACGCCUCCGCCAAGUGGAAACCAAGCGGAGUUCGGCCUCCUCUCUCGGCAGCGUCCUCGUGCCUCGUUUU-UCAC-U
-----------------.(((...(.(((((.(..(((((((((((...((....))...))))))....(((.........))).)))))..).))))).)...)-))..-. ( -35.40)
>DroSec_CAF1 36243 94 - 1
-----------------CGGAUUUCCAGGCAGGCAGACGCCUCCGCCAAGUGGAAACCAGGCGGAGUUCGGCCUUCUCUCUCGGCAGCGUCCUCGUGCCUCGUUCU-UCAC-U
-----------------.((....))(((((.(..((((((((((((..((....))..)))))))....(((.........))).)))))..).)))))......-....-. ( -38.80)
>DroSim_CAF1 38518 113 - 1
NNNNNNNNGGGGCUCCACGGAUUUCCAGGCAGGCAGACUCCUCCGCCAAGUGGAAACCAGGACGAUUACGGCCUUCUCUCUCGGCAGCGUCCUCGUGCCUCGUUCUUUCACGU
........((((((((((((....)).(((.((.((....)))))))..))))).((.((((((......(((.........)))..)))))).)))))))............ ( -38.80)
>DroEre_CAF1 67007 93 - 1
-----------------CGGAUUUCCAGGCAGGCGGACGCCUCCGCCAAGUGAAAAGCAGGCGGAGUUCGGCCUCCUCUCUCGGCAGCGUCCUCGUGCCUCGUU-U-UCAC-U
-----------------.(((...(.(((((.(.(((((((((((((..((.....)).)))))))....(((.........))).)))))).).))))).)..-)-))..-. ( -40.60)
>DroYak_CAF1 37637 93 - 1
-----------------CGGAUUUCCAGGCAGGCAGACGCCUCCGCCAAGUGAAAACCAGGCGGCGUUCGGCCUCCUCUCUCGGCAGCGUCCUCGUGCCUCGUU-U-GCAC-U
-----------------.((....))(((((.(..((((((.(((((..((....))..))))).)....(((.........))).)))))..).)))))....-.-....-. ( -34.30)
>consensus
_________________CGGAUUUCCAGGCAGGCAGACGCCUCCGCCAAGUGGAAACCAGGCGGAGUUCGGCCUCCUCUCUCGGCAGCGUCCUCGUGCCUCGUU_U_UCAC_U
..................((....))(((((.(..((((((((((((..((....))..)))))))....(((.........))).)))))..).)))))............. (-30.66 = -32.06 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:59 2006