Locus 671

Sequence ID 2L_DroMel_CAF1
Location 1,970,630 – 1,970,730
Length 100
Max. P 0.987513
window1099 window1100

overview

Window 9

Location 1,970,630 – 1,970,730
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.75
Mean single sequence MFE -39.72
Consensus MFE -23.38
Energy contribution -25.46
Covariance contribution 2.08
Combinations/Pair 1.06
Mean z-score -2.59
Structure conservation index 0.59
SVM decision value 1.31
SVM RNA-class probability 0.941110
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1970630 100 + 22407834
AAUGCGUCUCACUCGCACUCAUUUUGGGGGUGG-----GCACUGAGUGG-----GGUGGGGUGCAAGAGCGAGCUAGACAGAAAUGGGGUGCUGGUGUGAGUGAGUGU----------GU
.(((((.((((((((((((((((.....))))(-----(((((..((.(-----..(((..(((....)))..)))..)....))..)))))))))))))))))))))----------)) ( -37.60)
>DroSec_CAF1 13077 100 + 1
AGUGCGUCUCGCUCGCACCCAUUUUGGGGGUGG-----GCACUGAGUGG-----GGUGGGGUGCAAGAGCGAGCUAGACAGAAAUGGGGUGCUGGUGUGAGUGAGUGU----------GU
.(..((.((((((((((((((((.....))))(-----(((((..((.(-----..(((..(((....)))..)))..)....))..)))))))))))))))))))).----------.) ( -39.50)
>DroSim_CAF1 17123 100 + 1
AGUGCGUCUCGCUCGCACCCAUUUUGGGGGUGG-----GCACUGAGUGG-----GGUGGGGUGCAAGAGCGAGCUAGACAGAAAUGGGGUGCUGGUGUGAGUGAGUGU----------GU
.(..((.((((((((((((((((.....))))(-----(((((..((.(-----..(((..(((....)))..)))..)....))..)))))))))))))))))))).----------.) ( -39.50)
>DroEre_CAF1 22243 112 + 1
AACGCGUCUCGCUCGCACCCAUUUCGGGGAUGGGAUAAGCACUGAGUGG-----GGUGGGGUGAAAGAGCGAGCUAGACAAAAAGGGGC---UGGUGUGAGUGAGUGUGUGUGUGUGUGC
.(((((.(((((((((.(((((..((....(((........)))..)).-----.)))))........((.((((...(.....).)))---).)))))))))))))))).......... ( -37.90)
>DroYak_CAF1 20254 109 + 1
AGCGCCUCUCGCUCGCACCCAUUUCGGGGGUGC-----GCACUGAGUGGAGUGGGGUGAGGUGAAAGAGCGAGCUAGACAGCAAGGGGCUGCUGGU----GUGAGUG--UGUGUGUGUGU
.(((((((((((((((((((.......))))))-----.((((......)))).............))))))(((((.((((.....)))))))))----..))).)--)))........ ( -44.10)
>consensus
AGUGCGUCUCGCUCGCACCCAUUUUGGGGGUGG_____GCACUGAGUGG_____GGUGGGGUGCAAGAGCGAGCUAGACAGAAAUGGGGUGCUGGUGUGAGUGAGUGU__________GU
...(((.(((((((((((((((((....((((.......)))))))))...................((((..(((........)))..)))))))))))))))))))............ (-23.38 = -25.46 +   2.08)

alignment

Postscript

secondary structure

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dotplot

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Window 0

Location 1,970,630 – 1,970,730
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.75
Mean single sequence MFE -25.23
Consensus MFE -18.50
Energy contribution -18.58
Covariance contribution 0.08
Combinations/Pair 1.12
Mean z-score -2.67
Structure conservation index 0.73
SVM decision value 2.08
SVM RNA-class probability 0.987513
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1970630 100 - 22407834
AC----------ACACUCACUCACACCAGCACCCCAUUUCUGUCUAGCUCGCUCUUGCACCCCACC-----CCACUCAGUGC-----CCACCCCCAAAAUGAGUGCGAGUGAGACGCAUU
..----------...(((((((............................((....))........-----.((((((.((.-----.......))...)))))).)))))))....... ( -21.00)
>DroSec_CAF1 13077 100 - 1
AC----------ACACUCACUCACACCAGCACCCCAUUUCUGUCUAGCUCGCUCUUGCACCCCACC-----CCACUCAGUGC-----CCACCCCCAAAAUGGGUGCGAGCGAGACGCACU
..----------.............................((((.((((((....((((......-----.......))))-----..((((.......)))))))))).))))..... ( -24.52)
>DroSim_CAF1 17123 100 - 1
AC----------ACACUCACUCACACCAGCACCCCAUUUCUGUCUAGCUCGCUCUUGCACCCCACC-----CCACUCAGUGC-----CCACCCCCAAAAUGGGUGCGAGCGAGACGCACU
..----------.............................((((.((((((....((((......-----.......))))-----..((((.......)))))))))).))))..... ( -24.52)
>DroEre_CAF1 22243 112 - 1
GCACACACACACACACUCACUCACACCA---GCCCCUUUUUGUCUAGCUCGCUCUUUCACCCCACC-----CCACUCAGUGCUUAUCCCAUCCCCGAAAUGGGUGCGAGCGAGACGCGUU
((.................((......)---).........((((.((((((..........(((.-----.......))).....(((((.......))))).)))))).))))))... ( -23.00)
>DroYak_CAF1 20254 109 - 1
ACACACACACA--CACUCAC----ACCAGCAGCCCCUUGCUGUCUAGCUCGCUCUUUCACCUCACCCCACUCCACUCAGUGC-----GCACCCCCGAAAUGGGUGCGAGCGAGAGGCGCU
...........--......(----.((.(((((.....)))))....(((((((.............((((......)))).-----((((((.......))))))))))))).)).).. ( -33.10)
>consensus
AC__________ACACUCACUCACACCAGCACCCCAUUUCUGUCUAGCUCGCUCUUGCACCCCACC_____CCACUCAGUGC_____CCACCCCCAAAAUGGGUGCGAGCGAGACGCACU
.........................................((((.((((((..........................(((.......))).(((.....))).)))))).))))..... (-18.50 = -18.58 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:32 2006