Locus 4126

Sequence ID X_DroMel_CAF1
Location 10,854,894 – 10,855,021
Length 127
Max. P 0.842960
window6778 window6779

overview

Window 8

Location 10,854,894 – 10,854,986
Length 92
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 72.08
Mean single sequence MFE -17.09
Consensus MFE -2.39
Energy contribution -2.83
Covariance contribution 0.45
Combinations/Pair 1.38
Mean z-score -2.88
Structure conservation index 0.14
SVM decision value 0.43
SVM RNA-class probability 0.735026
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10854894 92 - 22224390
AC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCCGG----GCCCAA----------AAAUAUUUGUAAUAAAUU
((-----((....)))-).(((((----((...(((...(((((((....)))))--)).....-..(((....)))...)----))....----------...)))))))........ ( -21.40)
>DroSec_CAF1 8757 92 - 1
AC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAACAGUAUG--CUUUAAA-AACCAUAUUUGGCCGG----GUCCAA----------AAAUAUUUGUAAUAAAUU
((-----((....)))-).(((((----((((((((((.((((.((....)).))--)).....-........)))))..)----))....----------...)))))))........ ( -14.65)
>DroSim_CAF1 8868 92 - 1
AC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCCGG----GCCCAA----------AAAUAUUUGUAAUAAAUU
((-----((....)))-).(((((----((...(((...(((((((....)))))--)).....-..(((....)))...)----))....----------...)))))))........ ( -21.40)
>DroYak_CAF1 8904 92 - 1
AC-----AGCCAACUG-UAACAAA----UAACGCACAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCCUG----GCCCAA----------AAAUAUUUGCAAUAAAUU
((-----((....)))-)..((((----((.........(((((((....)))))--)).....-.......(((((....----..))))----------)..))))))......... ( -18.30)
>DroAna_CAF1 3752 107 - 1
AC-----ACCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUAUG--CUUUAAAAAAGCAUAUUUGCCAGGAAGAGGCAAAAAAACGAGCCAAAUAUUAGCCAUAAAAU
..-----......(((-.......----.....((.....))......(((((((--(((.....))))))))))..))).....(((..........))).................. ( -15.70)
>DroPer_CAF1 27622 94 - 1
AUCCCAUAGGCCCCCGUUAAAAAACACUUGGCCGUUUAAUGCAUACAUAAGAAAGACUCUUAGA-AACCAAAAUUA--------------A----------UACAAGUUCUACUACACU
........((((...(((....)))....))))(((((((.......(((((.....)))))..-.......))))--------------)----------.))............... ( -11.09)
>consensus
AC_____AGCCAACUG_UAACAAA____UAACCGCCAACAGCACACAAAAGUAUG__CUUUAAA_AACCAUAUUUGGCCGG____GCCCAA__________AAAUAUUUGUAAUAAAUU
.........................................(((((....)))))....................(((.......)))............................... ( -2.39 =  -2.83 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,854,920 – 10,855,021
Length 101
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 74.74
Mean single sequence MFE -21.21
Consensus MFE -3.38
Energy contribution -4.85
Covariance contribution 1.47
Combinations/Pair 1.15
Mean z-score -3.37
Structure conservation index 0.16
SVM decision value 0.76
SVM RNA-class probability 0.842960
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10854920 101 - 22224390
CACUAA-AAAGCCAGGCGGCCCA----GGCCAAUCAAAGAAC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCC
......-...((((((((((...----.))).........((-----((....)))-)......----.....)))...(((((((....)))))--)).....-.........)))). ( -30.00)
>DroSec_CAF1 8783 98 - 1
CACUGA-AAAGCCAGG---CCCA----GGCCAAUCAAAGAAC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAACAGUAUG--CUUUAAA-AACCAUAUUUGGCC
......-...((((((---(...----.))).........((-----((....)))-)......----...........((((.((....)).))--)).....-.........)))). ( -17.50)
>DroSim_CAF1 8894 98 - 1
CACUGA-AAAGCCAGG---CCCA----GGCCAAUCAAAGUAC-----AGCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCC
..((..-..))...((---((..----(((.........(((-----((....)))-)).....----.....)))...(((((((....)))))--)).....-..........)))) ( -25.11)
>DroYak_CAF1 8930 99 - 1
CACUGAAAAAGCCAGG---CCCA----GGCCAAUCAAAGUAC-----AGCCAACUG-UAACAAA----UAACGCACAACAGCACACAAAAGUGUG--CUUUAAA-AACCAUAUUUGGCC
..........((((((---(...----.)))........(((-----((....)))-)).....----...........(((((((....)))))--)).....-.........)))). ( -24.80)
>DroAna_CAF1 3792 92 - 1
---UUA-AA----UGG---CCCA----AGCCAAUCAAAAAAC-----ACCCAACUG-UAACAAA----UAACCGCCAACAGCACACAAAAGUAUG--CUUUAAAAAAGCAUAUUUGCCA
---...-..----(((---(...----.))))..........-----......(((-(......----.........)))).......(((((((--(((.....)))))))))).... ( -14.66)
>DroPer_CAF1 27641 104 - 1
---UUA-AG----AGG---CCCAGACAGUCCAUUCAUUGAAUCCCAUAGGCCCCCGUUAAAAAACACUUGGCCGUUUAAUGCAUACAUAAGAAAGACUCUUAGA-AACCAAAAUUA---
---(((-((----((.---............((.((((((((......((((...(((....)))....)))))))))))).))............))))))).-...........--- ( -15.21)
>consensus
CACUGA_AAAGCCAGG___CCCA____GGCCAAUCAAAGAAC_____AGCCAACUG_UAACAAA____UAACCGCCAACAGCACACAAAAGUAUG__CUUUAAA_AACCAUAUUUGGCC
..........(((((............(((..................)))..............................(((((....)))))..................))))). ( -3.38 =  -4.85 +   1.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:58 2006