Locus 6604

Sequence ID	3L_DroMel_CAF1
Location	17,548,185 – 17,548,331
Length	146
Max. P	0.915612

overview

Window 8

Location	17,548,185 – 17,548,278
Length	93
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	78.82
Mean single sequence MFE	-36.87
Consensus MFE	-14.01
Energy contribution	-14.10
Covariance contribution	0.10
Combinations/Pair	1.12
Mean z-score	-2.81
Structure conservation index	0.38
SVM decision value	0.61
SVM RNA-class probability	0.800099
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17548185 93 - 23771897
CUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCACUGCAUUUGC-----------GGCUUGGUCAUCCAACCUGGUGG-----CCAAAGCCAAAUCAUGGGUU
((((((....))))))((((.((((.((((..((........))..))))-----------((((((((((((......)))))-----)).))))).)))).)))).. ( -34.80)
>DroSec_CAF1 34098 92 - 1
CUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCACUGCAGUGGC-----------GGCUUGGUCAUCCAACCUGGUGG-----CCA-AGCCAAAUCAUGGGUU
((((((....))))))((((.((((.((....))..(((((....)))))-----------((((((((((((......)))))-----)))-)))).)))).)))).. ( -41.70)
>DroSim_CAF1 36583 93 - 1
CUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCACUGCAGUUGC-----------GGCUUGGUCAUCCAACCUGGUGG-----CCAAAGCCAAAUCAUGGGUU
((((((....))))))((((.((((.(((((.((........)).)))))-----------((((((((((((......)))))-----)).))))).)))).)))).. ( -36.40)
>DroEre_CAF1 33890 97 - 1
CUGCAUACAAAUGCGGCUCGAGAUUCGCGAUCGCUGGCCACUGCAGUGGC-----------GGCUUGGUCAUCCAACCUGGUGGCCUGGCCAGAGCCAAAUCAUGG-UU
..((((....))))(((((.......((....))..(((((....)))))-----------((((.(((((((......))))))).)))).))))).........-.. ( -40.80)
>DroYak_CAF1 37041 97 - 1
CUGCAUACAAAUGCG-------AUUCGCGAUCGCUGACUAUUGCAGUGGCUUGUGGCUUGUGGCUUGGUCAUCCAACCUGGUGG-----CCAGCUCCAAAUCAUGGCUU
(((((.......(((-------(((...)))))).......))))).((((.(((..(((..(((.(((((((......)))))-----)))))..)))..))))))). ( -36.24)
>DroPer_CAF1 42172 79 - 1
CUGCAUACAAAUGCGACUGCA-----GCGAUUGCCGGCCAUCGCUGUAGU-----------CUCUUGGUCAUCCAACCUGG--------------CCAGAUCAUGGGGG
((.(((........(((((((-----(((((.(....).)))))))))))-----------)..(((((((.......)))--------------))))...))).)). ( -31.30)
>consensus
CUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCACUGCAGUGGC___________GGCUUGGUCAUCCAACCUGGUGG_____CCA_AGCCAAAUCAUGGGUU
((((((....))))))..........((....)).(((((..((..................)).)))))..(((...((((((.....)))...))).....)))... (-14.01 = -14.10 +   0.10)

alignment

secondary structure

dotplot

Window 9

Location	17,548,238 – 17,548,331
Length	93
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-29.55
Consensus MFE	-16.32
Energy contribution	-17.40
Covariance contribution	1.08
Combinations/Pair	1.07
Mean z-score	-2.47
Structure conservation index	0.55
SVM decision value	0.71
SVM RNA-class probability	0.828857
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17548238 93 + 23771897
UGGCCAGCGAUCGCGAAUCUCGAGCUGCAUUUGUAUGCAGCGCCACUCGAGCAUUCGACCAUUCAGCCAUUUGGCCAUUCAUAAUGAAAGUGA
((((((((((...(((((((((((((((((....))))))).....))))).))))).....)).))....)))))).((((.......)))) ( -32.20)
>DroPse_CAF1 37893 72 + 1
UGGCCGGCAAUCGC-----UGCAGUCGCAUUUGUAUGCAGCGCCAUGCGA--------CCG--------GCCGUCCAUUCAUAAUGAAAGUGA
.((((((...((((-----.((.((.((((....)))).))))...))))--------)))--------)))......((((.......)))) ( -25.30)
>DroSec_CAF1 34150 85 + 1
UGGCCAGCGAUCGCGAAUCUCGAGCUGCAUUUGUAUGCAGCGCCACUCGAGCAUUCGACCG--------UUUGGCCAUUCAUAAUGAAAGUGA
(((((((((....(((((((((((((((((....))))))).....))))).)))))..))--------.))))))).((((.......)))) ( -33.90)
>DroSim_CAF1 36636 85 + 1
UGGCCAGCGAUCGCGAAUCUCGAGCUGCAUUUGUAUGCAGCGCCACUCGAGCAUUCGACCG--------UUUGGCCAUUCAUAAUGAAAGUGA
(((((((((....(((((((((((((((((....))))))).....))))).)))))..))--------.))))))).((((.......)))) ( -33.90)
>DroEre_CAF1 33947 85 + 1
UGGCCAGCGAUCGCGAAUCUCGAGCCGCAUUUGUAUGCAGCGCCAUUCGAGCAUUCGGCCA--------UUUGGCCAUUCAUAAUGAAAGUGA
((((((((....))(((((((((((.((((....)))).)).....))))).)))).....--------..)))))).((((.......)))) ( -26.70)
>DroPer_CAF1 42216 72 + 1
UGGCCGGCAAUCGC-----UGCAGUCGCAUUUGUAUGCAGCGCCAUGCGA--------CCG--------GCCGUCCAUUCAUAAUGAAAGUGA
.((((((...((((-----.((.((.((((....)))).))))...))))--------)))--------)))......((((.......)))) ( -25.30)
>consensus
UGGCCAGCGAUCGCGAAUCUCGAGCCGCAUUUGUAUGCAGCGCCACUCGAGCAUUCGACCG________UUUGGCCAUUCAUAAUGAAAGUGA
((((((((....))(((((((((((.((((....)))).)).....))))).))))...............)))))).((((.......)))) (-16.32 = -17.40 +   1.08)

alignment

secondary structure

dotplot

Window 0

Location	17,548,238 – 17,548,331
Length	93
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-30.58
Consensus MFE	-17.96
Energy contribution	-19.35
Covariance contribution	1.39
Combinations/Pair	1.08
Mean z-score	-2.72
Structure conservation index	0.59
SVM decision value	1.10
SVM RNA-class probability	0.915612
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17548238 93 - 23771897
UCACUUUCAUUAUGAAUGGCCAAAUGGCUGAAUGGUCGAAUGCUCGAGUGGCGCUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCA
................((((((...((((....))))((((.(((((.....(((((((....))))))))))))))))((....)))))))) ( -32.50)
>DroPse_CAF1 37893 72 - 1
UCACUUUCAUUAUGAAUGGACGGC--------CGG--------UCGCAUGGCGCUGCAUACAAAUGCGACUGCA-----GCGAUUGCCGGCCA
.....(((((.....))))).(((--------(((--------(.......(((((((..(......)..))))-----)))...))))))). ( -26.20)
>DroSec_CAF1 34150 85 - 1
UCACUUUCAUUAUGAAUGGCCAAA--------CGGUCGAAUGCUCGAGUGGCGCUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCA
................((((((..--------((((((....(((((.....(((((((....)))))))))))).....)))))).)))))) ( -34.20)
>DroSim_CAF1 36636 85 - 1
UCACUUUCAUUAUGAAUGGCCAAA--------CGGUCGAAUGCUCGAGUGGCGCUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCA
................((((((..--------((((((....(((((.....(((((((....)))))))))))).....)))))).)))))) ( -34.20)
>DroEre_CAF1 33947 85 - 1
UCACUUUCAUUAUGAAUGGCCAAA--------UGGCCGAAUGCUCGAAUGGCGCUGCAUACAAAUGCGGCUCGAGAUUCGCGAUCGCUGGCCA
................((((((.(--------(.((.((((.(((((.....(((((((....)))))))))))))))))).))...)))))) ( -30.20)
>DroPer_CAF1 42216 72 - 1
UCACUUUCAUUAUGAAUGGACGGC--------CGG--------UCGCAUGGCGCUGCAUACAAAUGCGACUGCA-----GCGAUUGCCGGCCA
.....(((((.....))))).(((--------(((--------(.......(((((((..(......)..))))-----)))...))))))). ( -26.20)
>consensus
UCACUUUCAUUAUGAAUGGCCAAA________CGGUCGAAUGCUCGAAUGGCGCUGCAUACAAAUGCAGCUCGAGAUUCGCGAUCGCUGGCCA
................((((((...............((((.(((((.....(((((((....))))))))))))))))((....)))))))) (-17.96 = -19.35 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:29 2006