Locus 7963

Sequence ID	X_DroMel_CAF1
Location	19,849,455 – 19,849,596
Length	141
Max. P	0.999941

overview

Window 7

Location	19,849,455 – 19,849,567
Length	112
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	67.67
Mean single sequence MFE	-40.07
Consensus MFE	-27.61
Energy contribution	-28.23
Covariance contribution	0.62
Combinations/Pair	1.15
Mean z-score	-2.12
Structure conservation index	0.69
SVM decision value	4.71
SVM RNA-class probability	0.999941
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19849455 112 + 22224390
CAUUCCUCUAGGACUCCGGACACUGUAGACACUUGUGUAGCUCCCGAGCUGUGGAUCCGGGGAUCCGGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGAC
...(((((..(((((((((((((.....(((....)))((((....)))))))..))))))).))))))))..((((..((((((...............)))))))))).. ( -44.26)
>DroSec_CAF1 7254 107 + 1
CAUUCUUCUAGGACUCUGGACACGAAACACG-----GGAGCGCCCGAGCUAUGGAUCCUGGGAUCCAGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGAC
........((((.(((((((..(......((-----((....)))).....((((((....)))))).)..))))))).((((((...............)))))))))).. ( -42.66)
>DroSim_CAF1 3957 107 + 1
CAUUCCUCUAGGACUCCGGACACGGAACACG-----GGAGCGCCCGAGCUCUGGAGCCGGGGAUCCAGGCAUCCGGGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...(((((..(((((((((...((((.(.((-----((....)))).).))))...)))))).))).((...)))))))................................. ( -33.30)
>consensus
CAUUCCUCUAGGACUCCGGACACGGAACACG_____GGAGCGCCCGAGCUAUGGAUCCGGGGAUCCAGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGAC
...(((....)))(((((((..(..............((((......))))((((((....)))))).)..))))))).((((((...............))))))...... (-27.61 = -28.23 +   0.62)

alignment

secondary structure

dotplot

Window 8

Location	19,849,455 – 19,849,567
Length	112
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	67.67
Mean single sequence MFE	-41.33
Consensus MFE	-29.15
Energy contribution	-31.23
Covariance contribution	2.09
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.71
SVM decision value	2.85
SVM RNA-class probability	0.997379
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19849455 112 - 22224390
GUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCCGGAUCCCCGGAUCCACAGCUCGGGAGCUACACAAGUGUCUACAGUGUCCGGAGUCCUAGAGGAAUG
....((((((((..(((.....)))..))))))))((((((((....)))))(((((..(((((((....))))(((....))).....))))))))........))).... ( -47.10)
>DroSec_CAF1 7254 107 - 1
GUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCUGGAUCCCAGGAUCCAUAGCUCGGGCGCUCC-----CGUGUUUCGUGUCCAGAGUCCUAGAAGAAUG
.(((((((.((((((((.....(((.((((((...)))))).))).))))))).(((..(..(((.((((....))-----)).)))..)..))).).))))).))...... ( -46.60)
>DroSim_CAF1 3957 107 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNUCCCCGGAUGCCUGGAUCCCCGGCUCCAGAGCUCGGGCGCUCC-----CGUGUUCCGUGUCCGGAGUCCUAGAGGAAUG
....................................((((((((.((((.(....).))))((((.((((....))-----)).)))).))))))))..(((....)))... ( -30.30)
>consensus
GUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCUGGAUCCCCGGAUCCACAGCUCGGGCGCUCC_____CGUGUUCCGUGUCCGGAGUCCUAGAGGAAUG
....((((((((..(((.....)))..)))))))).(((((..(..(((((....))))).......((((((.........)))))).)..)))))..(((....)))... (-29.15 = -31.23 +   2.09)

alignment

secondary structure

dotplot

Window 9

Location	19,849,495 – 19,849,596
Length	101
Sequences	3
Columns	101
Reading direction	forward
Mean pairwise identity	52.81
Mean single sequence MFE	-30.92
Consensus MFE	-17.85
Energy contribution	-18.79
Covariance contribution	0.95
Combinations/Pair	1.05
Mean z-score	-1.27
Structure conservation index	0.58
SVM decision value	1.67
SVM RNA-class probability	0.971417
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19849495 101 + 22224390
CUCCCGAGCUGUGGAUCCGGGGAUCCGGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGACGCACGUGUCCCACGUUACAAGUUCUCCCU
.....(((((((((..((((((.((..(((.(((.((....))))).)))......))))))))..))......(((((...))))).)).)))))..... ( -38.20)
>DroSec_CAF1 7289 101 + 1
CGCCCGAGCUAUGGAUCCUGGGAUCCAGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGACGCACGUGUCCCACUUUACAGGUUCACCCC
.....(((((.((((((....))))))(((((.((((..((((((...............))))))))))((....)))))))........)))))..... ( -37.76)
>DroSim_CAF1 3992 101 + 1
CGCCCGAGCUCUGGAGCCGGGGAUCCAGGCAUCCGGGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
..((((.((.(((((.(....).)))))))...))))................................................................ ( -16.80)
>consensus
CGCCCGAGCUAUGGAUCCGGGGAUCCAGGGAUCCAGGGAGCCCGGAACCCAUAAAAGACCCCGGGCCCUGACGCACGUGUCCCAC_UUACA_GUUC_CCC_
..(((((.((.((((((....)))))).)).))..))).((((((...............))))))................................... (-17.85 = -18.79 +   0.95)

alignment

secondary structure

dotplot

Window 0

Location	19,849,495 – 19,849,596
Length	101
Sequences	3
Columns	101
Reading direction	reverse
Mean pairwise identity	52.81
Mean single sequence MFE	-35.63
Consensus MFE	-22.47
Energy contribution	-24.33
Covariance contribution	1.86
Combinations/Pair	1.05
Mean z-score	-1.29
Structure conservation index	0.63
SVM decision value	2.09
SVM RNA-class probability	0.987700
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19849495 101 - 22224390
AGGGAGAACUUGUAACGUGGGACACGUGCGUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCCGGAUCCCCGGAUCCACAGCUCGGGAG
(((((...((((..(((((...)))))....))))((((((..(((.....)))..)))))))))))...((((.(((((....))))).......)))). ( -44.60)
>DroSec_CAF1 7289 101 - 1
GGGGUGAACCUGUAAAGUGGGACACGUGCGUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCUGGAUCCCAGGAUCCAUAGCUCGGGCG
((((((..((........))..))).....(((((((((((..(((.....)))..))))))..)))))..)))((((((....))))))..((....)). ( -45.40)
>DroSim_CAF1 3992 101 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNUCCCCGGAUGCCUGGAUCCCCGGCUCCAGAGCUCGGGCG
................................................................(((((..(((((((.(....).))))).))))))).. ( -16.90)
>consensus
_GGG_GAAC_UGUAA_GUGGGACACGUGCGUCAGGGCCCGGGGUCUUUUAUGGGUUCCGGGCUCCCUGGAUCCCUGGAUCCCCGGAUCCACAGCUCGGGCG
.................................((((((((..(((.....)))..))))))))((((..(...((((((....))))))..)..)))).. (-22.47 = -24.33 +   1.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:56 2006