Locus 957

Sequence ID	X_DroMel_CAF1
Location	2,721,008 – 2,721,187
Length	179
Max. P	0.999986

overview

Window 4

Location	2,721,008 – 2,721,113
Length	105
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	86.59
Mean single sequence MFE	-23.78
Consensus MFE	-19.17
Energy contribution	-19.43
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.81
SVM decision value	0.53
SVM RNA-class probability	0.772208
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2721008 105 + 22224390
G-----AUGGGC-AAAAGGGGGGCGUGGCGGAUCGUAGUGCAAAUUGCGAAAGUGGAAAAU-------GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAA
.-----.((.((-(..(..(((((((.((...(((((((....)))))))..)).).....-------......((((((((......))))))))..))))).)...)..))).)). ( -23.90)
>DroSec_CAF1 109654 106 + 1
C-----AUGGGCCGAAAAGGGGGCGUGGCGGAUGGUAGUGCAAAUUGCGAAAGUGGAAAAU-------GGCAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAA
(-----(((..((......))..))))(((.((.((.(((....(..(....)..).....-------(((((.((((((((......)))))))).))))))))..)).)).))).. ( -27.80)
>DroSim_CAF1 97719 106 + 1
G-----AUGGGCCGAAAAGGGGGCGUGGCGGCUGGUAGUGCAAAUUGCGAAAGUGGAAAAU-------GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAA
.-----((.(((((....(....)....))))).)).(((((..(..(....)..)....(-------((.((.((((((((......)))))))).))..))).......))))).. ( -25.10)
>DroYak_CAF1 118686 108 + 1
GGGAAAAUGG----------GGUCGUGGCGGAUCGUAGUGCAAAUUGCAAAAGUGGAAAAUGGAAAAUGGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAA
..........----------.......(((.(((((..(((.....)))...((((..(((......(....).((((((((......)))))))))))..))))..))))).))).. ( -18.30)
>consensus
G_____AUGGGC_GAAAAGGGGGCGUGGCGGAUCGUAGUGCAAAUUGCGAAAGUGGAAAAU_______GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAA
......................(((((.((....((.(.((((.(..(....)..)..................((((((((......)))))))).)))).)))...)).))))).. (-19.17 = -19.43 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	2,721,042 – 2,721,153
Length	111
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-24.92
Consensus MFE	-24.92
Energy contribution	-24.92
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.15
Structure conservation index	1.00
SVM decision value	5.41
SVM RNA-class probability	0.999986
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2721042 111 + 22224390
CAAAUUGCGAAAGUGGAAAAU-------GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..).....-------...((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... ( -26.40)
>DroSec_CAF1 109689 111 + 1
CAAAUUGCGAAAGUGGAAAAU-------GGCAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..).....-------...((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... ( -26.40)
>DroSim_CAF1 97754 111 + 1
CAAAUUGCGAAAGUGGAAAAU-------GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..).....-------...((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... ( -26.40)
>DroEre_CAF1 124147 111 + 1
CAAAUUGCAAAAGUGGAAAAU-------GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..).....-------...((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... ( -22.70)
>DroYak_CAF1 118716 118 + 1
CAAAUUGCAAAAGUGGAAAAUGGAAAAUGGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..)...............((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... ( -22.70)
>consensus
CAAAUUGCGAAAGUGGAAAAU_______GGAAAAUGUUUAUUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUA
....(..(....)..)...............((((((((((((((((((((((((.(((((.(((.....))).)))))....)))))))......)))).))))))))))))).... (-24.92 = -24.92 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	2,721,042 – 2,721,153
Length	111
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	96.66
Mean single sequence MFE	-18.20
Consensus MFE	-18.02
Energy contribution	-18.02
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.99
SVM decision value	4.02
SVM RNA-class probability	0.999761
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2721042 111 - 22224390
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUUCC-------AUUUUCCACUUUCGCAAUUUG
....(((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..)))))))))))...-------..................... ( -17.90)
>DroSec_CAF1 109689 111 - 1
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUGCC-------AUUUUCCACUUUCGCAAUUUG
...((((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..))))))))))))..-------..................... ( -19.40)
>DroSim_CAF1 97754 111 - 1
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUUCC-------AUUUUCCACUUUCGCAAUUUG
....(((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..)))))))))))...-------..................... ( -17.90)
>DroEre_CAF1 124147 111 - 1
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUUCC-------AUUUUCCACUUUUGCAAUUUG
....(((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..)))))))))))...-------..................... ( -17.90)
>DroYak_CAF1 118716 118 - 1
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUUCCAUUUUCCAUUUUCCACUUUUGCAAUUUG
....(((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..)))))))))))............................... ( -17.90)
>consensus
UAAUAAAUGUUUAUUAAUCAUAUUUGUAAACAAAUUGCCAUUGCGCACCAUUUGUGAGCAAUUAUUUAUUUAUGCCAAUAAACAUUUUCC_______AUUUUCCACUUUCGCAAUUUG
....(((((((((((...((((...(((((..((((((.....((((.....)))).)))))).))))).))))..)))))))))))............................... (-18.02 = -18.02 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	2,721,075 – 2,721,187
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-25.70
Consensus MFE	-25.70
Energy contribution	-25.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.65
Structure conservation index	1.00
SVM decision value	3.40
SVM RNA-class probability	0.999152
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2721075 112 + 22224390
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). ( -25.70)
>DroSec_CAF1 109722 112 + 1
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). ( -25.70)
>DroSim_CAF1 97787 112 + 1
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). ( -25.70)
>DroEre_CAF1 124180 112 + 1
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). ( -25.70)
>DroYak_CAF1 118756 112 + 1
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). ( -25.70)
>consensus
UUGGCAUAAAUAAAUAAUUGCUCACAAAUGGUGCGCAAUGGCAAUUUGUUUACAAAUAUGAUUAAUAAACAUUUAUUAAGCGCUGUCUAAGCGAAGUCAAGCAAUAAUUGCA
(((((.(((((((((.(((((.(((.....))).)))))....))))))))).........(((((((....))))))).((((.....))))..)))))(((.....))). (-25.70 = -25.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:07 2006