Locus 2214

Sequence ID	X_DroMel_CAF1
Location	5,975,189 – 5,975,394
Length	205
Max. P	0.893205

overview

Window 0

Location	5,975,189 – 5,975,287
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.03
Mean single sequence MFE	-35.20
Consensus MFE	-21.46
Energy contribution	-21.94
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-2.39
Structure conservation index	0.61
SVM decision value	0.60
SVM RNA-class probability	0.796950
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5975189 98 - 22224390
GAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGACUAAUUAAAAGCCUUUAUGG---CUCACAGACACUCA-------------------
(((((........(((((..(((........)))..))))).((((((.......(((....)))........((((.....))---))))))))))))).------------------- ( -33.50)
>DroPse_CAF1 5674 101 - 1
GAGUGGACUCCAGUCUGUUGUUGUGUCAUUCGGAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGGCCAAUUAAAAGCCUUUAAGUGCAUACACAGACACAGC-------------------
(((....)))..((((((.((.(((.((((..((.(((.....(((.(((((((....))))))))))......)))))..))))))))))))))).....------------------- ( -32.80)
>DroSim_CAF1 9223 98 - 1
GAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGACUAAUUAAAAGCCUUUAUGG---CUCACAGACACUCA-------------------
(((((........(((((..(((........)))..))))).((((((.......(((....)))........((((.....))---))))))))))))).------------------- ( -33.50)
>DroYak_CAF1 9274 98 - 1
GAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGACUAAUUAAAAGCCUUUAUGG---CUCACAGACACUCA-------------------
(((((........(((((..(((........)))..))))).((((((.......(((....)))........((((.....))---))))))))))))).------------------- ( -33.50)
>DroPer_CAF1 9258 120 - 1
GAGUGGACUCCAGUCUGUUGUUGUGUCAUUCGGAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGGCCAAUUAAAAGCCUUUAAGUGCAUACACAGACACAGCGUACAGACGUACAGACUGA
(((....)))((((((...((((((((........(((.....(((.(((((((....))))))))))......))).....(((....))).))))))))((((....)))))))))). ( -42.70)
>consensus
GAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAGGAUUUGUGCUCAGGUGUCCUUGGACUAAUUAAAAGCCUUUAUGG___CUCACAGACACUCA___________________
(((((........(((((..(((........)))..))))).((((((...(((((((....))).........))))...........))))))))))).................... (-21.46 = -21.94 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	5,975,247 – 5,975,361
Length	114
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-28.71
Consensus MFE	-28.32
Energy contribution	-28.10
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.99
SVM decision value	0.98
SVM RNA-class probability	0.893205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5975247 114 - 22224390
----ACAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUUGCCAGUGCCAUCUUCGAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAG
----....................((((((........((.(((..(((((..(....)..))))).))).)).....))))))........((((..(((........)))..)))) ( -27.62)
>DroSim_CAF1 9281 114 - 1
----CCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUCGAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAG
----....................((((((........((.(((..(((((..(....)..))))).))).)).....))))))........((((..(((........)))..)))) ( -29.72)
>DroYak_CAF1 9332 118 - 1
UUUUCCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCAACCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUCGAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAG
..........(((((((.....((.((((..((.....))......(((((..(....)..))))))))).)).....))))))).......((((..(((........)))..)))) ( -28.80)
>consensus
____CCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUCGAGUGGACUCCAGUCUGUUGUGCUGUCAUUUGCAUGGCAG
..........(((((((.....((.((((..((.....))......(((((..(....)..))))))))).)).....))))))).......((((..(((........)))..)))) (-28.32 = -28.10 +  -0.22)

alignment

secondary structure

dotplot

Window 2

Location	5,975,287 – 5,975,394
Length	107
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	86.88
Mean single sequence MFE	-19.03
Consensus MFE	-16.02
Energy contribution	-15.80
Covariance contribution	-0.22
Combinations/Pair	1.08
Mean z-score	-1.68
Structure conservation index	0.84
SVM decision value	0.09
SVM RNA-class probability	0.578688
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5975287 107 - 22224390
CAGGCACCCCGAGCCUCGAAU----C-CCUUC--CCGCCG----ACAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUUGCCAGUGCCAUCUUC
..(((((..((.((...(((.----.-..)))--..))))----..........................................(((((..(....)..))))).)))))...... ( -18.50)
>DroSim_CAF1 9321 107 - 1
CAGGCACCCCGAGCCCCGAGU----C-CCUUC--CCGCCG----CCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUC
..(((((...(.((..((.(.----.-....)--.))..)----))........................................(((((..(....)..))))).)))))...... ( -20.00)
>DroYak_CAF1 9372 118 - 1
CAGGCACCCUGAACCUGUUCUCUUUCCUCUUCCUCCGCCGUUUUCCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCAACCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUC
..(((((...(((....)))..................................................................(((((..(....)..))))).)))))...... ( -18.60)
>consensus
CAGGCACCCCGAGCCUCGAAU____C_CCUUC__CCGCCG____CCAUUUUCCAUUUCCAUUUGCCACUUUCACAUUUUGCCACCCGGCGACUGUCCACUUUCGCCAGUGCCAUCUUC
..(((((.............................................((........))......................(((((..(....)..))))).)))))...... (-16.02 = -15.80 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:58 2006