Locus 7394

Sequence ID	X_DroMel_CAF1
Location	18,428,507 – 18,428,628
Length	121
Max. P	0.992075

overview

Window 9

Location	18,428,507 – 18,428,598
Length	91
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	90.49
Mean single sequence MFE	-40.96
Consensus MFE	-36.52
Energy contribution	-36.60
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.89
SVM decision value	2.07
SVM RNA-class probability	0.987285
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18428507 91 + 22224390
-CAGCAUAUGGCGGGGAUCGCAGCCUCCUUGAGGCGCGCAGCUCCAAGGACUCCCGCUGGGAGUCACUUGC------------UCGGCGAGGAAGGAACUGCAA
-..((.....(((.....))).(((((...)))))))((((.(((...(((((((...))))))).(((((------------...)))))...))).)))).. ( -40.70)
>DroSec_CAF1 51357 91 + 1
-CAGCAUAUGGCGGGGAUCGCAGCCUCCUUGAGGCGCGCAGCUCCAAGGACUCCCGCUGGGAGUCACUUGC------------UCGGCGAGGAAGGAACUGCAA
-..((.....(((.....))).(((((...)))))))((((.(((...(((((((...))))))).(((((------------...)))))...))).)))).. ( -40.70)
>DroSim_CAF1 51615 92 + 1
ACAGCAUAUGGCGGGGAUCGCAGCCUCCUUGAGGCGCGCAGCUCCAAGGACUCCCGCUGGGAGUCACUUGC------------UCGGCGAGGAAGGAACUGCAA
...((.....(((.....))).(((((...)))))))((((.(((...(((((((...))))))).(((((------------...)))))...))).)))).. ( -40.70)
>DroEre_CAF1 54131 92 + 1
ACAGCAUAUGGCGGGGAUCGCAGCCUCCUGGAGACGCACAGCUCCAAGGACUCCCGCUGGGAGUCACUUGC------------GCGGCGAGGAAGGAACUGCAA
...((.....)).......(((((((((((....)((...((..(((((((((((...))))))).)))).------------)).)).))).)))..)))).. ( -35.80)
>DroYak_CAF1 33385 104 + 1
ACAGCAUAUGGCGGGUAUCGCAGCCUCCUUGAGGCGCGCAGCUCCAAGGACUCCCGCUGGGAGUCACUUGCUCUCGGAGCGAGGCAGUGGGGCAGGAACUGCAA
..........((((....(((.(((((...))))))))..((((((..(((((((...))))))).(((((((...)))))))....)))))).....)))).. ( -46.90)
>consensus
ACAGCAUAUGGCGGGGAUCGCAGCCUCCUUGAGGCGCGCAGCUCCAAGGACUCCCGCUGGGAGUCACUUGC____________UCGGCGAGGAAGGAACUGCAA
...((.....(((.....))).(((((...)))))))((((.(((...(((((((...))))))).(((((...............)))))...))).)))).. (-36.52 = -36.60 +   0.08)

alignment

secondary structure

dotplot

Window 0

Location	18,428,507 – 18,428,598
Length	91
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	90.49
Mean single sequence MFE	-39.50
Consensus MFE	-36.62
Energy contribution	-36.50
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.83
Structure conservation index	0.93
SVM decision value	2.31
SVM RNA-class probability	0.992075
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18428507 91 - 22224390
UUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCAAGGAGGCUGCGAUCCCCGCCAUAUGCUG-
..((((((((......((...------------))(((.(((((((...))))))))))))))))))(((((((...))))).(((.....))).....))..- ( -38.90)
>DroSec_CAF1 51357 91 - 1
UUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCAAGGAGGCUGCGAUCCCCGCCAUAUGCUG-
..((((((((......((...------------))(((.(((((((...))))))))))))))))))(((((((...))))).(((.....))).....))..- ( -38.90)
>DroSim_CAF1 51615 92 - 1
UUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCAAGGAGGCUGCGAUCCCCGCCAUAUGCUGU
..((((((((......((...------------))(((.(((((((...))))))))))))))))))(((((((...))))).(((.....))).....))... ( -38.90)
>DroEre_CAF1 54131 92 - 1
UUGCAGUUCCUUCCUCGCCGC------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGUGCGUCUCCAGGAGGCUGCGAUCCCCGCCAUAUGCUGU
(((((((((((....((((((------------.((((.(((((((...)))))))))))..)).).))).....)))).))))))).....((.....))... ( -35.80)
>DroYak_CAF1 33385 104 - 1
UUGCAGUUCCUGCCCCACUGCCUCGCUCCGAGAGCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCAAGGAGGCUGCGAUACCCGCCAUAUGCUGU
..((((((((.........((((((...)))).))(((.(((((((...))))))))))))))))))(((((((...))))).(((.....))).....))... ( -45.00)
>consensus
UUGCAGUUCCUUCCUCGCCGA____________GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCAAGGAGGCUGCGAUCCCCGCCAUAUGCUGU
..((((((((......((...............))(((.(((((((...))))))))))))))))))(((((((...))))).(((.....))).....))... (-36.62 = -36.50 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	18,428,535 – 18,428,628
Length	93
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	83.64
Mean single sequence MFE	-32.68
Consensus MFE	-21.81
Energy contribution	-23.03
Covariance contribution	1.22
Combinations/Pair	1.04
Mean z-score	-2.38
Structure conservation index	0.67
SVM decision value	0.20
SVM RNA-class probability	0.630767
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18428535 93 - 22224390
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCA
.(((((......)))))...((((.......(((((((((......((...------------))(((.(((((((...)))))))))))))))))))..)))). ( -34.20)
>DroSec_CAF1 51385 93 - 1
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCA
.(((((......)))))...((((.......(((((((((......((...------------))(((.(((((((...)))))))))))))))))))..)))). ( -34.20)
>DroSim_CAF1 51644 93 - 1
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUCCUCGCCGA------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCA
.(((((......)))))...((((.......(((((((((......((...------------))(((.(((((((...)))))))))))))))))))..)))). ( -34.20)
>DroEre_CAF1 54160 93 - 1
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUCCUCGCCGC------------GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGUGCGUCUCC
.(((((......)))))...(((((.......((((((((.........((------------....))(((((((...)))))))...))))))))...))))) ( -33.00)
>DroYak_CAF1 33414 105 - 1
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUGCCCCACUGCCUCGCUCCGAGAGCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCA
.(((((......)))))...((((.......(((((((((.........((((((...)))).))(((.(((((((...)))))))))))))))))))..)))). ( -40.30)
>DroPer_CAF1 28839 71 - 1
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUUC-----GA------------GCUAG-----CCCAGCGGGAGACCCAAG------------CA
.(((((......)))))((((((((.....))..(((((.....-----))------------)))..-----))))))((....))....------------.. ( -20.20)
>consensus
AUUAGAUUUCAUUCUAAGCUGGGGAAUUAAUUGCAGUUCCUUCCUCGCCGA____________GCAAGUGACUCCCAGCGGGAGUCCUUGGAGCUGCGCGCCUCA
.(((((......)))))(((.(((((((......))))))).......................((((.(((((((...))))))))))).)))........... (-21.81 = -23.03 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:49 2006