Locus 4270

Sequence ID	3R_DroMel_CAF1
Location	11,399,239 – 11,399,589
Length	350
Max. P	0.835978

overview

Window 9

Location	11,399,239 – 11,399,338
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.32
Mean single sequence MFE	-27.18
Consensus MFE	-24.76
Energy contribution	-24.96
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.91
SVM decision value	0.73
SVM RNA-class probability	0.835978
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399239 99 - 27905053
CUUCUCAGCUGAUCAAAUCACAAC---------------------GCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAUCCGGGCAGGGAA
..((((..(((.(((((((.....---------------------((.....)).((.(((((.....((((........)))).)))))))..))))))))))((......)).)))). ( -26.50)
>DroSec_CAF1 146928 99 - 1
CUUCUCAGCUGAUCAAAUCACAAC---------------------GCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAUCCGGCCAGGGAA
..((((...((.(((((((.....---------------------((.....)).((.(((((.....((((........)))).)))))))..)))))))))(((.....))).)))). ( -26.60)
>DroSim_CAF1 138016 99 - 1
CUUCUCAGCUGAUCAAAUCACAAC---------------------GCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAUCCGGCCAGGGAA
..((((...((.(((((((.....---------------------((.....)).((.(((((.....((((........)))).)))))))..)))))))))(((.....))).)))). ( -26.60)
>DroEre_CAF1 135040 120 - 1
CUUCUCAGCUGAUCAAAUCACAACGCACAACGCACAAGGCACAACGCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAUCCGCCCAGGGAA
.......(((..(((((((............(((....((.....))....))).((.(((((.....((((........)))).)))))))..)))))))..))).(((......))). ( -29.20)
>DroYak_CAF1 137954 99 - 1
AUUCUCAGCUGAUCAAAUCACAAC---------------------GCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAGCCGCGCAGGGAA
.(((((.(((..(((((((.....---------------------((.....)).((.(((((.....((((........)))).)))))))..)))))))..))).((...)).))))) ( -27.00)
>consensus
CUUCUCAGCUGAUCAAAUCACAAC_____________________GCACAUUGCACACGCUCGCCGCCGGAAUAAAACAUUUCCAUGAGCUGACGAUUUGACAGGCAUCCGGCCAGGGAA
.......(((..(((((((..........................((.....)).((.(((((.....((((........)))).)))))))..)))))))..))).(((......))). (-24.76 = -24.96 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	11,399,338 – 11,399,436
Length	98
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	88.43
Mean single sequence MFE	-17.18
Consensus MFE	-13.43
Energy contribution	-13.68
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.78
SVM decision value	0.09
SVM RNA-class probability	0.577644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399338 98 - 27905053
CAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACAUCCACUUCCACAUCCACAUCCAGAUGCAGAGUCAAAUCCCACCCACGCACACA
...(((((((........))))))).((((..-.....((......)).((((...((((........))))..))))..............))))... ( -19.30)
>DroSec_CAF1 147027 85 - 1
CAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACA------------UCCACAUCCAGAUGCAGAGUCAAAUCCCACCCACGC-CACA
...(((((((........))))))).......-.(((....(..((------------((........))))..).)))...............-.... ( -14.90)
>DroSim_CAF1 138115 86 - 1
CAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACA------------UCCACAUCCAGAUGCAGAGUCAAAUCCCACCCACGCACACA
...(((((((........))))))).((((..-...........((------------((........))))..((......))........))))... ( -17.70)
>DroEre_CAF1 135160 99 - 1
CAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCACAGCCACAGCCACAUCCACAUCCACAUCCACAUCCAGAUCCUGAGUCAAAUCCCACCCACGCACACA
...(((((((........))))))).((((....((....))..........................(((.....))).............))))... ( -16.80)
>consensus
CAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA_AGACAGAGCCACA____________UCCACAUCCAGAUGCAGAGUCAAAUCCCACCCACGCACACA
...(((((((........))))))).((((....(.......).........................(((.....))).............))))... (-13.43 = -13.68 +   0.25)

alignment

secondary structure

dotplot

Window 1

Location	11,399,357 – 11,399,474
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.01
Mean single sequence MFE	-35.70
Consensus MFE	-28.08
Energy contribution	-29.08
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	0.05
SVM RNA-class probability	0.558557
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399357 117 - 27905053
-UGAAUGCAGGCCAUCAAUGG-GGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACAUCCACUUCCACAUCCACAUCCAGAUGCAGAGUCA
-.((.((((((((........-)))).(((.(((((.((....(((((((........))))))).(((.(.-.......).)))...)).)))))..))).........))))...)). ( -34.60)
>DroSec_CAF1 147045 106 - 1
-UGGAUGCAGGCCAUCAAUGGGGGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACA------------UCCACAUCCAGAUGCAGAGUCA
-((((((..((((.((....)))))).(((.(((..((((((.(((((((........)))))))..))...-.).)))..)))..------------))).))))))(((.....))). ( -36.60)
>DroSim_CAF1 138134 106 - 1
-UGGAUGCAGGCCAUCAAUGGGGGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA-AGACAGAGCCACA------------UCCACAUCCAGAUGCAGAGUCA
-((((((..((((.((....)))))).(((.(((..((((((.(((((((........)))))))..))...-.).)))..)))..------------))).))))))(((.....))). ( -36.60)
>DroEre_CAF1 135179 115 - 1
----AUGCAGGCCAUCAAUGG-GGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCACAGCCACAGCCACAUCCACAUCCACAUCCACAUCCAGAUCCUGAGUCA
----.......(((....)))-(((((((((((((..((....(((((((........))))))).(((.....((....))......))).........))..))))).))))).))). ( -33.50)
>DroYak_CAF1 138093 106 - 1
GUGGAUGCACGCCAUCAAUGG-GGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGAGCCA-AGACUGAGCCAC------------AUCCACAUCCAGAUCCUGAGUCA
(((((((....(((....)))-((((((...(((..((.....(((((((........)))))))))..)))-...))).))).)------------)))))).....(((.....))). ( -37.20)
>consensus
_UGGAUGCAGGCCAUCAAUGG_GGCCAGGACUGGAGCUGCCAGCUGCCAUAAUCAUUAGUGGCAGAGUGCCA_AGACAGAGCCACA___________AUCCACAUCCAGAUGCAGAGUCA
.((((((..((((.(.....).)))).(((((((.....))))(((((((........))))))).................................))).))))))(((.....))). (-28.08 = -29.08 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	11,399,474 – 11,399,589
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.05
Mean single sequence MFE	-30.07
Consensus MFE	-25.83
Energy contribution	-26.70
Covariance contribution	0.87
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.86
SVM decision value	0.05
SVM RNA-class probability	0.557043
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399474 115 - 27905053
UGAUUCGCCGGACUUGGCAUUUCCGCCCACCCACAAUCACAUUCAUCCAAGCUCAGUCAACACUCGAAACUCACUUGUUUCGCCAUCGUUUUGCGACUGCAGUUCGUGGUGCAUG-----
(((((.(..((....(((......)))..))..))))))(((.(((((.(((((((((.......(((((......)))))((.........))))))).)))).).)))).)))----- ( -27.40)
>DroSec_CAF1 147151 115 - 1
UGAUUCGCCGGACUUGGCAUUUCCGCCCACCCACAAUCACAUUCAUCCAAGCUCAGUCAACACUCGAAACUCACUUGUUUCGCCAUCGUUUUGCGACUGCAGUUCGUGGUUGAUG-----
(((((.(..((....(((......)))..))..))))))...(((.(((.((((((((.......(((((......)))))((.........))))))).)))...))).)))..----- ( -27.00)
>DroSim_CAF1 138240 115 - 1
UGAUUCACCGGACUUGGCAUUUCCGCCCACCCACAAUCACAUUCAUCCAAGCUCAGUCAACACUCGAAACUCACUUGUUUCGCCAUCGUUUUGCGACUGCAGUUCGUGGUGGAUG-----
(((((....((....(((......)))...))..)))))(((((((((.(((((((((.......(((((......)))))((.........))))))).)))).).))))))))----- ( -30.90)
>DroYak_CAF1 138199 120 - 1
UGACUCACCGGACUUGGCACUUCCGCCCACCCAAAAUCGCAUUCAUCCGAGCUCAGUAAACACUCGAAACUCACUUGUUUCGCCAUCGUUUUGCGACUGCAUCUCGUGGUGGAUGUGGAU
.........((....(((......)))...))....(((((((((((((((..((((.......((((((......))))))....((.....))))))...)))).))))))))))).. ( -35.00)
>consensus
UGAUUCACCGGACUUGGCAUUUCCGCCCACCCACAAUCACAUUCAUCCAAGCUCAGUCAACACUCGAAACUCACUUGUUUCGCCAUCGUUUUGCGACUGCAGUUCGUGGUGGAUG_____
(((((....((....(((......)))...))..)))))(((((((((.(((((((((.......(((((......)))))((.........))))))).)))).).))))))))..... (-25.83 = -26.70 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:04 2006