Locus 1705

Sequence ID	3R_DroMel_CAF1
Location	4,896,639 – 4,896,774
Length	135
Max. P	0.966492

overview

Window 7

Location	4,896,639 – 4,896,734
Length	95
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	82.47
Mean single sequence MFE	-33.70
Consensus MFE	-26.93
Energy contribution	-27.02
Covariance contribution	0.09
Combinations/Pair	1.24
Mean z-score	-1.85
Structure conservation index	0.80
SVM decision value	0.58
SVM RNA-class probability	0.787740
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4896639 95 + 27905053
ACUGCCUGG----CUUAAU-----UUGUUAUUUCCUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAGCUGCUGUUGACAGCGCCUGACA
.(((...((----..(((.-----...)))...))....)))..(((((....)))))(((((((((((....))))))..((.((((....))))))))))). ( -31.80)
>DroPse_CAF1 32108 101 + 1
ACUACAUCGACCGUAUGAUUUCUUCUCUAAUUGUCUUUAUAGGACGCCGUUGGCGGCUGUGGGUGGUCCAAUGGGACCAAGGCCACUGUUGACGGCA---GCCA
........(((.((..((.....))....)).)))......((..(((((..(((...((((.((((((....))))))...)))))))..))))).---.)). ( -34.80)
>DroSec_CAF1 4669 95 + 1
ACUGCCUGG----CUUAAU-----UUGUUAUUUCAUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAUCCGCUGUUGACAGCGCCUGACA
........(----((....-----.((......)).....))).(((((....)))))(((((((((((....))))))....(((((....))))).))))). ( -32.80)
>DroSim_CAF1 4601 95 + 1
ACUGCCUGG----CUUAAU-----UUGUUAUUUCCUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAGCCGCUGUUGACAGCGCCUGACA
.(((...((----..(((.-----...)))...))....)))..(((((....)))))(((((((((((....))))))....(((((....))))).))))). ( -31.90)
>DroEre_CAF1 4215 94 + 1
ACUGCCUGG----CUUA------AUGGUUAUUUCAUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAGCCGCUGUUGACAGCGCCUGACA
..(((.((.----...(------((((.....)))))..)))))(((((....)))))(((((((((((....))))))....(((((....))))).))))). ( -35.80)
>DroYak_CAF1 4710 99 + 1
ACUGCCUGG----CUUAUU-UCCAUUACUAUUUGCUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAGCCGCUGUUGACAGCGCCUGACA
...((..((----(((...-.((.........((((....))))(((((....)))))...))((((((....)))))))))))((((....))))))...... ( -35.10)
>consensus
ACUGCCUGG____CUUAAU_____UUGUUAUUUCCUUUACAGCACAACGUUGCCGUUGGUCGGGGGUCCAAUGGGACCCAAGCCGCUGUUGACAGCGCCUGACA
............................................(((((....)))))(((((((((((....))))))....(((((....))))).))))). (-26.93 = -27.02 +   0.09)

alignment

secondary structure

dotplot

Window 8

Location	4,896,639 – 4,896,734
Length	95
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	82.47
Mean single sequence MFE	-36.10
Consensus MFE	-26.17
Energy contribution	-26.31
Covariance contribution	0.14
Combinations/Pair	1.23
Mean z-score	-2.93
Structure conservation index	0.72
SVM decision value	1.01
SVM RNA-class probability	0.900696
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4896639 95 - 27905053
UGUCAGGCGCUGUCAACAGCAGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGGAAAUAACAA-----AUUAAG----CCAGGCAGU
((((.(((((((....))))(((..((((((....)))))).....(((((....))))).)))................-----.....)----)).)))).. ( -36.10)
>DroPse_CAF1 32108 101 - 1
UGGC---UGCCGUCAACAGUGGCCUUGGUCCCAUUGGACCACCCACAGCCGCCAACGGCGUCCUAUAAAGACAAUUAGAGAAGAAAUCAUACGGUCGAUGUAGU
.(((---.(((((.....(((((..((((((....))))))......)))))..))))))))(((((..(((.....((.......)).....)))..))))). ( -30.90)
>DroSec_CAF1 4669 95 - 1
UGUCAGGCGCUGUCAACAGCGGAUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAUGAAAUAACAA-----AUUAAG----CCAGGCAGU
((((.(((((((....))))((...((((((....))))))))(..(((((....)))))..).................-----.....)----)).)))).. ( -35.10)
>DroSim_CAF1 4601 95 - 1
UGUCAGGCGCUGUCAACAGCGGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGGAAAUAACAA-----AUUAAG----CCAGGCAGU
((((....((((....))))(((((((((((....))))))((.(((((((....)))))....))...)).........-----...)))----)).)))).. ( -36.60)
>DroEre_CAF1 4215 94 - 1
UGUCAGGCGCUGUCAACAGCGGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAUGAAAUAACCAU------UAAG----CCAGGCAGU
((((.(((.......(((((((...((((((....))))))))...(((((....))))).))))).((((.......)))------)..)----)).)))).. ( -36.50)
>DroYak_CAF1 4710 99 - 1
UGUCAGGCGCUGUCAACAGCGGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGCAAAUAGUAAUGGA-AAUAAG----CCAGGCAGU
((((....((((....))))(((((((((((....))))))(((..(((((....)))))((((....))))........))).-...)))----)).)))).. ( -41.40)
>consensus
UGUCAGGCGCUGUCAACAGCGGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGGAAAUAACAA_____AUUAAG____CCAGGCAGU
.(((((.(((((....))))).)).((((((....))))))..)))(((((....))))).(((((.................................))))) (-26.17 = -26.31 +   0.14)

alignment

secondary structure

dotplot

Window 9

Location	4,896,657 – 4,896,774
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.03
Mean single sequence MFE	-43.73
Consensus MFE	-21.18
Energy contribution	-21.85
Covariance contribution	0.67
Combinations/Pair	1.52
Mean z-score	-2.28
Structure conservation index	0.48
SVM decision value	1.60
SVM RNA-class probability	0.966492
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4896657 117 - 27905053
CCCUCCUCCCCGGACGCCUCCGAGUCCUCGUCCUCGGUGGUGUCAGGCGCUGUCAACAGCAGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGGAAAUAA
...((((..((.((((((.(((((........))))).)))))).))........((((((....((((((....)))))).....(((((....)))))))))))..))))..... ( -51.40)
>DroPse_CAF1 32135 114 - 1
CCAACAUCGCCAGCUGUGUCCGAGUCGUCAUCGCCGGUGGUGGC---UGCCGUCAACAGUGGCCUUGGUCCCAUUGGACCACCCACAGCCGCCAACGGCGUCCUAUAAAGACAAUUA
...((((.(....).))))....(((.....(((((.(((((((---((..((((....))))..((((((....))))))....))))))))).))))).........)))..... ( -42.24)
>DroWil_CAF1 5805 114 - 1
CCCACAUCCCCAGCCCUUUCCGAAUCAUCCUCAUCUGUGGUGACG---GCCAUCAAUGCUGGCCUAGGUCCAAUUGGACCACCCACAACAGCCAAUGGAGUGCUGUAAAUACAACAA
..........((((...((((((.......))..((((.(((..(---((((.......)))))..(((((....)))))...))).)))).....)))).))))............ ( -32.40)
>DroYak_CAF1 4732 117 - 1
CCCUCCUCCCCGGACGCCUCCGAGUCCUCGUCGUCGGUGGUGUCAGGCGCUGUCAACAGCGGCUUGGGUCCCAUUGGACCCCCGACCAACGGCAACGUUGUGCUGUAAAGCAAAUAG
..........((((((((.(((((.......).)))).))))))((.(((((....))))).)).((((((....)))))).))..(((((....)))))((((....))))..... ( -48.80)
>DroAna_CAF1 23 114 - 1
CCCUCCUCCCCAUCCGCCUCGGAGUCCUCAUCCUCGGUGGUUUCGGCAGCGGUGAACAGUGGCUUGGGUCCCAUCGGGCCGCCCACCACCGCCAAUGGGGUGCUGUAAG---AAUAU
.....(.(((((((((((..(((.......)))..)))))....(((.(.((((....(((((((((......))))))))).)))).).))).)))))).).......---..... ( -44.70)
>DroPer_CAF1 38783 114 - 1
CCAACAUCGCCAGCUGUGUCCGAGUCGUCAUCGCCGGUGGUGGC---UGCCGUCAACAGUGGCCUUGGUCCCAUUGGACCACCCACAGCCGCCAACGGCGUCCUAUAAAGACAAGUA
............(((.((((...........(((((.(((((((---((..((((....))))..((((((....))))))....))))))))).))))).........))))))). ( -42.85)
>consensus
CCCACAUCCCCAGCCGCCUCCGAGUCCUCAUCGUCGGUGGUGUC___CGCCGUCAACAGUGGCCUGGGUCCCAUUGGACCACCCACAACCGCCAACGGCGUGCUGUAAAGACAAUAA
...............................(((((.((((((.....((((.......))))..((((((....)))))).......)))))).)))))................. (-21.18 = -21.85 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:20 2006