Locus 2425

Sequence ID	X_DroMel_CAF1
Location	6,497,921 – 6,498,052
Length	131
Max. P	0.999975

overview

Window 2

Location	6,497,921 – 6,498,022
Length	101
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	92.98
Mean single sequence MFE	-25.58
Consensus MFE	-23.64
Energy contribution	-24.88
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-3.09
Structure conservation index	0.92
SVM decision value	5.08
SVM RNA-class probability	0.999972
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6497921 101 + 22224390
GUGGUGUAAACUUAAUUAUAGAAAAUUAAGCAAUUGCCCGAUUUGCAUGCCAAAAGGUUGAUAAGAAAUCGAGCAAAA--AACAAGAUGA-AGUGCACCACGGG
((((((((..(((((((......)))))))...((((.((((((.((.(((....))))).....)))))).))))..--..........-..))))))))... ( -27.60)
>DroSec_CAF1 51815 101 + 1
GUGGUGUAAAUUUAAUUAUAGAAAAUUAAGCAAUUGCCCGAUUCGCAUGCCAAAAGGUUGAUAACAAAUCGAGCAAAA--AACAGGAUGA-AGUGCACCACGGG
((((((((..(((((((......)))))))...((((.(((((.....(((....)))........))))).))))..--..........-..))))))))... ( -24.32)
>DroSim_CAF1 51255 101 + 1
GUGGUGUAAAUUUAAUUAUAGAAAAUUAAGCAAUUGCCCGAUUUGCAUGCCAAAAGGUUGAUAACAAAUCGAGCAAAA--AACAGGAUGA-AGUGCACCACGGG
((((((((..(((((((......)))))))...((((.(((((((...(((....)))......))))))).))))..--..........-..))))))))... ( -28.40)
>DroEre_CAF1 51537 104 + 1
GUGGUGUAAUUAUAAUUAUAGAGAAUUAAGCAAUUGCCCGAUUUGCAUGCCAAAAGGUUGAUAACAAAUCGAGCAAAAAAAAAAGAAUGAUAGUUCACCACGGG
((((((.((((((((((......))))).....((((.(((((((...(((....)))......))))))).))))..............)))))))))))... ( -26.50)
>DroYak_CAF1 51619 102 + 1
GUGGUGUAAUUAUAAUUAUAGAGAAUUAAGCAAUUGCCCGAUUUGCAUGCCAAAAGGUUGAUAAGAAAUCGAACAAAA--GAAAGGAUGAUAGUGCACCACGGG
((((((((.((((.(((............((....)).((((((.((.(((....))))).....)))))).......--.....))).))))))))))))... ( -21.10)
>consensus
GUGGUGUAAAUUUAAUUAUAGAAAAUUAAGCAAUUGCCCGAUUUGCAUGCCAAAAGGUUGAUAACAAAUCGAGCAAAA__AACAGGAUGA_AGUGCACCACGGG
((((((((..(((((((......)))))))...((((.(((((((...(((....)))......))))))).)))).................))))))))... (-23.64 = -24.88 +   1.24)

alignment

secondary structure

dotplot

Window 3

Location	6,497,921 – 6,498,022
Length	101
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-26.22
Consensus MFE	-24.56
Energy contribution	-24.64
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-4.39
Structure conservation index	0.94
SVM decision value	5.13
SVM RNA-class probability	0.999975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6497921 101 - 22224390
CCCGUGGUGCACU-UCAUCUUGUU--UUUUGCUCGAUUUCUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAAUUUUCUAUAAUUAAGUUUACACCAC
...((((((....-..........--..((((((((((((.(..(((....)))..).).)))))))))))..((((((((......))))))))...)))))) ( -27.10)
>DroSec_CAF1 51815 101 - 1
CCCGUGGUGCACU-UCAUCCUGUU--UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCGAAUCGGGCAAUUGCUUAAUUUUCUAUAAUUAAAUUUACACCAC
...((((((....-.......((.--..(((((((((((((..((((....))))...)))))))))))))..))((((((......)))))).....)))))) ( -28.90)
>DroSim_CAF1 51255 101 - 1
CCCGUGGUGCACU-UCAUCCUGUU--UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAAUUUUCUAUAAUUAAAUUUACACCAC
...((((((....-.......((.--..(((((((((((((..((((....))))...)))))))))))))..))((((((......)))))).....)))))) ( -29.20)
>DroEre_CAF1 51537 104 - 1
CCCGUGGUGAACUAUCAUUCUUUUUUUUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAAUUCUCUAUAAUUAUAAUUACACCAC
...((((((...................(((((((((((((..((((....))))...))))))))))))).....(((((......)))))......)))))) ( -27.00)
>DroYak_CAF1 51619 102 - 1
CCCGUGGUGCACUAUCAUCCUUUC--UUUUGUUCGAUUUCUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAAUUCUCUAUAAUUAUAAUUACACCAC
...((((((..............(--..((((((((((((.(..(((....)))..).).)))))))))))..)..(((((......)))))......)))))) ( -18.90)
>consensus
CCCGUGGUGCACU_UCAUCCUGUU__UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAAUUUUCUAUAAUUAAAUUUACACCAC
...((((((...................(((((((((((((..((((....))))...))))))))))))).....(((((......)))))......)))))) (-24.56 = -24.64 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	6,497,946 – 6,498,052
Length	106
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	93.07
Mean single sequence MFE	-31.26
Consensus MFE	-28.00
Energy contribution	-28.52
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-1.35
Structure conservation index	0.90
SVM decision value	0.75
SVM RNA-class probability	0.841962
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6497946 106 - 22224390
GC-----GAUGCUCAUCAUGGCCAGCGCUCGAGAACCCGUGGUGCACU-UCAUCUUGUU--UUUUGCUCGAUUUCUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAA
((-----((((..((((((((....(......)...))))))))....-.)))).....--..((((((((((((.(..(((....)))..).).)))))))))))..)).... ( -27.20)
>DroSec_CAF1 51840 111 - 1
GCGAUGCGAUGCUCAUCAUGGCCAGCGCUCGAGAACCCGUGGUGCACU-UCAUCCUGUU--UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCGAAUCGGGCAAUUGCUUAA
(((((..((((..((((((((....(......)...))))))))....-.)))).....--...((((((((((((..((((....))))...))))))))))))))))).... ( -33.40)
>DroSim_CAF1 51280 111 - 1
GCGAUGCGAUGCUCAUCAUGGCCAGCGCUCGAAAACCCGUGGUGCACU-UCAUCCUGUU--UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAA
(((((..((((..((((((((....(....).....))))))))....-.)))).....--...((((((((((((..((((....))))...))))))))))))))))).... ( -33.10)
>DroEre_CAF1 51562 114 - 1
GCGAUGCGAUGCUCAUCAUGGCCAGCGCUCGAGAACCCGUGGUGAACUAUCAUUCUUUUUUUUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAA
(((((..((((.(((((((((....(......)...)))))))))..)))).............((((((((((((..((((....))))...))))))))))))))))).... ( -35.90)
>DroYak_CAF1 51644 112 - 1
GCGAUGCGAUGCUCAUCAUGGCCAGCGCUUGAGAACCCGUGGUGCACUAUCAUCCUUUC--UUUUGUUCGAUUUCUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAA
(((((..((((..((((((((....(......)...))))))))...))))........--...(((((((((((.(..(((....)))..).).))))))))))))))).... ( -26.70)
>consensus
GCGAUGCGAUGCUCAUCAUGGCCAGCGCUCGAGAACCCGUGGUGCACU_UCAUCCUGUU__UUUUGCUCGAUUUGUUAUCAACCUUUUGGCAUGCAAAUCGGGCAAUUGCUUAA
(((((..((((..((((((((....(....).....))))))))......))))..........((((((((((((..((((....))))...))))))))))))))))).... (-28.00 = -28.52 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:10 2006