Locus 4497

Sequence ID	3L_DroMel_CAF1
Location	12,986,046 – 12,986,206
Length	160
Max. P	0.999974

overview

Window 1

Location	12,986,046 – 12,986,166
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-28.19
Consensus MFE	-26.62
Energy contribution	-27.26
Covariance contribution	0.64
Combinations/Pair	1.06
Mean z-score	-2.75
Structure conservation index	0.94
SVM decision value	4.88
SVM RNA-class probability	0.999958
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12986046 120 + 23771897
CCCAACUACAUUUUCAAAAAGAACAAGUUUCGCUUCUUUUUAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUA
...............(((((((((.......).))))))))...........(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))). ( -32.20)
>DroSec_CAF1 103372 120 + 1
UACUACUACAUUUUCAUAAAGAACAAGUUUCGCUUCUUUUUAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUA
..................(((((.(((.....))).)))))...........(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))). ( -30.80)
>DroSim_CAF1 113006 120 + 1
UCCAACUACAUUUUCAUAAAGAACAAGUUUCGCUUCUUUUUAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUA
..................(((((.(((.....))).)))))...........(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))). ( -30.80)
>DroEre_CAF1 109369 120 + 1
CCCUCCUACAUUUUCAAAAAGAACAAGUUUCGCUUCUUUUUAACCUUUUCCAAAGCUGGUGCCUGUUCAGACUCAUCGACGUCCUUAUCGAGGUCUGACUUUUUGCCCUUGCCCAACUUA
........((....(((((((.(((.((.((((((.................)))).)).)).)))(((((((..((((........))))))))))))))))))....))......... ( -20.43)
>DroYak_CAF1 108156 120 + 1
CCCUCCUACAUUUUCAGAAAGAACAAGUUUCGCUUCUUUUUAACUUUUUCCAAAGCUGGUGCUUGUUCAGACUCAUCGACGUCCUUGUCGAGAUCUGACUUUUUGCCCUUGCCCAACUUA
........((....(((((((.((((((.((((((.................)))).)).))))))(((((.((.((((((....))))))))))))))))))))....))......... ( -26.73)
>consensus
CCCUACUACAUUUUCAAAAAGAACAAGUUUCGCUUCUUUUUAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUA
...............(((((((((.......).))))))))...........(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))). (-26.62 = -27.26 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	12,986,046 – 12,986,166
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-33.68
Consensus MFE	-30.88
Energy contribution	-29.92
Covariance contribution	-0.96
Combinations/Pair	1.15
Mean z-score	-2.53
Structure conservation index	0.92
SVM decision value	4.11
SVM RNA-class probability	0.999800
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12986046 120 - 23771897
UAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUAAAAAGAAGCGAAACUUGUUCUUUUUGAAAAUGUAGUUGGG
.(((((((((...(........((((((((((((......))))).).)))))).)..)).))))))).........((((((((((.(((...)))))))))))))............. ( -35.30)
>DroSec_CAF1 103372 120 - 1
UAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUAAAAAGAAGCGAAACUUGUUCUUUAUGAAAAUGUAGUAGUA
...((((.(((.((((......((((((((((((......))))).).))))))....)).))((((((....))))))..((((((.(((...))))))))).......)))..)))). ( -33.20)
>DroSim_CAF1 113006 120 - 1
UAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUAAAAAGAAGCGAAACUUGUUCUUUAUGAAAAUGUAGUUGGA
..(((((((((((.((......((((((((((((......))))).).))))))....))...((((((....))))))..............)))))))..(((....))).))))... ( -32.80)
>DroEre_CAF1 109369 120 - 1
UAAGUUGGGCAAGGGCAAAAAGUCAGACCUCGAUAAGGACGUCGAUGAGUCUGAACAGGCACCAGCUUUGGAAAAGGUUAAAAAGAAGCGAAACUUGUUCUUUUUGAAAAUGUAGGAGGG
((((((..((..((((......((((((((((((......))))).).))))))....)).))((((((....))))))........))..))))))..(((((((......))))))). ( -32.70)
>DroYak_CAF1 108156 120 - 1
UAAGUUGGGCAAGGGCAAAAAGUCAGAUCUCGACAAGGACGUCGAUGAGUCUGAACAAGCACCAGCUUUGGAAAAAGUUAAAAAGAAGCGAAACUUGUUCUUUCUGAAAAUGUAGGAGGG
((((((..((..((((......((((((((((((......))))).)).)))))....)).))((((((....))))))........))..))))))..(((((((......))))))). ( -34.40)
>consensus
UAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUAAAAAGAAGCGAAACUUGUUCUUUAUGAAAAUGUAGUAGGG
......(((((((.((......((((((((((((......))))).).))))))....))...((((((....))))))..............))))))).................... (-30.88 = -29.92 +  -0.96)

alignment

secondary structure

dotplot

Window 3

Location	12,986,086 – 12,986,206
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.58
Mean single sequence MFE	-28.12
Consensus MFE	-25.82
Energy contribution	-25.90
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-2.96
Structure conservation index	0.92
SVM decision value	4.55
SVM RNA-class probability	0.999918
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12986086 120 + 23771897
UAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUAUUUUCCUCCUUAAGUUUUUUUCGUUCCUUUUUAGACAGCU
............(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))).......................(((........))).... ( -28.80)
>DroSec_CAF1 103412 120 + 1
UAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUAUUUUCCUCCUUAAGUUUUUUUCGUUCCUUUUUGGACAGCU
............(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))).......................((.((.....)))).... ( -31.20)
>DroSim_CAF1 113046 120 + 1
UAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUAUUUUCCUCCUUAAGUUUUUUUCGUUCCUUUUUGGACAGCU
............(((((((.((..(((((((((..((((((....)))))))))))))......))....))))))))).......................((.((.....)))).... ( -31.20)
>DroEre_CAF1 109409 120 + 1
UAACCUUUUCCAAAGCUGGUGCCUGUUCAGACUCAUCGACGUCCUUAUCGAGGUCUGACUUUUUGCCCUUGCCCAACUUAUUUUCCUCCUUAAGUUUUUUUCGCUCCUUUUUUGACAACU
..........(((((..((.((....(((((((..((((........)))))))))))................((((((..........))))))......)).))..)))))...... ( -21.80)
>DroYak_CAF1 108196 120 + 1
UAACUUUUUCCAAAGCUGGUGCUUGUUCAGACUCAUCGACGUCCUUGUCGAGAUCUGACUUUUUGCCCUUGCCCAACUUAUUUUCCUCCUUAAGUUUUUUUCGCUCCUUUUUGGACAACU
........(((((((..((.((....(((((.((.((((((....)))))))))))))................((((((..........))))))......)).)).)))))))..... ( -27.60)
>consensus
UAACCUUUUCCAAAGCUGGUGCCUGUUCGGACUCAUCGACGUCCUUGUCGAGGUCCGACUUUUUGCCCUUGCCCAGCUUAUUUUCCUCCUUAAGUUUUUUUCGUUCCUUUUUGGACAGCU
........((((((((.((.((....(((((((..((((((....)))))))))))))......))))..))..((((((..........)))))).............))))))..... (-25.82 = -25.90 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	12,986,086 – 12,986,206
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-32.03
Consensus MFE	-30.38
Energy contribution	-29.02
Covariance contribution	-1.36
Combinations/Pair	1.21
Mean z-score	-3.06
Structure conservation index	0.95
SVM decision value	5.11
SVM RNA-class probability	0.999974
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12986086 120 - 23771897
AGCUGUCUAAAAAGGAACGAAAAAAACUUAAGGAGGAAAAUAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUA
((((.((((((...............(((....))).......(((((((...(........((((((((((((......))))).).)))))).)..)).)))))))))))...)))). ( -33.10)
>DroSec_CAF1 103412 120 - 1
AGCUGUCCAAAAAGGAACGAAAAAAACUUAAGGAGGAAAAUAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUA
((((.((((((...............(((....))).......(((((((...(........((((((((((((......))))).).)))))).)..)).)))))))))))...)))). ( -35.40)
>DroSim_CAF1 113046 120 - 1
AGCUGUCCAAAAAGGAACGAAAAAAACUUAAGGAGGAAAAUAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUA
((((.((((((...............(((....))).......(((((((...(........((((((((((((......))))).).)))))).)..)).)))))))))))...)))). ( -35.40)
>DroEre_CAF1 109409 120 - 1
AGUUGUCAAAAAAGGAGCGAAAAAAACUUAAGGAGGAAAAUAAGUUGGGCAAGGGCAAAAAGUCAGACCUCGAUAAGGACGUCGAUGAGUCUGAACAGGCACCAGCUUUGGAAAAGGUUA
..(((((.................((((((..........)))))).)))))((((......((((((((((((......))))).).))))))....)).))((((((....)))))). ( -27.17)
>DroYak_CAF1 108196 120 - 1
AGUUGUCCAAAAAGGAGCGAAAAAAACUUAAGGAGGAAAAUAAGUUGGGCAAGGGCAAAAAGUCAGAUCUCGACAAGGACGUCGAUGAGUCUGAACAAGCACCAGCUUUGGAAAAAGUUA
..(((((((................(((((..........))))))))))))((((......((((((((((((......))))).)).)))))....)).))((((((....)))))). ( -29.09)
>consensus
AGCUGUCCAAAAAGGAACGAAAAAAACUUAAGGAGGAAAAUAAGCUGGGCAAGGGCAAAAAGUCGGACCUCGACAAGGACGUCGAUGAGUCCGAACAGGCACCAGCUUUGGAAAAGGUUA
((((.((((((...............(((....))).......(((((((...(........((((((((((((......))))).).)))))).)..)).)))))))))))...)))). (-30.38 = -29.02 +  -1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:59 2006