Locus 4462

Sequence ID	2L_DroMel_CAF1
Location	12,807,033 – 12,807,192
Length	159
Max. P	0.894211

overview

Window 8

Location	12,807,033 – 12,807,153
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.17
Mean single sequence MFE	-21.14
Consensus MFE	-17.72
Energy contribution	-17.96
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.79
Structure conservation index	0.84
SVM decision value	0.98
SVM RNA-class probability	0.894211
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807033 120 - 22407834
CUCCACAAAAUCCCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAGCCAUAAAAAGGCAAAGUGAGAACUGAAUGAAAUCCCCGCUUGUCAUUAUCAAAGAGCAUAUAACAGACGAGAUA
.........(((.((.(.(((((((..((.........((((...(((.......)))...))))))..))))))).......((((............))))........).)).))). ( -20.10)
>DroSec_CAF1 72723 120 - 1
CUCCACAAAAUCCCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAACCAUGAAAAGGCAAAGUCAGAACUGAAUGAAAUCCCCGCUUGUCAUUAUCAAAGAGCAUAUAACAGGCGAGAUA
.........(((.((((.(((((((..((.........(((.(....).)))...(((...))).))..))))))).......((((............))))........)))).))). ( -21.80)
>DroSim_CAF1 75994 120 - 1
CUCCACAAAAUCCCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAGCCAUGAAAAGGCAAAGUGAGAACUGAAUGAAAUCCCCGCUUGUCAUUAUCAAAGAGCAUAUAACAGACGAGAUA
.........(((.((.(.(((((((..((.........((((...(((.......)))...))))))..))))))).......((((............))))........).)).))). ( -20.10)
>DroEre_CAF1 76174 119 - 1
CCCCACAAAAUUUCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAGCCAUAAAAAGGCAAAGUGAGAACUGAAUGAAAUC-CCGCUUGUCAUUAUCAAAGAGCGUAUAACAGACGAGAUA
.........((((((.(.(((((((..((.........((((...(((.......)))...))))))..)))))))....-.(((((............))))).......).)))))). ( -23.60)
>DroYak_CAF1 76039 120 - 1
CUUCACGAAAUCCCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAGCCAUAAAAAGGCAAAGUGAGAACUGAAUGAAAUCCCCGCUUGUCAUUAUCAAAGAGCAUAUAACAGACGAGAUA
.........(((.((.(.(((((((..((.........((((...(((.......)))...))))))..))))))).......((((............))))........).)).))). ( -20.10)
>consensus
CUCCACAAAAUCCCGCCAUCAUUCAAAUCAAAGACCAAUCACGAAGCCAUAAAAAGGCAAAGUGAGAACUGAAUGAAAUCCCCGCUUGUCAUUAUCAAAGAGCAUAUAACAGACGAGAUA
.........(((.((.(.(((((((..((.........((((...(((.......)))...))))))..))))))).......((((............))))........).)).))). (-17.72 = -17.96 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	12,807,073 – 12,807,192
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.98
Mean single sequence MFE	-28.78
Consensus MFE	-24.50
Energy contribution	-24.78
Covariance contribution	0.28
Combinations/Pair	1.14
Mean z-score	-1.35
Structure conservation index	0.85
SVM decision value	0.35
SVM RNA-class probability	0.699111
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807073 119 + 22407834
GAUUUCAUUCAGUUCUCACUUUGCCUUUUUAUGGCUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGGGAUUUUGUGGAGGGUCCUUGUCGUUAUAUACAAAUGCGAAUGUACUU-UUUA
.....(((((.....((((...(((.......)))...))))..........(((((.((((((((((((((((....))))))).)))))))))...)))))..))))).....-.... ( -28.90)
>DroSec_CAF1 72763 120 + 1
GAUUUCAUUCAGUUCUGACUUUGCCUUUUCAUGGUUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGGGAUUUUGUGGAGGGUCCUUGUCGUUAUAUACAAAUGCGAAUGUACUUUUUUA
.....(((((............(((...(((((....)))))..))).....(((((.((((((((((((((((....))))))).)))))))))...)))))..))))).......... ( -27.40)
>DroSim_CAF1 76034 120 + 1
GAUUUCAUUCAGUUCUCACUUUGCCUUUUCAUGGCUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGGGAUUUUGUGGAGGGUCCUUGACGUUAUAUACAAAUGCGAAUGUACUUUUUUA
.....(((((.....((((...(((.......)))...))))..........(((((.((((((..((((((((....))))))))...))))))...)))))..))))).......... ( -25.40)
>DroEre_CAF1 76213 119 + 1
GAUUUCAUUCAGUUCUCACUUUGCCUUUUUAUGGCUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGAAAUUUUGUGGGGAGUGCUCGUCGUUAUAUAUAAAUGCGAAUGUACUU-GUUA
..............(((((...(((.......)))(((((.(((..((........))..))).))))).....)))))((((((...((((...........))))..))))))-.... ( -28.30)
>DroYak_CAF1 76079 119 + 1
GAUUUCAUUCAGUUCUCACUUUGCCUUUUUAUGGCUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGGGAUUUCGUGAAGAGUCCUCGUCGUUAUAUACAAAGGCGAAUAUACUA-UUAA
......((((.....((((...(((.......)))...))))...(((((((...((.(((((((((((((((......)))))).))))))))).)))))))))))))......-.... ( -33.90)
>consensus
GAUUUCAUUCAGUUCUCACUUUGCCUUUUUAUGGCUUCGUGAUUGGUCUUUGAUUUGAAUGAUGGCGGGAUUUUGUGGAGGGUCCUUGUCGUUAUAUACAAAUGCGAAUGUACUU_UUUA
.....(((((.....((((...(((.......)))...))))...((.((((...((.((((((((((((((((....))))))).))))))))).)))))).))))))).......... (-24.50 = -24.78 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:22 2006