Locus 3977

Sequence ID	2L_DroMel_CAF1
Location	11,594,567 – 11,594,754
Length	187
Max. P	0.575645

overview

Window 9

Location	11,594,567 – 11,594,676
Length	109
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	89.27
Mean single sequence MFE	-25.18
Consensus MFE	-17.79
Energy contribution	-17.73
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.71
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.575645
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11594567 109 - 22407834
AUAUCGAAAUAGCUCAACAUCCACAAAUAUGUUGCCGAAGUGGAAUUUCUCUGUAGUUUCCAUUUCGCCCUAGUUUCUGUGAUUUUCAUUUGGAAUCU---------AGUUGCUUUUU
......(((.(((.((((((........)))))).((((((((((...((....)).))))))))))..((((.(((((((.....)))..)))).))---------))..))).))) ( -23.80)
>DroSec_CAF1 48685 118 - 1
AUAUCGAAAUAGCUCAACCUCCACAAAAAUGUUGCCGAAGUGGAGUUUCUCUGUAGUUUCCAUUUCGCCCUAGUUUCUGUGAUUUUCAUUUGGAAACAACAUCAAGCAUUUGCUUUUU
.....((..............((((.((((...(.((((((((((...((....)).)))))))))).)...)))).))))........(((....)))..))((((....))))... ( -23.80)
>DroSim_CAF1 51398 118 - 1
AUAUCGAAAUAGCUCAAGCUCCACAAAAAUGUUGCCGAAGUGGAGUUUCUCUGUAGUUUCCAUUUCGCCCUAGUUUCUGUGAUUUUCAUUUGGAAACAACAUCAAGCAUUUCCCUUUU
.....(((((.(((.......((((.((((...(.((((((((((...((....)).)))))))))).)...)))).))))........(((....))).....))))))))...... ( -26.40)
>DroYak_CAF1 50584 118 - 1
AUAUCGAAAUAGCUCAACCUCCACAAAAAUGCUGCCGAAGUGGAGUUUUUGUGUAGUUUCUAUUUCGCCCCAGUUUCUGUGAUUUUCAUUUGAAAAGAACAUCAAGCAUUUGCCUUUU
....((((((((...(((...(((((((((.(..(....)..).)))))))))..))).)))))))).....((((.(((..(((((....)))))..)))..))))........... ( -26.70)
>consensus
AUAUCGAAAUAGCUCAACCUCCACAAAAAUGUUGCCGAAGUGGAGUUUCUCUGUAGUUUCCAUUUCGCCCUAGUUUCUGUGAUUUUCAUUUGGAAACAACAUCAAGCAUUUGCCUUUU
.....................((((.((((...(.((((((((((............)))))))))).)...)))).)))).(((((....)))))...................... (-17.79 = -17.73 +  -0.06)

alignment

secondary structure

dotplot

Window 0

Location	11,594,637 – 11,594,754
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	91.82
Mean single sequence MFE	-29.60
Consensus MFE	-23.86
Energy contribution	-24.05
Covariance contribution	0.19
Combinations/Pair	1.10
Mean z-score	-1.51
Structure conservation index	0.81
SVM decision value	0.01
SVM RNA-class probability	0.540569
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11594637 117 + 22407834
UUCGGCAACAUAUUUGUGGAUGUUGAGCUAUUUCGAUAUUGUUGCCUUUGAAAUCGCGCAAACCAACUAAUGUUUUGACUUUCAGUCAAAGAAGGGCA--AACUAUGCCAUUGUUGAAC
((((((((.(((((..(((...(((.((.(((((((...........))))))).)).))).)))...)))))((((((.....))))))....((((--.....)))).)))))))). ( -29.70)
>DroSec_CAF1 48764 118 + 1
UUCGGCAACAUUUUUGUGGAGGUUGAGCUAUUUCGAUAUUGUUGCCUUUGAAAUCGCGCAAAGCAAAUAAUGUUUUGACUUUCAGUUAAAGAAGGGCAAAAACUAUGCCAUUGUUGUA-
....(((((((((((((((((((...((.(((((((...........))))))).)).(((((((.....))))))))))))))..))))))..((((.......))))..)))))).- ( -29.50)
>DroSim_CAF1 51477 118 + 1
UUCGGCAACAUUUUUGUGGAGCUUGAGCUAUUUCGAUAUUGUUGCCUUUGAAAUAGCGCAAAGCAACUAAUGUUUUGACUUUCAGUUAAAGAAGGGCAAAAACUAUGCCAUUGUUGUA-
....((((((.....((((.((((..((((((((((...........))))))))))...)))).......(((((..(((((.......)))))...)))))....)))))))))).- ( -32.60)
>DroYak_CAF1 50663 113 + 1
UUCGGCAGCAUUUUUGUGGAGGUUGAGCUAUUUCGAUAUUGUUGCCUUUGAAACCGCGCAA---AACUAAUGCUUUGACUUUCAGUUAAAGAAGGACA--AACUAUGCCAUUGUUGUG-
...(((((((....(((.(((((......))))).))).)))))))........(((((((---........(((((((.....)))))))..((.((--.....)))).))).))))- ( -26.60)
>consensus
UUCGGCAACAUUUUUGUGGAGGUUGAGCUAUUUCGAUAUUGUUGCCUUUGAAAUCGCGCAAAGCAACUAAUGUUUUGACUUUCAGUUAAAGAAGGGCA__AACUAUGCCAUUGUUGUA_
...(((((((....(((.(((((......))))).))).)))))))...........((((...........(((((((.....)))))))...((((.......)))).))))..... (-23.86 = -24.05 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:14 2006