Locus 3188

Sequence ID	2L_DroMel_CAF1
Location	9,108,365 – 9,108,509
Length	144
Max. P	0.991456

overview

Window 5

Location	9,108,365 – 9,108,475
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-27.68
Consensus MFE	-24.12
Energy contribution	-24.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.87
SVM decision value	2.27
SVM RNA-class probability	0.991456
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9108365 110 + 22407834
GCAUUCGUAAUA------CAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCC----UGCUUACUUAUUCAUAUGAAAUUGCCUGAUUACCGUUGGCCAAAUCGUUUUGCCCAGCACC
((((((((....------..)))))......)))......(((((((((...)))----..........(((....)))...)))))).....(((((.((((....)))).)))))... ( -27.50)
>DroSec_CAF1 10520 114 + 1
GCAUUCGUAAUA------CAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCCUGCCUGCUUACUUAUUCAUAUGAAAAUGCCUGAUUACCGUUGGCCAAAUCGUUUUGCCCAGCACC
((((((((....------..)))))......)))......((((((((((.....))))..........(((....)))...)))))).....(((((.((((....)))).)))))... ( -30.00)
>DroSim_CAF1 10603 114 + 1
GCAUUCGUAAUA------CAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCCUGCCUGCUUACUUAUUCAUAUGAAAUUGCCUGAUUACCGUUGGCCAAAUCGUUUUGCCCAGAACC
((((((((....------..)))))......)))......((((((((((.....))))..........(((....)))...))))))......((((.((((....)))).)))).... ( -26.00)
>DroEre_CAF1 10713 116 + 1
GCAUUCGUAAUACUCGAACAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCC----UGCUUACUUAUUCAUAUGAAAUUGCCUGAUUACCGUUGGCCAAAUCGUUUUGCCCAGCACC
......((((((.(((.....)))....))))))......(((((((((...)))----..........(((....)))...)))))).....(((((.((((....)))).)))))... ( -27.10)
>DroYak_CAF1 15549 110 + 1
GCAUUCGUAAUA------CAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCC----UGCUUACUUAUUCAUAUGAAAUUGCCUGAUUACCGUUGGCCAAAUCGCUUUGCCCAGCGCC
((((((((....------..)))))......)))......(((((((((...)))----..........(((....)))...))))))....((((((.((((....)))).)))))).. ( -27.80)
>consensus
GCAUUCGUAAUA______CAACGAAAUUUAUUGCACACACUCAGGCGGCAUUGCC____UGCUUACUUAUUCAUAUGAAAUUGCCUGAUUACCGUUGGCCAAAUCGUUUUGCCCAGCACC
((((((((............)))))......)))......(((((((((...)))..............(((....)))...)))))).....(((((.((((....)))).)))))... (-24.12 = -24.32 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	9,108,399 – 9,108,509
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.68
Mean single sequence MFE	-31.58
Consensus MFE	-25.13
Energy contribution	-24.65
Covariance contribution	-0.48
Combinations/Pair	1.11
Mean z-score	-1.77
Structure conservation index	0.80
SVM decision value	0.76
SVM RNA-class probability	0.843263
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9108399 110 - 22407834
AACACGUACCAAUACAGAGCUAUGUACACAC------UACGGUGCUGGGCAAAACGAUUUGGCCAACGGUAAUCAGGCAAUUUCAUAUGAAUAAGUAAGCA----GGCAAUGCCGCCUGA
......((((..((((......))))..(((------....))).(((.((((....)))).)))..)))).((((((...(((....)))..........----(((...))))))))) ( -29.50)
>DroSec_CAF1 10554 114 - 1
AACACGUACCAAUACAGAGCUAUAUACACAC------UACGGUGCUGGGCAAAACGAUUUGGCCAACGGUAAUCAGGCAUUUUCAUAUGAAUAAGUAAGCAGGCAGGCAAUGCCGCCUGA
......((((..................(((------....))).(((.((((....)))).)))..)))).((((((...(((....)))..........((((.....)))))))))) ( -31.60)
>DroSim_CAF1 10637 114 - 1
AACACGUACCAAUACAGAGCUAUGUACACAC------UAUGGUUCUGGGCAAAACGAUUUGGCCAACGGUAAUCAGGCAAUUUCAUAUGAAUAAGUAAGCAGGCAGGCAAUGCCGCCUGA
......((((....((((((((((.......------))))))))))(((...........)))...)))).((((((...(((....)))..........((((.....)))))))))) ( -35.50)
>DroEre_CAF1 10753 116 - 1
AACACGUACCAAUACGGAGCCGUGUACACACGAAGCCCACGGUGCUGGGCAAAACGAUUUGGCCAACGGUAAUCAGGCAAUUUCAUAUGAAUAAGUAAGCA----GGCAAUGCCGCCUGA
.((.(((.((((..((....((((....))))..(((((......)))))....))..))))...)))))..((((((...(((....)))..........----(((...))))))))) ( -33.70)
>DroYak_CAF1 15583 116 - 1
AACACGUACCAAUACAGAGCUAUGUACAUACGACGACGACGGCGCUGGGCAAAGCGAUUUGGCCAACGGUAAUCAGGCAAUUUCAUAUGAAUAAGUAAGCA----GGCAAUGCCGCCUGA
......((((....(((.(((.(((.(.......))))..))).)))((((((....))).)))...)))).((((((...(((....)))..........----(((...))))))))) ( -27.60)
>consensus
AACACGUACCAAUACAGAGCUAUGUACACAC______UACGGUGCUGGGCAAAACGAUUUGGCCAACGGUAAUCAGGCAAUUUCAUAUGAAUAAGUAAGCA____GGCAAUGCCGCCUGA
......((((....(((.(((...................))).)))((((((....))).)))...)))).((((((...(((....)))..............(((...))))))))) (-25.13 = -24.65 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:28 2006