Locus 1755

Sequence ID	X_DroMel_CAF1
Location	4,871,521 – 4,871,668
Length	147
Max. P	0.932273

overview

Window 2

Location	4,871,521 – 4,871,628
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.35
Mean single sequence MFE	-22.82
Consensus MFE	-15.10
Energy contribution	-15.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.66
SVM decision value	0.25
SVM RNA-class probability	0.654732
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4871521 107 - 22224390
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAAUCUAA------A--UCAUUU--UUUUUU--UUACAGACAA
.(((((......)))..........((((.((.(((((..((....)).)))))..)).))))-)).(((.(((((((((.....------.--.....)--))))))--)).))).... ( -23.50)
>DroSec_CAF1 23023 103 - 1
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAAUCGAG------A--CAAUUC--UUUGAU------AGAGAA
.(((((......))........((.....)).......)))..((((((((((...(((((((-((...))))))......))).------.--))))))--))))..------...... ( -19.70)
>DroSim_CAF1 23712 103 - 1
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAAUCGAG------A--CAAUUC--UUUGAU------AUACAA
.(((((......))........((.....)).......)))..((((((((((...(((((((-((...))))))......))).------.--))))))--))))..------...... ( -19.70)
>DroEre_CAF1 25901 110 - 1
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAUUCGUUUU-GCACUGCAAGAAAAAAUGGUG------U--CAAAUGAUGUUGUGCGCU-CAGAAAA
..(((......((((((((((((......(((.(((((..((....)).))))).))).((((-((...))))))......))))------(--(....)).))))))))..-))).... ( -26.90)
>DroYak_CAF1 23215 104 - 1
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCCAGAAAAAAAGGCU------AUACAAAU---UUCGAGGAC------GAA
...(((......)))...((..((.........(((((..((....)).)))))..(((.(((-(....(((.........))).------...)))).---..)))))..------)). ( -23.00)
>DroAna_CAF1 76224 109 - 1
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUGGUUCAGGCACUGAAAGAAAAAGGGGUCUUAGCUGUGUAGAU---UUUUAA--A------UUA
((((((......))......((((.........(((((..((....)).))))).....(((((...)))))........))))...))))........---......--.------... ( -24.10)
>consensus
AGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU_GCACUGCAAGAAAAAAUCGAG______A__CAAAU___UUUGAU______AGACAA
.(((((......))).......((.....))..(((((..((....)).)))))..........))...................................................... (-15.10 = -15.10 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	4,871,549 – 4,871,668
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.92
Mean single sequence MFE	-28.77
Consensus MFE	-24.34
Energy contribution	-25.03
Covariance contribution	0.70
Combinations/Pair	1.04
Mean z-score	-2.31
Structure conservation index	0.85
SVM decision value	1.22
SVM RNA-class probability	0.932273
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4871549 119 - 22224390
GUGGUGCAGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAA
(..((((((((.......)))....((((..............(((......))).......((.....))..(((((..((....)).)))))....)))))-))))..)......... ( -29.00)
>DroSec_CAF1 23047 119 - 1
GUGGUGCAGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAA
(..((((((((.......)))....((((..............(((......))).......((.....))..(((((..((....)).)))))....)))))-))))..)......... ( -29.00)
>DroSim_CAF1 23736 119 - 1
GUGGUGCAGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCAAGAAAAAA
(..((((((((.......)))....((((..............(((......))).......((.....))..(((((..((....)).)))))....)))))-))))..)......... ( -29.00)
>DroEre_CAF1 25932 119 - 1
GUGGUGCCGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAUUCGUUUU-GCACUGCAAGAAAAAA
(..((((.(((.......)))......................(((......)))..........((((.((((((((..((....)).)))).)))).))))-))))..)......... ( -29.60)
>DroYak_CAF1 23240 119 - 1
GUGGUGCAGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU-GCACUGCCAGAAAAAA
(..((((((((.......)))....((((..............(((......))).......((.....))..(((((..((....)).)))))....)))))-))))..)......... ( -28.10)
>DroAna_CAF1 76253 118 - 1
GCCGUGCC--CGAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUGGUUCAGGCACUGAAAGAAAAAG
...(((((--.((((............................(((......))).......((.....))..(((((..((....)).)))))....)))).)))))............ ( -27.90)
>consensus
GUGGUGCAGGCCAACAACGCCCCACAAACAAUCACUUACAAGCUGCUAAAUUGCAUAAUCACCCAAAAAGGAAUCAACGGCCGCAAGGAGUUGAAAUCGUUUU_GCACUGCAAGAAAAAA
(((((((.(((.......)))....((((..............(((......))).......((.....))..(((((..((....)).)))))....))))..)))))))......... (-24.34 = -25.03 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:11 2006