Locus 4753

Sequence ID	3L_DroMel_CAF1
Location	13,365,537 – 13,365,665
Length	128
Max. P	0.908058

overview

Window 1

Location	13,365,537 – 13,365,632
Length	95
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.94
Mean single sequence MFE	-37.82
Consensus MFE	-27.05
Energy contribution	-26.80
Covariance contribution	-0.25
Combinations/Pair	1.10
Mean z-score	-2.07
Structure conservation index	0.72
SVM decision value	0.62
SVM RNA-class probability	0.802636
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13365537 95 + 23771897
AAAGCCGCUCGGCAA-----AAGUCCUGGAUGC--GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAUGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU-----------
....((((((((...-----.((.((..(...(--(...((((((((((((.......)))))))))))).-.-))..)..)).))....----.)))))..)))...----------- ( -38.20)
>DroSec_CAF1 37142 95 + 1
AAAGCCACUCGCCAA-----AAGUCCUGGAUGC--GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU-----------
...(((((.(((((.-----......))).)).--))))).((((((((((.......))))))))))...-(-(((.((((........----.))))..))))...----------- ( -36.70)
>DroSim_CAF1 37040 95 + 1
AAAGCCGCUCGGCCA-----AAGUCCUGGAUGC--GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU-----------
...((.(((((((((-----..(((...)))..--.)))).((((((....))))))..))))).))....-(-(((.((((........----.))))..))))...----------- ( -37.50)
>DroEre_CAF1 37538 95 + 1
AAAGCCGCUCAGCAA-----AAGUCCUGGAUGC--GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU-----------
...(((((.((.((.-----......))..)).--))))).((((((((((.......))))))))))...-(-(((.((((........----.))))..))))...----------- ( -33.40)
>DroYak_CAF1 38565 106 + 1
AAAGCCGCUCAGCAA-----AAGUCCUGGAUGC--GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGUGCCUAAGA----ACCGGGAUCCGAAUCGGGAUCGGGA
....(((.((.....-----..(((((((...(--..((((((((((((((.......)))))))))((..-.-....)))))))...).----.)))))))(((...))))).))).. ( -39.00)
>DroPer_CAF1 13292 105 + 1
AAGGC---UUGCCAAAUGAGAGGUCCUUGUUCCCGGUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAAUAAGCGGCACCAGGUCCAGGACAGCACCGGGACUGAGAC-----------
..(((---((..(....)..)))))(((..((((((((.(.((((((....)))))).....(((((.....))))).....(((...))).)))))))))..)))..----------- ( -42.10)
>consensus
AAAGCCGCUCGGCAA_____AAGUCCUGGAUGC__GUGGCAUGUGGCUUGUGCCACAAACGAGCCGCAGGA_U_CGAACUGGGCCUAAGA____ACCGGGAUCGGAAU___________
......................(((((((......(((((.((((((....)))))).....)))))...........((.......))......)))))))................. (-27.05 = -26.80 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	13,365,569 – 13,365,665
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.79
Mean single sequence MFE	-38.64
Consensus MFE	-23.96
Energy contribution	-23.97
Covariance contribution	0.01
Combinations/Pair	1.28
Mean z-score	-2.10
Structure conservation index	0.62
SVM decision value	1.06
SVM RNA-class probability	0.908058
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13365569 96 + 23771897
CAUGUGGCUUGUGCCACAAACGAGCCGCAUGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU------------------CGGGAUCGGGAAUCGGUACUUGGGAAACAGCCC
((((((((((((.......)))))))))))).-.-....(((..((((((.----(((((..((.((..------------------.....)).))..))))).))))))...)))... ( -40.40)
>DroSec_CAF1 37174 96 + 1
CAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU------------------CGGGAUCGGGAAUCGGUACUCGGGAAGAAGCCC
..((((((((((.......))))))))))...-.-......((((......----.((((((((((..(------------------((....)))...))))).)))))......)))) ( -35.22)
>DroSim_CAF1 37072 96 + 1
CAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU------------------CGGGAUCGGGAAUCGGUACUCGGGAAGAAGCCC
..((((((((((.......))))))))))...-.-......((((......----.((((((((((..(------------------((....)))...))))).)))))......)))) ( -35.22)
>DroEre_CAF1 37570 102 + 1
CAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGGGCCUAAGA----ACCGGGAUCGGAAU------------CGGGAUCGGGAUCGGGAAUCGGUACUUGGGAAGAAGCCC
..((((((((((.......))))))))))...-.-....((...((((((.----(((((..((((..(------------((....)))..))))...))))).)))))).))...... ( -37.90)
>DroYak_CAF1 38597 114 + 1
CAUGUGGCUUGUGCCACAAACGAGCCGCAGGA-U-CGAACUGUGCCUAAGA----ACCGGGAUCCGAAUCGGGAUCGGGAUCGGGAUCGGGAUCGGGAAUCGGUACUUGGAAAGCAGCCC
..((((((((((.......))))))))))...-.-....((((..(((((.----(((((..(((((.((((..(((....)))..))))..)))))..))))).)))))...))))... ( -46.10)
>DroPer_CAF1 13328 88 + 1
CAUGUGGCUUGUGCCACAAACGAGCCGCAAUAAGCGGCACCAGGUCCAGGACAGCACCGGGACUGAGAC------------------CGGGAUCGAGA-------CCCGAGAA-------
..((((((....))))))..((((((((.....))))).((.(((((((..(.......)..))).)))------------------).)).)))...-------........------- ( -37.00)
>consensus
CAUGUGGCUUGUGCCACAAACGAGCCGCAGGA_U_CGAACUGGGCCUAAGA____ACCGGGAUCGGAAU__________________CGGGAUCGGGAAUCGGUACUCGGGAAGAAGCCC
..((((((((((.......))))))))))..........((((.(((...........))).)))).....................((((((((.....)))).))))........... (-23.96 = -23.97 +   0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:19 2006