Locus 5840

Sequence ID	3L_DroMel_CAF1
Location	15,762,559 – 15,762,819
Length	260
Max. P	0.999963

overview

Window 5

Location	15,762,559 – 15,762,671
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.10
Mean single sequence MFE	-31.68
Consensus MFE	-30.60
Energy contribution	-30.64
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	0.97
SVM decision value	4.93
SVM RNA-class probability	0.999963
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15762559 112 - 23771897
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCGCUAAAGUUGCUAAAGAAAGUGAACAAACAGAG--------
....(((((((((..((((((..(((((((((((((....))))).))))))))(((.....))).))))))..)))))......((((((......))).)))...)))).-------- ( -33.00)
>DroSec_CAF1 14154 112 - 1
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCGCUAAAGUUGCAAAAGAAAGUGAACAAACAGAG--------
....(((((((((..((((((..(((((((((((((....))))).))))))))(((.....))).))))))..)))))((.......)).................)))).-------- ( -32.60)
>DroSim_CAF1 15118 112 - 1
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCGCUAAAGUUGCAAAAGAAAGUGAACAAACAGAG--------
....(((((((((..((((((..(((((((((((((....))))).))))))))(((.....))).))))))..)))))((.......)).................)))).-------- ( -32.60)
>DroEre_CAF1 14277 112 - 1
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCGCUAAAGUUGCAAAAGAAAGUGAACAAACAGAG--------
....(((((((((..((((((..(((((((((((((....))))).))))))))(((.....))).))))))..)))))((.......)).................)))).-------- ( -32.60)
>DroAna_CAF1 9532 118 - 1
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGCAGCAAACAGAAAAUGGCGCUAAAGUUGCAAAAGAAAAC--ACAAACACAGACAUACUA
....(((((((((....(((..((((((((((((((....))))).)))))))))..))))))))..............((.......))..........--.......))))....... ( -27.60)
>consensus
CAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCGCUAAAGUUGCAAAAGAAAGUGAACAAACAGAG________
....(((((((((..((((((..(((((((((((((....))))).))))))))(((.....))).))))))..)))))((.......)).............))))............. (-30.60 = -30.64 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	15,762,591 – 15,762,710
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.64
Mean single sequence MFE	-35.57
Consensus MFE	-30.68
Energy contribution	-31.88
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.86
SVM decision value	2.88
SVM RNA-class probability	0.997555
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15762591 119 - 23771897
CCGGCUG-UGAGAGCCCAGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCG
(((((((-........))))........................((((..((((.(((((..((((((((((((((....))))).)))))))))..)))))))))..))))...))).. ( -36.30)
>DroSec_CAF1 14186 119 - 1
CUGGCUG-AGAGAGCCCAGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCG
.((((((-........)))).))...............(((...((((..((((.(((((..((((((((((((((....))))).)))))))))..)))))))))..)))).....))) ( -36.40)
>DroSim_CAF1 15150 119 - 1
CCGUCUG-AGAGAGCCCAGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCG
..(((((-........))).))................(((...((((..((((.(((((..((((((((((((((....))))).)))))))))..)))))))))..)))).....))) ( -34.00)
>DroEre_CAF1 14309 119 - 1
CCGGCUG-AAAGAGCCGAGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCG
.(((((.-....))))).....................(((...((((..((((.(((((..((((((((((((((....))))).)))))))))..)))))))))..)))).....))) ( -38.80)
>DroAna_CAF1 9570 118 - 1
--AGCAGUGGAGAGACGGGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGCAGCAAACAGAAAAUGGCG
--.((.((((...(((((.((.(((.................))).)).)))))........((((((((((((((....))))).))))))))))))).)).................. ( -32.33)
>consensus
CCGGCUG_AGAGAGCCCAGCACAUAAAAUUCAAUAAAACGCAUAUUUGGCUGUCAUUUGUUCCGAGUUUUGGGCGCCAAAGUGCCACAAAAUUUGCCACAGAGGCAAACAGAAAACGGCG
..((((......))))......................(((...((((..((((.(((((..((((((((((((((....))))).)))))))))..)))))))))..)))).....))) (-30.68 = -31.88 +   1.20)

alignment

secondary structure

dotplot

Window 7

Location	15,762,710 – 15,762,819
Length	109
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	90.77
Mean single sequence MFE	-28.11
Consensus MFE	-25.08
Energy contribution	-24.70
Covariance contribution	-0.38
Combinations/Pair	1.07
Mean z-score	-1.29
Structure conservation index	0.89
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15762710 109 - 23771897
AAGGAAAUCAAAAGCCGGCUAAGCGCCAAAAAAGCUGUAAGGAAAUAAUGUCUGGCCAGGCCAACGAG------CAAGGAGCGUUAUCCUUGGAGAGGUACGGUGCGAAAAAGCG
.................(((..(((((.......((.((((((..((((((....((..((......)------)..)).)))))))))))).))......))))).....))). ( -27.32)
>DroSec_CAF1 14305 109 - 1
AAGGAAAUCAAAAGCCGGCUAAGCGCCAAAAAAGCUGUAAGGAAAUAAUGUCUGGCCAAGCCAACGAG------CAAGGAGCGUUAUCCUUGGAGAGGCACCGUGCGAAAAAGCG
.............((((((.....))).......((.((((((..((((((....((..((......)------)..)).)))))))))))).)).))).....((......)). ( -27.60)
>DroSim_CAF1 15269 109 - 1
AAGGAAAUCAAAAGCCGGCUAAGCGCCAAAAAAGCUGUAAGGAAAUAAUGUCUGGCCAGGCCAACGAG------CAAGGAGCGUUAUCCUUGGAGAGGCACCGUGCGAAAAAGCG
.............((((((.....))).......((.((((((..((((((....((..((......)------)..)).)))))))))))).)).))).....((......)). ( -28.60)
>DroEre_CAF1 14428 105 - 1
----------AAAGCCGGCUAAGCGCCAAAAAAGCUGUAAGGAAAUAAUGUCUGGCCAAGUCAACGAGCGGCAUCAAGGAGCGUUAUCCUUGGAGAGGCACGGUGCGAAAAAGCG
----------...((((((.....))).......((.((((((..((((((((.(((............))).....))).))))))))))).)).))).....((......)). ( -28.90)
>consensus
AAGGAAAUCAAAAGCCGGCUAAGCGCCAAAAAAGCUGUAAGGAAAUAAUGUCUGGCCAAGCCAACGAG______CAAGGAGCGUUAUCCUUGGAGAGGCACCGUGCGAAAAAGCG
.............((((((.....))).......((.((((((..(((((((((((...)))...(........)..))).))))))))))).)).))).....((......)). (-25.08 = -24.70 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:41 2006