Locus 3506

Sequence ID	X_DroMel_CAF1
Location	9,416,485 – 9,416,579
Length	94
Max. P	0.993769

overview

Window 9

Location	9,416,485 – 9,416,579
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	79.89
Mean single sequence MFE	-19.12
Consensus MFE	-8.52
Energy contribution	-8.12
Covariance contribution	-0.40
Combinations/Pair	1.25
Mean z-score	-2.71
Structure conservation index	0.45
SVM decision value	1.58
SVM RNA-class probability	0.965154
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9416485 94 + 22224390
AGUGUCCAACACAAUAGGAGUCUGCUCCUCGCAGCUC---CUUCCAUUUUGUCACUUUUUUUGUUUUUUUACAGAAGAGCACUUCCACUGAACAUUA
(((((.(((......(((((.((((.....)))))))---))......))).....((((((((......))))))))))))).............. ( -22.10)
>DroSec_CAF1 1815 92 + 1
AGUGUCCAACACAACAGGAGUCUGCUCCUCGCAGCUC---CUCCCAUUUUGUUUUUU--UUUUUUUUUUUAGAGAGGAGCACUUCCACUGAACAUUA
(((((.((.......(((((.((((.....)))))))---)).......((((((((--(((........))))))))))).......)).))))). ( -22.90)
>DroSim_CAF1 1527 88 + 1
AGUGUCCAACACAACAAGAGUCUGCUCCUCGCAGCUC---CUCCCAUUUUGUCACUU------UUUUUUUAGAAAGGAGCACUUCCACUGAACAUUA
(((((.((.........(((.((((.....)))))))---.........(((..(((------(((....))))))..))).......)).))))). ( -17.90)
>DroEre_CAF1 1746 80 + 1
ACUGCCCAACACAACAGGAGUCUGCUCCUCGCAGCUC---CUCUCAUUUUGUCACUU------U--------CAAAAAGCAAUUCCACUGCACAUUA
..(((..........(((((.((((.....)))))))---))....(((((......------.--------))))).)))................ ( -16.10)
>DroYak_CAF1 1737 83 + 1
ACUGCCCAGCACAACAGGAGUCUGCUCCUCGCAGCUCCUCCUCUCAUCUUGUCACUU------U--------CAAAGAGCAAUGCCACUGAACAUUG
...((...((.....(((((.((((.....))))))))).......((((.......------.--------..))))))...))............ ( -16.60)
>consensus
AGUGUCCAACACAACAGGAGUCUGCUCCUCGCAGCUC___CUCCCAUUUUGUCACUU______UUUUUUUA_AAAAGAGCACUUCCACUGAACAUUA
(((((............(((.((((.....))))))).........((((........................))))))))).............. ( -8.52 =  -8.12 +  -0.40)

alignment

secondary structure

dotplot

Window 0

Location	9,416,485 – 9,416,579
Length	94
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	79.89
Mean single sequence MFE	-26.44
Consensus MFE	-16.30
Energy contribution	-16.50
Covariance contribution	0.20
Combinations/Pair	1.21
Mean z-score	-2.88
Structure conservation index	0.62
SVM decision value	2.42
SVM RNA-class probability	0.993769
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9416485 94 - 22224390
UAAUGUUCAGUGGAAGUGCUCUUCUGUAAAAAAACAAAAAAAGUGACAAAAUGGAAG---GAGCUGCGAGGAGCAGACUCCUAUUGUGUUGGACACU
...((((..(..((((....))))..).....)))).....((((.(((.(..(.((---(((((((.....)))).))))).)..).)))..)))) ( -26.10)
>DroSec_CAF1 1815 92 - 1
UAAUGUUCAGUGGAAGUGCUCCUCUCUAAAAAAAAAAA--AAAAAACAAAAUGGGAG---GAGCUGCGAGGAGCAGACUCCUGUUGUGUUGGACACU
...((((((..(.(((((((((((((............--............)))))---)))).)).(((((....))))).)).)..)))))).. ( -28.76)
>DroSim_CAF1 1527 88 - 1
UAAUGUUCAGUGGAAGUGCUCCUUUCUAAAAAAA------AAGUGACAAAAUGGGAG---GAGCUGCGAGGAGCAGACUCUUGUUGUGUUGGACACU
...(((((...(((((.....)))))........------....((((.((..((((---...((((.....)))).))))..)).))))))))).. ( -24.90)
>DroEre_CAF1 1746 80 - 1
UAAUGUGCAGUGGAAUUGCUUUUUG--------A------AAGUGACAAAAUGAGAG---GAGCUGCGAGGAGCAGACUCCUGUUGUGUUGGGCAGU
.....(((.......(..(((....--------.------)))..)(((.(..(.((---(((((((.....)))).))))).)..).))).))).. ( -24.70)
>DroYak_CAF1 1737 83 - 1
CAAUGUUCAGUGGCAUUGCUCUUUG--------A------AAGUGACAAGAUGAGAGGAGGAGCUGCGAGGAGCAGACUCCUGUUGUGCUGGGCAGU
...(((((((((((....(((((..--------.------............))))).(((((((((.....)))).))))))))..)))))))).. ( -27.76)
>consensus
UAAUGUUCAGUGGAAGUGCUCUUUU_UAAAAAAA______AAGUGACAAAAUGGGAG___GAGCUGCGAGGAGCAGACUCCUGUUGUGUUGGACACU
...((((((((......)))........................((((.((((((((......((((.....)))).)))))))).))))))))).. (-16.30 = -16.50 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:05 2006