Locus 5337

Sequence ID	2R_DroMel_CAF1
Location	17,277,853 – 17,277,970
Length	117
Max. P	0.995610

overview

Window 3

Location	17,277,853 – 17,277,970
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.54
Mean single sequence MFE	-21.38
Consensus MFE	-6.28
Energy contribution	-6.68
Covariance contribution	0.40
Combinations/Pair	1.12
Mean z-score	-2.17
Structure conservation index	0.29
SVM decision value	1.54
SVM RNA-class probability	0.962770
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17277853 117 + 20766785
AAUCAUAUUUUAAUUUUAUGCAAAUUAUACGCUGAUUAUGCUGUCAGCAUCACUAAAGGUUCCGCACAUUU---CAUUAUGUAUCUACAUACAUGAACAUGUAUGUACAAUGAAAUCUCA
..................(((.........((((((......)))))).........(....)))).((((---(((..(((....((((((((....)))))))))))))))))).... ( -23.20)
>DroPse_CAF1 3203 96 + 1
AUUUAUGUUUUAAUUUAAUGCAAAUUGUACACUGAUUAUGCUGUCAGCCUCGAUAGAGGCCCCACAUAUGUACACAUUUUAAUGAU----AUAUGUACAU--------------------
...(((((.(((.(..((((.....((((((.((((......))))(((((....)))))........))))))))))..).))).----))))).....-------------------- ( -18.50)
>DroSec_CAF1 876 113 + 1
ACUCAUAUUCUAAUUUUAUGCAAAUUAUACGCUGAUUAUGCUGUCAGCAUCACUGGAGGUUCCGCACAUUU---CAUUAUGUAUCUACAUACAUGAACAU----GUACAAUGAAAUCUCA
............(((((((((.........((((((......))))))......((.....))))((((((---((((((((....))))).))))).))----))...))))))).... ( -23.10)
>DroSim_CAF1 2851 113 + 1
AAUCAUAUUUUAAUUUUAUGCAAAUUAUACGCUGAUUAUGCUGUCAGCAUCACUGGAGGUUCCGCACAUUU---CAUUAUGUAUCUACAUACAUGAACAU----GUACAAUGAAAUCUCA
..((((.............((.........((((((......))))))......((.....))))((((((---((((((((....))))).))))).))----))...))))....... ( -23.10)
>DroPer_CAF1 3262 100 + 1
AUUCAUGUUUUAAUUUAAUGCAAAUUGUACACUGAUUAUGCUGUCAGCCUCGAUAGAGGCCCCACAUAUGUACACAUUUUAACGAUACAUAUAUGUACAU--------------------
.........................((((((.....((((.((((.(((((....))))).......(((....)))......))))))))..)))))).-------------------- ( -19.00)
>consensus
AAUCAUAUUUUAAUUUUAUGCAAAUUAUACGCUGAUUAUGCUGUCAGCAUCACUAGAGGUUCCGCACAUUU___CAUUAUGUAUCUACAUACAUGAACAU____GUACAAUGAAAUCUCA
..((((....((((((.....))))))...((((((......))))))............................................))))........................ ( -6.28 =  -6.68 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	17,277,853 – 17,277,970
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.54
Mean single sequence MFE	-26.04
Consensus MFE	-9.72
Energy contribution	-9.56
Covariance contribution	-0.16
Combinations/Pair	1.25
Mean z-score	-2.56
Structure conservation index	0.37
SVM decision value	2.60
SVM RNA-class probability	0.995610
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17277853 117 - 20766785
UGAGAUUUCAUUGUACAUACAUGUUCAUGUAUGUAGAUACAUAAUG---AAAUGUGCGGAACCUUUAGUGAUGCUGACAGCAUAAUCAGCGUAUAAUUUGCAUAAAAUUAAAAUAUGAUU
....((((((((((((((((((....))))))))......))))))---))))(((((((....(((...(((((((........))))))).))))))))))................. ( -28.20)
>DroPse_CAF1 3203 96 - 1
--------------------AUGUACAUAU----AUCAUUAAAAUGUGUACAUAUGUGGGGCCUCUAUCGAGGCUGACAGCAUAAUCAGUGUACAAUUUGCAUUAAAUUAAAACAUAAAU
--------------------.(((((((((----.........)))))))))(((((..((((((....))))))....)))))...((((((.....))))))................ ( -24.00)
>DroSec_CAF1 876 113 - 1
UGAGAUUUCAUUGUAC----AUGUUCAUGUAUGUAGAUACAUAAUG---AAAUGUGCGGAACCUCCAGUGAUGCUGACAGCAUAAUCAGCGUAUAAUUUGCAUAAAAUUAGAAUAUGAGU
...............(----((((((((((((....))))))....---...(((((((.....))....(((((((........))))))).......)))))......)))))))... ( -26.50)
>DroSim_CAF1 2851 113 - 1
UGAGAUUUCAUUGUAC----AUGUUCAUGUAUGUAGAUACAUAAUG---AAAUGUGCGGAACCUCCAGUGAUGCUGACAGCAUAAUCAGCGUAUAAUUUGCAUAAAAUUAAAAUAUGAUU
.(((.((((...((((----((.(((((.(((((....))))))))---)))))))))))).))).....(((((((........))))))).((((((.....)))))).......... ( -25.30)
>DroPer_CAF1 3262 100 - 1
--------------------AUGUACAUAUAUGUAUCGUUAAAAUGUGUACAUAUGUGGGGCCUCUAUCGAGGCUGACAGCAUAAUCAGUGUACAAUUUGCAUUAAAUUAAAACAUGAAU
--------------------((((.((((((((((((((....))).))))))))))).((((((....))))))....))))....((((((.....))))))................ ( -26.20)
>consensus
UGAGAUUUCAUUGUAC____AUGUUCAUGUAUGUAGAUACAUAAUG___AAAUGUGCGGAACCUCUAGUGAUGCUGACAGCAUAAUCAGCGUAUAAUUUGCAUAAAAUUAAAAUAUGAAU
....................................................((((((((..(......)(((((((........)))))))....))))))))................ ( -9.72 =  -9.56 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:25 2006