Locus 4857

Sequence ID	3R_DroMel_CAF1
Location	12,740,716 – 12,740,850
Length	134
Max. P	0.999270

overview

Window 3

Location	12,740,716 – 12,740,817
Length	101
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	91.36
Mean single sequence MFE	-41.14
Consensus MFE	-32.78
Energy contribution	-32.66
Covariance contribution	-0.12
Combinations/Pair	1.14
Mean z-score	-2.69
Structure conservation index	0.80
SVM decision value	2.26
SVM RNA-class probability	0.991307
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12740716 101 + 27905053
UUAAUAUUCAUUGCCGGCUUCUGCUGCUGUUGCUGUUUUUGCUCCUGCCGGG---AAGUGGAAGUAUUUCGGCGG-----GGCUGUGGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((..(.......((.(((((((..---(..(....)..)..))))))-----))).)..)).)))))))).)))...))). ( -42.00)
>DroSec_CAF1 115968 101 + 1
UUAAUAUUCAUUGCCGGCUCCUGCUGCUGUUGCUGUUUUUGCUCCUGCCGGG---AAGUGGAAGUAUUUCGGAGG-----GGCUGUGGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((..(.......((((((.(((..---(..(....)..)..))))))-----))).)..)).)))))))).)))...))). ( -43.10)
>DroSim_CAF1 117582 101 + 1
UUAAUAUUCAUUGCCGGCUCCUGCUGCUGUUGCUGUUUUUGCUCCUGCCGGG---AAGUGGAAGUAUUUCGGAGG-----GGCUGUGGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((..(.......((((((.(((..---(..(....)..)..))))))-----))).)..)).)))))))).)))...))). ( -43.10)
>DroEre_CAF1 122556 104 + 1
UUAAUAUUCAUUGCCGGCUCCUGCUGCUGCUGCUGUUUUUGCUCCUGCCGGGGGGCAGUGGAGGUACUUCGAAGG-----GGCUGUUGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((.(((.(((((((((((....)))))))..((((...)))))))).-----)))....)).)))))))).)))...))). ( -42.60)
>DroYak_CAF1 112430 106 + 1
UUAAUAUUCAUUGCCGGCUCCUGCUGCUGUUGCUGUUUUUGCUCCUGUCGCA---AAGUCAAGGUAUUUCGAAGGUAUCGGGCUGUUGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((.((((.((((((.......)))---))).)..((((((.....)))))).)))....)).)))))))).)))...))). ( -34.90)
>consensus
UUAAUAUUCAUUGCCGGCUCCUGCUGCUGUUGCUGUUUUUGCUCCUGCCGGG___AAGUGGAAGUAUUUCGGAGG_____GGCUGUGGCUGCAGCAGGUGCUCAUGCAG
...........(((.(((.((((((((.((..(.(((......(((.(((((...............)))))))).....))).)..)).)))))))).)))...))). (-32.78 = -32.66 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	12,740,716 – 12,740,817
Length	101
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.36
Mean single sequence MFE	-30.91
Consensus MFE	-27.21
Energy contribution	-27.21
Covariance contribution	0.00
Combinations/Pair	1.09
Mean z-score	-2.51
Structure conservation index	0.88
SVM decision value	3.47
SVM RNA-class probability	0.999270
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12740716 101 - 27905053
CUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCGCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACAGCAACAGCAGCAGAAGCCGGCAAUGAAUAUUAA
.(((.((.((..(((((((.........(-----(.((((..............---..)))).)).((.......))....)))))))..)))))))........... ( -28.69)
>DroSec_CAF1 115968 101 - 1
CUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCUCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACAGCAACAGCAGCAGGAGCCGGCAAUGAAUAUUAA
.(((.((.((.((((((((..........-----((((((..............---..))).))).((.......))....)))))))).)))))))........... ( -30.39)
>DroSim_CAF1 117582 101 - 1
CUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCUCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACAGCAACAGCAGCAGGAGCCGGCAAUGAAUAUUAA
.(((.((.((.((((((((..........-----((((((..............---..))).))).((.......))....)))))))).)))))))........... ( -30.39)
>DroEre_CAF1 122556 104 - 1
CUGCAUGAGCACCUGCUGCAGCAACAGCC-----CCUUCGAAGUACCUCCACUGCCCCCCGGCAGGAGCAAAAACAGCAGCAGCAGCAGGAGCCGGCAAUGAAUAUUAA
.(((.((.((.((((((((.((.......-----.................(((((....)))))..((.......)).)).)))))))).)))))))........... ( -35.10)
>DroYak_CAF1 112430 106 - 1
CUGCAUGAGCACCUGCUGCAGCAACAGCCCGAUACCUUCGAAAUACCUUGACUU---UGCGACAGGAGCAAAAACAGCAACAGCAGCAGGAGCCGGCAAUGAAUAUUAA
.(((.((.((.((((((((..........(((.....))).......(((..((---(((.......)))))..))).....)))))))).)))))))........... ( -30.00)
>consensus
CUGCAUGAGCACCUGCUGCAGCCACAGCC_____CCUCCGAAAUACUUCCACUU___CCCGGCAGGAGCAAAAACAGCAACAGCAGCAGGAGCCGGCAAUGAAUAUUAA
.(((.((.((.((((((((...............((((((...................))).))).((.......))....)))))))).)))))))........... (-27.21 = -27.21 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	12,740,749 – 12,740,850
Length	101
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	92.13
Mean single sequence MFE	-25.91
Consensus MFE	-20.48
Energy contribution	-20.32
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.97
Structure conservation index	0.79
SVM decision value	1.05
SVM RNA-class probability	0.906217
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12740749 101 - 27905053
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCGCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACA
..........((((((((((((.(..((......))..).))))))))..)))).....(((-----(.((((..............---..)))).)).))....... ( -26.49)
>DroSec_CAF1 116001 101 - 1
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCUCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACA
..........((((((((((((.(..((......))..).))))))))..)))).....((.-----((((((..............---..))).))).))....... ( -24.39)
>DroSim_CAF1 117615 101 - 1
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCCACAGCC-----CCUCCGAAAUACUUCCACUU---CCCGGCAGGAGCAAAAACA
..........((((((((((((.(..((......))..).))))))))..)))).....((.-----((((((..............---..))).))).))....... ( -24.39)
>DroEre_CAF1 122589 104 - 1
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCAACAGCC-----CCUUCGAAGUACCUCCACUGCCCCCCGGCAGGAGCAAAAACA
..........((((((((((((.(((......((((((...((....)))))))).......-----..)))..)))))))...(((((....))))))).)))..... ( -28.16)
>DroYak_CAF1 112463 106 - 1
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCAACAGCCCGAUACCUUCGAAAUACCUUGACUU---UGCGACAGGAGCAAAAACA
............(((((((((((.........((((((...((....))))))))..)))).(((.....)))....))).))))((---(((.......))))).... ( -26.10)
>consensus
UAAAAAAAUAUUGUCAGGUGCUGGAACAAAAAGCUGCAUGAGCACCUGCUGCAGCCACAGCC_____CCUCCGAAAUACUUCCACUU___CCCGGCAGGAGCAAAAACA
..........((((((((((((.(..((......))..).)))))))((((......))))................................)))))........... (-20.48 = -20.32 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:30 2006