Locus 2969

Sequence ID	X_DroMel_CAF1
Location	7,905,156 – 7,905,409
Length	253
Max. P	0.964758

overview

Window 4

Location	7,905,156 – 7,905,268
Length	112
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	91.62
Mean single sequence MFE	-18.43
Consensus MFE	-17.99
Energy contribution	-17.77
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-1.48
Structure conservation index	0.98
SVM decision value	0.47
SVM RNA-class probability	0.748169
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7905156 112 - 22224390
GACAAAAUCAACAUCCAGCGGCAGCGCGGCCAUAAACAAAGCCAAAAUCAAAAGUCAUUCGGAUAUAUACAUAUAUUCGCCCAUAAUAGCGAAUAAACAGUAACAGAACGAG
(((..............(((....)))(((..........)))..........)))..(((......(((...(((((((........)))))))....)))......))). ( -20.30)
>DroSec_CAF1 5806 104 - 1
CACAAC------AUCCAGCGGCAGCGCGGCCAUAAACAAAGCCAAAAUCAAAAGUCAUUCGGAUAUAU--AUAUAUUUGCACAUAAAAGCGAAUAAACAGUAACAGAACGGG
......------((((.(((....)))(((..........))).................))))....--...(((((((........)))))))................. ( -17.30)
>DroSim_CAF1 8925 110 - 1
CACAACAUCAACAUCCAGCGGCAGCGCGGCCAUAAACAAAGCCAAAAUCAAAAGUCAUUCGGAUAUAU--AUAUAUUUGCACAUAAAAGCGAAUAAACAGUAACAGAACGAG
.......((...((((.(((....)))(((..........))).................))))....--...(((((((........)))))))..............)). ( -17.70)
>consensus
CACAACAUCAACAUCCAGCGGCAGCGCGGCCAUAAACAAAGCCAAAAUCAAAAGUCAUUCGGAUAUAU__AUAUAUUUGCACAUAAAAGCGAAUAAACAGUAACAGAACGAG
.((.........((((.(((....)))(((..........))).................)))).........(((((((........)))))))....))........... (-17.99 = -17.77 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	7,905,268 – 7,905,369
Length	101
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	88.92
Mean single sequence MFE	-14.07
Consensus MFE	-13.23
Energy contribution	-12.57
Covariance contribution	-0.66
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.94
SVM decision value	0.73
SVM RNA-class probability	0.836611
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7905268 101 - 22224390
AAUCUGUAUGUUGUAUAUGUUCAAUUCAAAAUUCAGCAACAAUAGCAACAACGCAAUUC--------AGCAACAACAACAAACAAAACCGACAAGCUAAACUUGGCUAA
....(((.((((((...((((..............((.......))......((.....--------.)))))))))))).))).........(((((....))))).. ( -15.00)
>DroSec_CAF1 5910 107 - 1
AAUCUGUAUGUUGUAUAUGUUUAAUUUA-AAUUCAACAACAAAAGCAAAAACGCAAUUCAACAAUUCAGCAACAAC-ACAAGCAAAACCGACGAGCUAAACUCGGCUAA
....(((.((((((...((((.(((...-.))).))))......((......))..............))))))))-).............((((.....))))..... ( -13.60)
>DroSim_CAF1 9035 107 - 1
AAUCUGUAUGUUGUAUAUGUUCAAUUUA-AAUUCAACAACAAAAGCAACAACGCAAUUCAACAAUUCAGCAACAAC-ACAAGCAAAACCGACGAGCUAAACUCGGCUAA
....(((.((((((...((((.(((...-.))).))))......((......))..............))))))))-).............((((.....))))..... ( -13.60)
>consensus
AAUCUGUAUGUUGUAUAUGUUCAAUUUA_AAUUCAACAACAAAAGCAACAACGCAAUUCAACAAUUCAGCAACAAC_ACAAGCAAAACCGACGAGCUAAACUCGGCUAA
....(((.((((((...((((.(((.....))).))))......((......))..............))))))...)))...........((((.....))))..... (-13.23 = -12.57 +  -0.66)

alignment

secondary structure

dotplot

Window 6

Location	7,905,300 – 7,905,409
Length	109
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	91.40
Mean single sequence MFE	-17.67
Consensus MFE	-17.60
Energy contribution	-17.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	1.00
SVM decision value	1.57
SVM RNA-class probability	0.964758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7905300 109 - 22224390
UUUUUAUUUUUACAGUUGCAACUUUUUAACAAUCGUGUACAAUCUGUAUGUUGUAUAUGUUCAAUUCAAAAUUCAGCAACAAUAGCAACAACGCAAUUC--------AGCAACAACA
..............(((((..............((((((((((......)))))))))).........................((......)).....--------.))))).... ( -17.60)
>DroSec_CAF1 5942 115 - 1
UUUUUAUUUUUACAGUUGCAACUUUUUAACAAUCGUGUACAAUCUGUAUGUUGUAUAUGUUUAAUUUA-AAUUCAACAACAAAAGCAAAAACGCAAUUCAACAAUUCAGCAACAAC-
..............(((((.....(((((....((((((((((......))))))))))......)))-)).............((......))..............)))))...- ( -17.70)
>DroSim_CAF1 9067 115 - 1
UUUUUAUUUUUACAGUUGCAACUUUUUAACAAUCGUGUACAAUCUGUAUGUUGUAUAUGUUCAAUUUA-AAUUCAACAACAAAAGCAACAACGCAAUUCAACAAUUCAGCAACAAC-
..............(((((.....(((((....((((((((((......))))))))))......)))-)).............((......))..............)))))...- ( -17.70)
>consensus
UUUUUAUUUUUACAGUUGCAACUUUUUAACAAUCGUGUACAAUCUGUAUGUUGUAUAUGUUCAAUUUA_AAUUCAACAACAAAAGCAACAACGCAAUUCAACAAUUCAGCAACAAC_
..............(((((..............((((((((((......)))))))))).........................((......))..............))))).... (-17.60 = -17.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:02 2006