Locus 3987

Sequence ID	X_DroMel_CAF1
Location	10,563,356 – 10,563,501
Length	145
Max. P	0.999099

overview

Window 8

Location	10,563,356 – 10,563,464
Length	108
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	75.57
Mean single sequence MFE	-26.91
Consensus MFE	-18.54
Energy contribution	-19.34
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.85
Structure conservation index	0.69
SVM decision value	3.37
SVM RNA-class probability	0.999099
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10563356 108 - 22224390
CCCAUCAAC--C--C------CAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAGGACAGCUGUGGUCAGCAAAAUAGAGAAACAGAUUUUACACUUAUCCCAAAUG-CAA
...((((((--(--.------(((......))).)))).(((..((((((((((((.............))))))))))))....))).....)))...................-... ( -25.42)
>DroSec_CAF1 3521 103 - 1
CC-----GU--C--C------CAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAAGACAGCUGUGUUCAGCAAAAUAGAGAAAACGAUUUUACACUUAUGCCAAUUG-CAC
.(-----((--.--(------(((........))))...(((..((((((..((((.............))))..))))))....)))...)))............(((.....)-)). ( -19.82)
>DroSim_CAF1 3522 103 - 1
CC-----GU--C--C------CAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAAGACAGCUGUGGUCAGCAAAAUAGAGAAAACGAUUUUACACUUAUCCCAAAUG-UGC
..-----..--.--.------.....((((((.(((...(((..((((((((((((.............))))))))))))....))).....(((.........)))))).)))-))) ( -30.62)
>DroEre_CAF1 3491 89 - 1
CC-----CU--CCUC------CAUUCGCACAAGUGCUUACUCACAUGCUGGCCACAAA-------CAGUUGUGGUCAGCAGAAUAGAGACAG---------ACUUAUCCCAAGUC-CAC
..-----..--.(((------.(((((((....))).........((((((((((((.-------...)))))))))))))))).)))...(---------((((.....)))))-... ( -32.30)
>DroYak_CAF1 3563 105 - 1
C------CUUCCCUCCCCUGGCAUUCGCACAUGUGCUUACUCAGUUGCUGGCCACGAA-------CAGCGAUGGUCAGCAAAAUAGAGAACGAGAUUUUACAUUCAUCCCAAAUUGCA-
.------.....(((....(((((........)))))..(((..((((((((((((..-------...)).))))))))))....)))...)))........................- ( -26.40)
>consensus
CC_____CU__C__C______CAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAA_GACAGCUGUGGUCAGCAAAAUAGAGAAAAAGAUUUUACACUUAUCCCAAAUG_CAC
.........................(((....)))....(((..((((((((((((.............))))))))))))....)))............................... (-18.54 = -19.34 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	10,563,395 – 10,563,501
Length	106
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	80.27
Mean single sequence MFE	-20.12
Consensus MFE	-14.57
Energy contribution	-14.82
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.72
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10563395 106 - 22224390
AACAUGACCCCCUGCACCCCCUGCACCGCCC-CAUCCCCCCAUCAACC--CCAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAGGACAGCUGUGGUCAGC
....(((.....((((.....))))......-............((((--.(((......))).))))..)))...((((((((((.............)))))))))) ( -21.92)
>DroSec_CAF1 3560 92 - 1
AACAUGACCGCC---------UGCACCGCCC-CAUCACCC-----GUC--CCAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAAGACAGCUGUGUUCAGC
....(((((((.---------(((.......-........-----...--......)))...))))))).......((((..((((.............))))..)))) ( -17.38)
>DroSim_CAF1 3561 92 - 1
AACAUGACCCCC---------UGCACCGCCC-CAUCACCC-----GUC--CCAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAAGACAGCUGUGGUCAGC
....((((((..---------(((.......-........-----...--......)))...).))))).......((((((((((.............)))))))))) ( -19.18)
>DroEre_CAF1 3521 88 - 1
AACAUGACCCCC---------UGCAACAACAGCAACCCCC-----CUCCUCCAUUCGCACAAGUGCUUACUCACAUGCUGGCCACAAA-------CAGUUGUGGUCAGC
...(((......---------(((.......)))......-----...........(((....))).......)))(((((((((((.-------...))))))))))) ( -22.00)
>consensus
AACAUGACCCCC_________UGCACCGCCC_CAUCACCC_____GUC__CCAUUCGCACAUGUGGUUACUCACUUGCUGGCCACAAACAAAAGACAGCUGUGGUCAGC
..............................................................(((......)))..((((((((((.............)))))))))) (-14.57 = -14.82 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:40 2006