Locus 7321

Sequence ID	3R_DroMel_CAF1
Location	19,358,699 – 19,358,838
Length	139
Max. P	0.957065

overview

Window 3

Location	19,358,699 – 19,358,802
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	76.02
Mean single sequence MFE	-19.65
Consensus MFE	-12.12
Energy contribution	-14.50
Covariance contribution	2.38
Combinations/Pair	1.17
Mean z-score	-2.14
Structure conservation index	0.62
SVM decision value	1.47
SVM RNA-class probability	0.957065
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19358699 103 + 27905053
AACAGAGCUAUUGCAGCAGUAACUGUAAAAUAAUAAAAAUAAUACGUGUUAACACAAUAAACAUAACUUAUUGUGUUUGCGAUCUUCGAUCAAGCAAGCUAGG
.....((((.((((((......)))))).................((((.((((((((((.......)))))))))).))((((...))))..)).))))... ( -22.40)
>DroSec_CAF1 9813 93 + 1
AACAGAGCUUAUGCAGCAAUAACAG-------AU---ACAAAUACAUGUAAACACAAUACACAUAACCUAUUGUGUUUGCGGUCUUCGAUCAAGCAGGCUAAG
.....((((..(((...........-------..---..........((((((((((((.........))))))))))))((((...))))..)))))))... ( -21.50)
>DroSim_CAF1 9889 93 + 1
AACAGAGCUUAUGCAGCAAUAACAG-------AU---AACAAUACAUGUAAACACAAUACACAUAACCUAUUGUGUUUGCGGUCUUCGAUCAAGCAGGCUAAG
.....((((..(((...........-------..---..........((((((((((((.........))))))))))))((((...))))..)))))))... ( -21.50)
>DroYak_CAF1 10085 84 + 1
AACAUAGUUA--ACAGCAGGAACAG-------AA---AACAAUACUUGUAGU---AAGUAACA----UUAUUGUGUUUGGUAUCUUGGAUCAAGCAAGCUAAG
..........--..(((........-------..---.((((((..(((...---.....)))----.))))))(((((((.......)))))))..)))... ( -13.20)
>consensus
AACAGAGCUAAUGCAGCAAUAACAG_______AU___AACAAUACAUGUAAACACAAUAAACAUAACCUAUUGUGUUUGCGAUCUUCGAUCAAGCAAGCUAAG
.....((((..(((.................................(((((((((((((.......)))))))))))))((((...))))..)))))))... (-12.12 = -14.50 +   2.38)

alignment

secondary structure

dotplot

Window 4

Location	19,358,722 – 19,358,838
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	72.37
Mean single sequence MFE	-25.01
Consensus MFE	-9.19
Energy contribution	-12.03
Covariance contribution	2.84
Combinations/Pair	1.19
Mean z-score	-1.84
Structure conservation index	0.37
SVM decision value	0.49
SVM RNA-class probability	0.755258
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19358722 116 + 27905053
UGUAAAAUAAUAAAAAUAAUACGUGUUAACACAAUAAACAUAACUUAUUGUGUUUGCGAUCUUCGAUCAAGCAAGCUAGGAUGUUGAGAAACAGUUCCUGUCACUUGAAAUGGCCU
(((.....................((.((((((((((.......)))))))))).))((((...))))..))).((((.....(..((..((((...))))..))..)..)))).. ( -22.40)
>DroSec_CAF1 9836 106 + 1
AG-------AU---ACAAAUACAUGUAAACACAAUACACAUAACCUAUUGUGUUUGCGGUCUUCGAUCAAGCAGGCUAAGAUGUUGAGAAACAGUUCCUAUCUCUUGAAGUGACAU
..-------..---.........(((((((((((((.........)))))))))))))(((..(..(((((.(((......((((....)))).......)))))))).).))).. ( -23.42)
>DroSim_CAF1 9912 106 + 1
AG-------AU---AACAAUACAUGUAAACACAAUACACAUAACCUAUUGUGUUUGCGGUCUUCGAUCAAGCAGGCUAAGAUGUUGAGAAACAGUUCCUAUCUCUUGAAGUGACCU
..-------..---..........((((((((((((.........))))))))))))((((..(..(((((.(((......((((....)))).......)))))))).).)))). ( -26.22)
>DroEre_CAF1 10021 95 + 1
AC-------AA---AACAAUACUUGGGGU---AAG----A----UUAUUGUGCUUGCCAUCUUGGAGCAAGCAAAAUGAGGUGCUGAAAAGCAGCUUCUCUAUCUUGAAGGGGCCU
..-------..---........(..((((---(((----(----(((((.((((((((......).))))))).)))))(.((((....)))).).))).)))))..)........ ( -26.90)
>DroYak_CAF1 10106 99 + 1
AG-------AA---AACAAUACUUGUAGU---AAGUAACA----UUAUUGUGUUUGGUAUCUUGGAUCAAGCAAGCUAAGCUGCUGAAAAGCAGUUCCUCUAUCUUGGAUUGGCCU
..-------..---.((((((..(((...---.....)))----.))))))(((((((.......)))))))..(((((((((((....))))))(((........)))))))).. ( -26.10)
>consensus
AG_______AU___AACAAUACAUGUAAACACAAUAAACAUAACUUAUUGUGUUUGCGAUCUUCGAUCAAGCAAGCUAAGAUGUUGAGAAACAGUUCCUAUCUCUUGAAGUGGCCU
........................((((((((((((.........)))))))))))).........(((((..........((((....))))..........)))))........ ( -9.19 = -12.03 +   2.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:06 2006