Locus 4174

Sequence ID	2L_DroMel_CAF1
Location	11,969,668 – 11,969,765
Length	97
Max. P	0.812800

overview

Window 4

Location	11,969,668 – 11,969,765
Length	97
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	85.70
Mean single sequence MFE	-20.32
Consensus MFE	-13.52
Energy contribution	-13.36
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-2.20
Structure conservation index	0.67
SVM decision value	0.46
SVM RNA-class probability	0.746336
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11969668 97 + 22407834
AU------GCCAUUCGAAUGCUAUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAACCGGGGAGAUUUUUUUUCCCCUCCAUUCCCAUUUUUUCGAUUCUUU
..------.....(((((.....((((...((((((.....)))))).)))).......(((((((.....)))))))..............)))))...... ( -22.50)
>DroSec_CAF1 189065 95 + 1
AU------GCCAUUCGAAUGCUAUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAACCGAGG-GACUUUUUUUUCCCUCCAUUCCC-UUUUUUCGAUUCUUU
..------.....(((((.....((((...((((((.....)))))).)))).......((((-((........)))))).......-....)))))...... ( -20.50)
>DroSim_CAF1 155422 95 + 1
AU------GCCAUUCGAAUGCUAUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAACCGAGG-GACUUUUUUUCCCCUCCAUUCCC-UUUUUUCGAUUCUUU
..------.....(((((.....((((...((((((.....)))))).)))).......((((-(..........))))).......-....)))))...... ( -18.50)
>DroEre_CAF1 163697 92 + 1
AU------GCCAUUCGAAUGCUGUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAACCGACG-GA---UUUUUUCCCUCCAUUCCC-AUUUUUCGAUUCUUC
..------.....(((((...((((((...((((((.....)))))).)))))).....((.(-((---.....))).)).......-....)))))...... ( -19.30)
>DroYak_CAF1 160295 86 + 1
AUUCUGUUGCCAUUCGAAUGCUAUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAAGCGAGG-GG---UUUUUCCCCUCCACUCC--AUU-----------U
...................(((.((((...((((((.....)))))).))))....)))((((-((---.....))))))......--...-----------. ( -20.80)
>consensus
AU______GCCAUUCGAAUGCUAUGCUACAAAUUAUGUGAAAUGAUUGAGCACAAAACCGAGG_GA_UUUUUUUCCCCUCCAUUCCC_UUUUUUCGAUUCUUU
...............(((((...((((...((((((.....)))))).)))).......((((.((.......)).))))))))).................. (-13.52 = -13.36 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	11,969,668 – 11,969,765
Length	97
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	85.70
Mean single sequence MFE	-22.79
Consensus MFE	-16.30
Energy contribution	-15.98
Covariance contribution	-0.32
Combinations/Pair	1.19
Mean z-score	-2.08
Structure conservation index	0.72
SVM decision value	0.65
SVM RNA-class probability	0.812800
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11969668 97 - 22407834
AAAGAAUCGAAAAAAUGGGAAUGGAGGGGAAAAAAAAUCUCCCCGGUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCAUAGCAUUCGAAUGGC------AU
......(((((...((((((((((.(((((.........)))))(((.....)))...))))))).)))....(((......)))))))).....------.. ( -20.30)
>DroSec_CAF1 189065 95 - 1
AAAGAAUCGAAAAAA-GGGAAUGGAGGGAAAAAAAAGUC-CCUCGGUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCAUAGCAUUCGAAUGGC------AU
......(((((....-..((((.((((((........))-)))).))))(((((((((..............))).))))))...))))).....------.. ( -23.84)
>DroSim_CAF1 155422 95 - 1
AAAGAAUCGAAAAAA-GGGAAUGGAGGGGAAAAAAAGUC-CCUCGGUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCAUAGCAUUCGAAUGGC------AU
......(((((....-..((((.((((((........))-)))).))))(((((((((..............))).))))))...))))).....------.. ( -22.94)
>DroEre_CAF1 163697 92 - 1
GAAGAAUCGAAAAAU-GGGAAUGGAGGGAAAAAA---UC-CGUCGGUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCACAGCAUUCGAAUGGC------AU
......(((((....-.(((((.((.(((.....---))-).)).)))))((((((((..............))).)))))....))))).....------.. ( -21.54)
>DroYak_CAF1 160295 86 - 1
A-----------AAU--GGAGUGGAGGGGAAAAA---CC-CCUCGCUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCAUAGCAUUCGAAUGGCAACAGAAU
.-----------...--.(((((((((((.....---))-))))....((((((((((..............))).))))))))))))...((....)).... ( -25.34)
>consensus
AAAGAAUCGAAAAAA_GGGAAUGGAGGGGAAAAAAA_UC_CCUCGGUUUUGUGCUCAAUCAUUUCACAUAAUUUGUAGCAUAGCAUUCGAAUGGC______AU
..................(((((((((((........)).))))....((((((((((..............))).))))))))))))............... (-16.30 = -15.98 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:34 2006