Locus 5331

Sequence ID	2R_DroMel_CAF1
Location	17,263,097 – 17,263,192
Length	95
Max. P	0.908300

overview

Window 4

Location	17,263,097 – 17,263,192
Length	95
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	77.63
Mean single sequence MFE	-24.97
Consensus MFE	-13.29
Energy contribution	-13.93
Covariance contribution	0.64
Combinations/Pair	1.35
Mean z-score	-2.24
Structure conservation index	0.53
SVM decision value	1.06
SVM RNA-class probability	0.908300
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17263097 95 + 20766785
AUAGCUGA-GUUAAUGAUUGGAAAUUAAUUUGUCAGCCGGG-AGAAUGGGCCA-AUGGGA-UUACGCAAUUGCGUAGACAAAUUGCUGACAAUUAGCAG-
...(((((-((((((........))))))((((((((..((-........))(-((..(.-((((((....)))))).)..))))))))))))))))..- ( -26.90)
>DroVir_CAF1 72864 88 + 1
AUUGUUGA-CUUAAUGAUUGGAUAUUAAUUUGGCAGGCUGU-GUUA-GCCUCA-AUAGUACCUACUU-------CAGACAAAUUGUUGUCGAUUAGCCG-
...(((((-.....(((..((.(((((..(((..((((((.-..))-))))))-))))))))....)-------))(((((....)))))..)))))..- ( -16.80)
>DroSim_CAF1 56535 95 + 1
AUAGCUGA-GUUAAUGAUUGGAAAUUAAUUCGUCAGCCGGG-GGAACGGGCCA-AUGGGA-UUACGCAAUUGCGUAGACAAAUUGCUGACAAUUAGCAG-
...(((((-((((((........))))))))((((((((..-....)))..((-((..(.-((((((....)))))).)..)))))))))....)))..- ( -30.10)
>DroEre_CAF1 55878 95 + 1
AUAGUUGA-GUUAAUGAUUGGAAAUUAAUUUGUCAGCCGGG-GGAAUGGGCCA-AUGGGA-UUACGCAAUUGCGUAGACAAAUUGCUGACAAUUAGCAG-
........-((((((..(..(....(((((((((..(((..-((......)).-.)))..-.(((((....)))))))))))))))..)..))))))..- ( -26.60)
>DroWil_CAF1 77528 91 + 1
AUAGUUAAACUUAAUGAUUGGAAAUUAAUUUGACAGGCUGA-AGCAUUUGCUGUGUGUAG-AUGCUUA-------AGACAAAUUGUUGUCGAUUAACCAG
...((((((.(((((........))))))))))).((...(-(((((((((.....))))-)))))).-------.(((((....)))))......)).. ( -23.20)
>DroYak_CAF1 55086 96 + 1
AUAGUUGA-GUUAAUGAUUGGAAAUUAAUUUGUCAGCCGGGGGGAAUGGGCCA-AUGGGA-UUACGCAAUUGCGUAGACAAAUUGCUGACAAUUAGCAG-
........-((((((..(..(....(((((((((..(((..((.......)).-.)))..-.(((((....)))))))))))))))..)..))))))..- ( -26.20)
>consensus
AUAGUUGA_GUUAAUGAUUGGAAAUUAAUUUGUCAGCCGGG_GGAAUGGGCCA_AUGGGA_UUACGCAAUUGCGUAGACAAAUUGCUGACAAUUAGCAG_
...(((((..(((((........))))).((((((((.....((......)).........((((((....)))))).......)))))))))))))... (-13.29 = -13.93 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	17,263,097 – 17,263,192
Length	95
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	77.63
Mean single sequence MFE	-17.47
Consensus MFE	-7.86
Energy contribution	-9.37
Covariance contribution	1.50
Combinations/Pair	1.25
Mean z-score	-2.17
Structure conservation index	0.45
SVM decision value	0.31
SVM RNA-class probability	0.682835
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17263097 95 - 20766785
-CUGCUAAUUGUCAGCAAUUUGUCUACGCAAUUGCGUAA-UCCCAU-UGGCCCAUUCU-CCCGGCUGACAAAUUAAUUUCCAAUCAUUAAC-UCAGCUAU
-..(((..((((((((........(((((....))))).-......-(((........-.))))))))))).(((((........))))).-..)))... ( -19.90)
>DroVir_CAF1 72864 88 - 1
-CGGCUAAUCGACAACAAUUUGUCUG-------AAGUAGGUACUAU-UGAGGC-UAAC-ACAGCCUGCCAAAUUAAUAUCCAAUCAUUAAG-UCAACAAU
-.((((..(((((((....))))).)-------)....(((.....-..((((-(...-..))))))))....................))-))...... ( -15.51)
>DroSim_CAF1 56535 95 - 1
-CUGCUAAUUGUCAGCAAUUUGUCUACGCAAUUGCGUAA-UCCCAU-UGGCCCGUUCC-CCCGGCUGACGAAUUAAUUUCCAAUCAUUAAC-UCAGCUAU
-..(((....((((((........(((((....))))).-......-.....((....-..))))))))((.(((((........))))).-)))))... ( -20.50)
>DroEre_CAF1 55878 95 - 1
-CUGCUAAUUGUCAGCAAUUUGUCUACGCAAUUGCGUAA-UCCCAU-UGGCCCAUUCC-CCCGGCUGACAAAUUAAUUUCCAAUCAUUAAC-UCAACUAU
-..(((.......)))(((((((((((((....))))).-......-.((((......-...)))))))))))).................-........ ( -18.80)
>DroWil_CAF1 77528 91 - 1
CUGGUUAAUCGACAACAAUUUGUCU-------UAAGCAU-CUACACACAGCAAAUGCU-UCAGCCUGUCAAAUUAAUUUCCAAUCAUUAAGUUUAACUAU
.(((((((.((((((....))))).-------.((((((-.............)))))-)..............................).))))))). ( -11.42)
>DroYak_CAF1 55086 96 - 1
-CUGCUAAUUGUCAGCAAUUUGUCUACGCAAUUGCGUAA-UCCCAU-UGGCCCAUUCCCCCCGGCUGACAAAUUAAUUUCCAAUCAUUAAC-UCAACUAU
-..(((.......)))(((((((((((((....))))).-......-.((((..........)))))))))))).................-........ ( -18.70)
>consensus
_CUGCUAAUUGUCAGCAAUUUGUCUACGCAAUUGCGUAA_UCCCAU_UGGCCCAUUCC_CCCGGCUGACAAAUUAAUUUCCAAUCAUUAAC_UCAACUAU
...(((.......)))(((((((((((((....)))))..........((((..........)))))))))))).......................... ( -7.86 =  -9.37 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:16 2006