Locus 4667

Sequence ID	2R_DroMel_CAF1
Location	15,242,298 – 15,242,417
Length	119
Max. P	0.978361

overview

Window 4

Location	15,242,298 – 15,242,417
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.48
Mean single sequence MFE	-31.76
Consensus MFE	-25.25
Energy contribution	-24.88
Covariance contribution	-0.38
Combinations/Pair	1.06
Mean z-score	-2.13
Structure conservation index	0.79
SVM decision value	1.81
SVM RNA-class probability	0.978361
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15242298 119 + 20766785
UC-UUUUGUAAGCAAAACAAUAUUAUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACGUCGACAAACCUGUUGUGAAAA
..-(((((....))))).........((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))((.(((((....))))))).... ( -30.70)
>DroEre_CAF1 65995 117 + 1
UC-UAUGGUACAUAAAAAAAU-UUAUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACAUUAACAA-CUUGCUGCCAAAA
..-..(((((((.........-....((((((((((((.......)))))....(((((.(....))))))....((((...))))....))))))).........-..)).)))))... ( -30.25)
>DroWil_CAF1 166009 113 + 1
UC-UUUAGGAGAAAUUCAA----AUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGAUUAUCAG-A-UAAUGACAAUA
..-....(((....))).(----((((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))))))).(((.-.-...)))..... ( -34.80)
>DroYak_CAF1 69307 118 + 1
UUUUUUUGUAAAUCAAAAAAU-UAUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUGAAAGG-AAGUGUGCCAAAC
.(((((((.....)))))))(-(((.((((((((((((.......)))))....(((((.(....))))))....((((...))))....))))))).))))..((-.......)).... ( -31.30)
>consensus
UC_UUUUGUAAAUAAAAAAAU_UAAUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACAUUAACAA_A_UGAUGCCAAAA
..........................((((((((((((.......)))))....(((((.......)))))...................)))))))....................... (-25.25 = -24.88 +  -0.38)

alignment

secondary structure

dotplot

Window 5

Location	15,242,298 – 15,242,417
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.48
Mean single sequence MFE	-32.38
Consensus MFE	-27.36
Energy contribution	-27.43
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.85
SVM decision value	0.22
SVM RNA-class probability	0.641493
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15242298 119 - 20766785
UUUUCACAACAGGUUUGUCGACGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAUAAUAUUGUUUUGCUUACAAAA-GA
....((.((((((((....))).((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))......))))).)).........-.. ( -31.90)
>DroEre_CAF1 65995 117 - 1
UUUUGGCAGCAAG-UUGUUAAUGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAUAA-AUUUUUUUAUGUACCAUA-GA
..(((((((....-)))))))(((((....(((((....))))))))))...(((((((.....)))))))((((.......)))).(((((..((((-(....)))))...)))))-.. ( -34.50)
>DroWil_CAF1 166009 113 - 1
UAUUGUCAUUA-U-CUGAUAAUCUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAU----UUGAAUUUCUCCUAAA-GA
.(((((((...-.-.))))))).(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...----................-.. ( -30.80)
>DroYak_CAF1 69307 118 - 1
GUUUGGCACACUU-CCUUUCAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAUA-AUUUUUUGAUUUACAAAAAAA
.............-.........((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))....-.(((((((.....))))))). ( -32.30)
>consensus
UUUUGGCAACA_G_CUGUUAAUGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAAA_AUUUUUUUAUUUACAAAA_GA
.......................((((((((..(((((...)))))......(((((((.....)))))))((((.......)))))))))))).......................... (-27.36 = -27.43 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:10 2006