Locus 5956

Sequence ID	3R_DroMel_CAF1
Location	15,716,113 – 15,716,334
Length	221
Max. P	0.933380

overview

Window 6

Location	15,716,113 – 15,716,228
Length	115
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	64.68
Mean single sequence MFE	-23.31
Consensus MFE	-12.51
Energy contribution	-13.32
Covariance contribution	0.81
Combinations/Pair	1.24
Mean z-score	-1.66
Structure conservation index	0.54
SVM decision value	1.23
SVM RNA-class probability	0.933380
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15716113 115 - 27905053
CUGGACCGCAGGGUUCAAGGUUUUGGGUGUAAAAAUACAAUUUUCCCUUAAUUUAACGUUAUAUGUGGAAUAUAAUUUGCUUGGGA-AAAAGGCAUUAUAUAAUAUAUACACCA-AU
.((((((....))))))........((((((.........(((((((..........(((((((.....)))))))......))))-)))......((((...)))))))))).-.. ( -23.59)
>DroSec_CAF1 12348 95 - 1
CUGGACCGUAGGGUUCAAGGUCUCGGCUGUGAAAAUAUAAUUUUCCCUUCAUU-----------AUGUAUCAUCAUUUGCUUGGGAAAAGAGACAUU----------UACACAA-AU
.((((((....))))))..(((((...(((....)))...(((((((......-----------(((......)))......))))))))))))...----------.......-.. ( -24.40)
>DroSim_CAF1 12662 99 - 1
CUGGACCGUAGGGUUCAAGGUCUCGGCUGUGAAAAUAUAAUUUUCCCUUCAUU-----------------UAACAUUUUUCUGGGAAAAGAGGCAUUAUACAAUAUAUACACAA-AU
.((((((....))))))..(((((...(((....)))...(((((((......-----------------............))))))))))))....................-.. ( -21.37)
>DroYak_CAF1 14073 117 - 1
CUGACCCUUCUGGGUCAAGGUCUUGCCAGUAAGAAAGUAAUUUUCACAGACCUUACAAAUGUAUGUAAAAUGUCAUUCAGUUGGCAAAAUUAACAUAAUACAAUAUUUAAACAAAAU
.((((((....)))))).(((.(((((((...(((((...)))))...(((.(((((......)))))...)))......))))))).))).......................... ( -23.90)
>consensus
CUGGACCGUAGGGUUCAAGGUCUCGGCUGUAAAAAUAUAAUUUUCCCUUAAUU___________GUG_AAUAUCAUUUGCUUGGGAAAAGAGACAUUAUACAAUAUAUACACAA_AU
.((((((....))))))..(((((...(((....)))...(((((((...................................))))))))))))....................... (-12.51 = -13.32 +   0.81)

alignment

secondary structure

dotplot

Window 7

Location	15,716,228 – 15,716,334
Length	106
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	79.42
Mean single sequence MFE	-33.76
Consensus MFE	-17.55
Energy contribution	-18.42
Covariance contribution	0.87
Combinations/Pair	1.12
Mean z-score	-1.97
Structure conservation index	0.52
SVM decision value	0.27
SVM RNA-class probability	0.660931
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15716228 106 - 27905053
CCUGCGAUCGAAUCAGAGCUGAGCCGAUCGACGGAAAAAGACGCUGACUAAUCGGCUGGGAAAUCCGCCAGAUCGGAUUAAGC--UCAUUUCGAAGGGAGCGGCAAUA
.((((..(((((...(((((...((((((..((((.......(((((....))))).......))))...))))))....)))--))..))))).....))))..... ( -37.64)
>DroSec_CAF1 12443 106 - 1
CCUGCGAUCGAAUCAGAGCUGAGCCGAUCGACGGAAAAAGACGCUGACUAAUCGGCUGGGAAAUCCGACAGAUCGGCUUAAGC--UCAUUUCGAAGGGAGCGGCAAAA
.((((..(((((...((((((((((((((..((((.......(((((....))))).......))))...))))))))).)))--))..))))).....))))..... ( -42.84)
>DroSim_CAF1 12761 106 - 1
CCUGCGAUCGAAUCAGAGCUGAGCCGAUCGACGGAAAAAGGCGCUGACUAAUCGGCUGGGAAAUCCGACAAAUCGGCUUAAGC--UCAUUUCGAAGGGAGCGGCAAAA
.((((..(((((...(((((((((((((...((((.......(((((....))))).......))))....)))))))).)))--))..))))).....))))..... ( -38.24)
>DroEre_CAF1 12674 84 - 1
CCUGCGAUCGAAUCAGAGGUGAGCCAAGCGACGGAAA-AAUCGCCGACUGAUCGGCGGGG----------------------CACUCAUUUCGAAGGGG-CGGCAACG
(((((...(((.((((.(((((.((.......))...-..)))))..))))))))))))(----------------------(.(((........))))-)(....). ( -27.20)
>DroYak_CAF1 14190 108 - 1
CUUGCGAUCAAAUCAGAGGUGAGCCAAGCGACGGAAAAAACCGCUGACAAAUCGACUGGGAAGUCCGACAGAUCGGAUUAAGCAAACAUUUUGAAGGGGGCGAUUAUA
.((((..((...((((.(((...((.......)).....))).))))((((.....((...(((((((....)))))))...)).....))))..))..))))..... ( -22.90)
>consensus
CCUGCGAUCGAAUCAGAGCUGAGCCGAUCGACGGAAAAAGACGCUGACUAAUCGGCUGGGAAAUCCGACAGAUCGGAUUAAGC__UCAUUUCGAAGGGAGCGGCAAAA
(((.((((((..(((....)))..)))))).(((((......(((((....)))))........(((......)))............))))).)))........... (-17.55 = -18.42 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:52 2006