Locus 956

Sequence ID	X_DroMel_CAF1
Location	2,720,461 – 2,720,566
Length	105
Max. P	0.998272

overview

Window 2

Location	2,720,461 – 2,720,566
Length	105
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	91.86
Mean single sequence MFE	-14.18
Consensus MFE	-11.40
Energy contribution	-11.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.25
Structure conservation index	0.80
SVM decision value	1.74
SVM RNA-class probability	0.974865
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2720461 105 + 22224390
AUAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUUUGCCCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((...(((.....))).....)))))..----...---................. ( -12.26)
>DroSec_CAF1 109136 102 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGGUUUU---CCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......))))))..............((((..((---((....))))...----)))---)................ ( -16.26)
>DroSim_CAF1 97182 102 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU---CCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((...((.....---.))...)))))..----...---................. ( -12.16)
>DroEre_CAF1 123558 109 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU---CCCACCGGAAUUUCAAUCCGGCCUUUUUUUCACUUACUCC
......((((((........((((......)))).......))))))(((....(((((..(((.....---.)))..)))))........))).................. ( -16.76)
>DroYak_CAF1 118153 105 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGCUUUU---CCCACCGGAAUUC----CCCACUUUUUUCUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((..(((.....---.)))..)))))..----....................... ( -13.46)
>consensus
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU___CCCUCCGGAAUUU____CCC___AUUUUUUCACUUGCUCC
......((((((........((((......)))).......))))))............(((((............)))))............................... (-11.40 = -11.40 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	2,720,461 – 2,720,566
Length	105
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	91.86
Mean single sequence MFE	-19.52
Consensus MFE	-16.86
Energy contribution	-16.70
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.41
Structure conservation index	0.86
SVM decision value	3.05
SVM RNA-class probability	0.998272
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2720461 105 - 22224390
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGGGCAAAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUAU
((((((((((.......---...----..(((((....((........))...))))).....((((.....................))))......)))))))))).... ( -18.40)
>DroSec_CAF1 109136 102 - 1
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGG---AAAACCCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.......---...----..(((((...(((---....)))...))))).....((((.....................))))......)))))))))).... ( -20.00)
>DroSim_CAF1 97182 102 - 1
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGG---AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.......---...----..(((((...((.---.....))...))))).....((((.....................))))......)))))))))).... ( -18.20)
>DroEre_CAF1 123558 109 - 1
GGAGUAAGUGAAAAAAAGGCCGGAUUGAAAUUCCGGUGGG---AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((........(((........(((((..(((.---.....)))..)))))....))).............(((........)))......)))))))))).... ( -21.10)
>DroYak_CAF1 118153 105 - 1
GGAGCAAGUGAGAAAAAAGUGGG----GAAUUCCGGUGGG---AAAAGCCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.............----..(((((..(((.---.....)))..))))).....((((.....................))))......)))))))))).... ( -19.90)
>consensus
GGAGCAAGUGAAAAAAU___GGG____AAAUUCCGGAGGG___AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((...................(((((...((.........))...))))).....((((.....................))))......)))))))))).... (-16.86 = -16.70 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:03 2006