Locus 1378

Sequence ID	X_DroMel_CAF1
Location	4,117,836 – 4,118,036
Length	200
Max. P	0.826940

overview

Window 7

Location	4,117,836 – 4,117,956
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.69
Mean single sequence MFE	-25.38
Consensus MFE	-21.35
Energy contribution	-20.42
Covariance contribution	-0.94
Combinations/Pair	1.16
Mean z-score	-1.79
Structure conservation index	0.84
SVM decision value	0.70
SVM RNA-class probability	0.826940
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4117836 120 - 22224390
CUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCUCCUACACAGUGAACAACAAGCAGUUCAUUAACAUACUAUAGG
.(((((((..((((((.....))))))....((((.......)))).)).)))))....(((.......))).............(((((((........)))))))............. ( -25.40)
>DroSec_CAF1 8955 120 - 1
CUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGUAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCUUACACAGUGAACAACAGGCAGUUCAUUAACAUACUAUAAG
(((((.((((((((((.....))))))....(((..((....))..)))........)))).....)))))..............(((((((........)))))))............. ( -23.50)
>DroSim_CAF1 4359 120 - 1
CUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCUUACACAGUGAACAACAAGCAGUUCAUUAACAUACUAUAAG
.(((((((..((((((.....))))))....((((.......)))).)).)))))....(((.......))).............(((((((........)))))))............. ( -25.40)
>DroYak_CAF1 4641 113 - 1
AUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUGGGAGCCGC-AUGAAACUUGGUGAAUUGAAGCUCUUCUCUUACACAGCGAAAA--AAUCAGUUAAUU----UAUUAUAAA
.(((((((..((((((.....))))))(((((......)))))....))-)))))...(((((((((((.(((............)))((...--..))..))))))----))))).... ( -27.20)
>consensus
CUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCUUACACAGUGAACAACAAGCAGUUCAUUAACAUACUAUAAG
.(((((((..((((((.....))))))....((((.......)))).)).)))))..(((((........(((............)))........)))))................... (-21.35 = -20.42 +  -0.94)

alignment

secondary structure

dotplot

Window 8

Location	4,117,876 – 4,117,996
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-31.95
Consensus MFE	-27.89
Energy contribution	-28.45
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	0.51
SVM RNA-class probability	0.762231
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4117876 120 - 22224390
UCCGUUCGCACACAUGCCUCGCCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCUCC
..((...(((....)))..))..(((..(((((.((.....(((((((..((((((.....))))))....((((.......)))).)).)))))....)))))))..).))........ ( -30.00)
>DroSec_CAF1 8995 120 - 1
UCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGUAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCU
...((..((.((..(((....)))..))))..))(((((..((((.((((((((((.....))))))....(((..((....))..)))........))))))))..)))))........ ( -31.40)
>DroSim_CAF1 4399 120 - 1
UCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCU
.(((...(((....)))..))).(((..(((((.((.....(((((((..((((((.....))))))....((((.......)))).)).)))))....)))))))..).))........ ( -33.10)
>DroYak_CAF1 4675 119 - 1
UCCGUUCGCACACAUGCCUCUGCGCUUGGUUCACGCUUCUAUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUGGGAGCCGC-AUGAAACUUGGUGAAUUGAAGCUCUUCUCU
...((..(((....)))....))(((..((((((.(.....(((((((..((((((.....))))))(((((......)))))....))-)))))....)))))))..).))........ ( -33.30)
>consensus
UCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCUAGGAGCAGCAAUGAAACUUGCUGAAUUGAAGCUCUUCCCU
.(((...(((....)))..))).(((..(((((.((.....(((((((..((((((.....))))))....((((.......)))).)).)))))....)))))))..).))........ (-27.89 = -28.45 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	4,117,916 – 4,118,036
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.36
Mean single sequence MFE	-26.38
Consensus MFE	-23.35
Energy contribution	-24.10
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.89
SVM decision value	-0.01
SVM RNA-class probability	0.528872
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4117916 120 - 22224390
GAUCAAGCUGGCUGUGAACUAUUUAACAUUUAAACUCAACUCCGUUCGCACACAUGCCUCGCCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCU
(((..(((((((.((((((((...........(((........))).(((....))).........))))))))))..............((((((.....))))))..))))).))).. ( -24.80)
>DroSec_CAF1 9035 120 - 1
GAUCAAGCUGGCUGUGAACUAUUUAACAUUUAAACCCAACUCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCU
(((..(((((((.((((((((((((.....)))).....(.(((...(((....)))..))).)..))))))))))..............((((((.....))))))..))))).))).. ( -28.00)
>DroSim_CAF1 4439 120 - 1
GAUCAAGCUGGCUGUGAACUAUUUAACAUUUAAACCCAACUCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCU
(((..(((((((.((((((((((((.....)))).....(.(((...(((....)))..))).)..))))))))))..............((((((.....))))))..))))).))).. ( -28.00)
>DroYak_CAF1 4714 120 - 1
GAUCAAGAUGGCAGUGAACUAUUUAACAUUUAAACUCAACUCCGUUCGCACACAUGCCUCUGCGCUUGGUUCACGCUUCUAUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCU
......((((((.((((((((...........(((........)))((((..........))))..))))))))((..........))..((((((.....))))))....)).)))).. ( -24.70)
>consensus
GAUCAAGCUGGCUGUGAACUAUUUAACAUUUAAACCCAACUCCGUUCGCACACAUGCCUCGGCGCUUGGUUCACGCUUCUCUUCAUGCAAUGUCAUGACAAAUGACACUCAGCUCAUCCU
(((..(((((((.((((((((((((.....)))).....(.(((...(((....)))..))).)..))))))))))..............((((((.....))))))..))))).))).. (-23.35 = -24.10 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:51 2006