Locus 1784

Sequence ID	2L_DroMel_CAF1
Location	4,879,508 – 4,879,604
Length	96
Max. P	0.999912

overview

Window 4

Location	4,879,508 – 4,879,604
Length	96
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	89.27
Mean single sequence MFE	-26.95
Consensus MFE	-23.68
Energy contribution	-23.28
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-3.69
Structure conservation index	0.88
SVM decision value	4.51
SVM RNA-class probability	0.999912
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4879508 96 + 22407834
AUUAUCAUAUUGCU--UGGCUACCCUCACAGAAAGCUUUUGCUGAAAAAUAGUUGAUGAUCUUUUCAUAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
..............--..((((((((((((((((((....)))((((((((..(((........))))))))).)).))))))))))))).))..... ( -28.60)
>DroSec_CAF1 29179 94 + 1
AUUAUCAUAUUGCU--UGGCUGCCCUCACAGAAAGCU--UGCUCAAAAAUAGUUGGUGAUCAUUUCAUAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
..............--..(((((((((((((((((((--...........)))).((((.....)))).........))))))))))))).))..... ( -25.60)
>DroSim_CAF1 30216 96 + 1
AUUAUCAUAUUGCUUUUGGCUGCCCUCACAGAAAGCU--UGCUCAAAAAUAGUUGGUGAUCAUUUCAUAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
..................(((((((((((((((((((--...........)))).((((.....)))).........))))))))))))).))..... ( -25.60)
>DroEre_CAF1 30687 89 + 1
AUUAUCAUUUUGCU--UUGCUACCCUCACAGAAAGCU--UGCUCAUAAAUAGUUG-UGAUUU----UGAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
.............(--(((((((((((((((((....--...((((((....)))-)))...----.((.....)).))))))))))))).))))).. ( -27.50)
>DroYak_CAF1 30632 89 + 1
AUUAUCAUUUUGCU--UUGCUACCCUCACAGAAAGCU--UGCUCAAAAAUAGUUG-UGGUUU----UGAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
.............(--(((((((((((((((((....--...((((((.((....-)).)))----)))........))))))))))))).))))).. ( -27.46)
>consensus
AUUAUCAUAUUGCU__UGGCUACCCUCACAGAAAGCU__UGCUCAAAAAUAGUUG_UGAUCUUUUCAUAUUUUCUCGUUCUGUGAGGGUAUGUAAACU
..................((((((((((((((((((....)))..............((.............))...))))))))))))).))..... (-23.68 = -23.28 +  -0.40)

alignment

secondary structure

dotplot

Window 5

Location	4,879,508 – 4,879,604
Length	96
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	89.27
Mean single sequence MFE	-25.66
Consensus MFE	-21.91
Energy contribution	-22.71
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-4.29
Structure conservation index	0.85
SVM decision value	4.18
SVM RNA-class probability	0.999828
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4879508 96 - 22407834
AGUUUACAUACCCUCACAGAACGAGAAAAUAUGAAAAGAUCAUCAACUAUUUUUCAGCAAAAGCUUUCUGUGAGGGUAGCCA--AGCAAUAUGAUAAU
.((((...(((((((((((((.((((((...(((........)))....))))))(((....))))))))))))))))...)--)))........... ( -30.10)
>DroSec_CAF1 29179 94 - 1
AGUUUACAUACCCUCACAGAACGAGAAAAUAUGAAAUGAUCACCAACUAUUUUUGAGCA--AGCUUUCUGUGAGGGCAGCCA--AGCAAUAUGAUAAU
.((((.....((((((((((....((((((((((.....))).....)))))))(((..--..))))))))))))).....)--)))........... ( -21.70)
>DroSim_CAF1 30216 96 - 1
AGUUUACAUACCCUCACAGAACGAGAAAAUAUGAAAUGAUCACCAACUAUUUUUGAGCA--AGCUUUCUGUGAGGGCAGCCAAAAGCAAUAUGAUAAU
......((((((((((((((....((((((((((.....))).....)))))))(((..--..)))))))))))))..((.....))..))))..... ( -22.40)
>DroEre_CAF1 30687 89 - 1
AGUUUACAUACCCUCACAGAACGAGAAAAUCA----AAAUCA-CAACUAUUUAUGAGCA--AGCUUUCUGUGAGGGUAGCAA--AGCAAAAUGAUAAU
.((((...(((((((((((((.(......(((----((((..-.....)))).)))...--..).)))))))))))))...)--)))........... ( -25.90)
>DroYak_CAF1 30632 89 - 1
AGUUUACAUACCCUCACAGAACGAGAAAAUCA----AAACCA-CAACUAUUUUUGAGCA--AGCUUUCUGUGAGGGUAGCAA--AGCAAAAUGAUAAU
.((((...(((((((((((((.(......(((----(((...-.......))))))...--..).)))))))))))))...)--)))........... ( -28.20)
>consensus
AGUUUACAUACCCUCACAGAACGAGAAAAUAUGAAAAGAUCA_CAACUAUUUUUGAGCA__AGCUUUCUGUGAGGGUAGCCA__AGCAAUAUGAUAAU
.(((....(((((((((((((((((((......................))))))(((....))))))))))))))))......)))........... (-21.91 = -22.71 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:13 2006