Locus 4419

Sequence ID	X_DroMel_CAF1
Location	11,654,669 – 11,654,789
Length	120
Max. P	0.988759

overview

Window 3

Location	11,654,669 – 11,654,765
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-21.58
Consensus MFE	-14.90
Energy contribution	-15.86
Covariance contribution	0.96
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.69
SVM decision value	0.60
SVM RNA-class probability	0.796036
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11654669 96 - 22224390
AGCGAGCGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGGUCGCUUCCACACACACACACACGGCGACCAUAAGUAACGCAUUUGUCUUU
.....(((...((((((((..(((........))).))))))))(((((((.................)))))))........))).......... ( -26.93)
>DroSec_CAF1 27915 94 - 1
AGCGAGCAAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGCUCGCUUCCACACAC--ACACACGACGACCAUAAGUAACGCAUUUGUCUUU
(((((((....((((((((..(((........))).))))))))))))))).........--......(((((...............)))))... ( -23.36)
>DroSim_CAF1 24414 92 - 1
AGCGAGCGAAAGAGAGACCAUCGACCACCCCCUCCCUGUUUCUCGCUCGCUUCCACACA----CACACGACGACCAUACGUAACGCCUUUGUCUUU
.((((((((..(((((((....((........))...)))))))..)))))........----......(((......)))..))).......... ( -19.40)
>DroEre_CAF1 30107 72 - 1
UGCGAGAGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCGCGCUCGCUUCCACAC------------------------ACGCAUUUGUCUUU
.(((((.(.....((((((..(((........))).)))))).).)))))........------------------------.............. ( -14.80)
>DroYak_CAF1 27380 90 - 1
UGCGAGAGAAAUAGAGACAAUCGACCACCCCCUCGCUGUUUCUCUCUCGCUCGCACUC------ACACAGCGACCAUAAGUAACGCAUUUGCCUUU
.((((((((....((((((..(((........))).))))))))))))))((((....------.....))))...........((....)).... ( -23.40)
>consensus
AGCGAGCGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGCUCGCUUCCACACA____CACACGACGACCAUAAGUAACGCAUUUGUCUUU
.((((((....((((((((..(((........))).)))))))))))))).............................................. (-14.90 = -15.86 +   0.96)

alignment

secondary structure

dotplot

Window 4

Location	11,654,699 – 11,654,789
Length	90
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	87.56
Mean single sequence MFE	-20.30
Consensus MFE	-14.90
Energy contribution	-15.86
Covariance contribution	0.96
Combinations/Pair	1.06
Mean z-score	-3.31
Structure conservation index	0.73
SVM decision value	2.13
SVM RNA-class probability	0.988759
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11654699 90 - 22224390
ACACAAACCUAAAAGCGACAU-ACUAGCGAGCGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGGUCGCUUCCACACACACACAC
..............((.....-....))((((((..((((((((..(((........))).))))))))..)))))).............. ( -22.30)
>DroSec_CAF1 27945 88 - 1
ACACAAACCUAAAAGCGACAU-ACUAGCGAGCAAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGCUCGCUUCCACACAC--ACAC
.....................-...(((((((....((((((((..(((........))).))))))))))))))).........--.... ( -21.50)
>DroSim_CAF1 24444 87 - 1
ACACAAACCUAAAAGCGACAUUACUAGCGAGCGAAAGAGAGACCAUCGACCACCCCCUCCCUGUUUCUCGCUCGCUUCCACACA----CAC
.........................(((((((((.(((.((...................)).))).)))))))))........----... ( -17.41)
>DroEre_CAF1 30121 82 - 1
ACACAAACUUAAAAGCGACAU-GCUUGCGAGAGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCGCGCUCGCUUCCACAC--------
............((((.....-))))(((((.(.....((((((..(((........))).)))))).).)))))........-------- ( -17.20)
>DroYak_CAF1 27410 84 - 1
ACACAAACUCAAAAGCGACAU-ACUUGCGAGAGAAAUAGAGACAAUCGACCACCCCCUCGCUGUUUCUCUCUCGCUCGCACUC------AC
..............((((...-....((((((((....((((((..(((........))).))))))))))))))))))....------.. ( -23.11)
>consensus
ACACAAACCUAAAAGCGACAU_ACUAGCGAGCGAAAGAGAGACAAUCGACCACCCCCUCGCUGUUUCUCGCUCGCUUCCACACA____CAC
..........................((((((....((((((((..(((........))).))))))))))))))................ (-14.90 = -15.86 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:37 2006